Chapter 3 Atmosphere chemistry application
61
32 Series of papers
Chapter 3 Atmosphere chemistry application
62
321 A computational investigation of the sulphuric acid catalysed 14-hydrogen transfer in higher Criegee intermediates
Presentation of the article
TitleA computational investigation of the sulphuric acid catalysed 14-hydrogen transfer in higher Criegee intermediates
Authors Sarrami F Mackenzie Rae FA and Karton A
Journal International Journal of Quantum Chemistry 2018 118 e25599
DOI httpsdxdoiorg 101002qua25599 Date of Publication February 2018
Graphical TOC
63
58
59
60
61
62
63
64
65
Chapter 3 Atmosphere chemistry application
66
322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Presentation of the article
Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Authors Sarrami F Yu LJ Wan W and Karton A
Journal Chemical Physics Letter 2017 675 27-34
DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017
Graphical TOC
67
68
69
70
71
72
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
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Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
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J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
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Chapter 3 Atmosphere chemistry application
62
321 A computational investigation of the sulphuric acid catalysed 14-hydrogen transfer in higher Criegee intermediates
Presentation of the article
TitleA computational investigation of the sulphuric acid catalysed 14-hydrogen transfer in higher Criegee intermediates
Authors Sarrami F Mackenzie Rae FA and Karton A
Journal International Journal of Quantum Chemistry 2018 118 e25599
DOI httpsdxdoiorg 101002qua25599 Date of Publication February 2018
Graphical TOC
63
58
59
60
61
62
63
64
65
Chapter 3 Atmosphere chemistry application
66
322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Presentation of the article
Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Authors Sarrami F Yu LJ Wan W and Karton A
Journal Chemical Physics Letter 2017 675 27-34
DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017
Graphical TOC
67
68
69
70
71
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74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
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Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
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Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
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Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
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J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
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metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
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M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
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63
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65
Chapter 3 Atmosphere chemistry application
66
322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Presentation of the article
Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Authors Sarrami F Yu LJ Wan W and Karton A
Journal Chemical Physics Letter 2017 675 27-34
DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017
Graphical TOC
67
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69
70
71
72
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
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2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
2007 3(2) 407
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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
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Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000
112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys
2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
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Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
58
59
60
61
62
63
64
65
Chapter 3 Atmosphere chemistry application
66
322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Presentation of the article
Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Authors Sarrami F Yu LJ Wan W and Karton A
Journal Chemical Physics Letter 2017 675 27-34
DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017
Graphical TOC
67
68
69
70
71
72
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
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2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys
Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem
Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem
Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J
Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G
Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem
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115 Curtiss L A Raghavachari K Trucks G W Pople J A J Chem Phys 1991
94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997
106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999
110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem
Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999
313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem
Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000
112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys
2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
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487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
59
60
61
62
63
64
65
Chapter 3 Atmosphere chemistry application
66
322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Presentation of the article
Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Authors Sarrami F Yu LJ Wan W and Karton A
Journal Chemical Physics Letter 2017 675 27-34
DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017
Graphical TOC
67
68
69
70
71
72
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem
Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
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313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem
Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000
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2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
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2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
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Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
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Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
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Chapter 3 Atmosphere chemistry application
66
322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Presentation of the article
Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Authors Sarrami F Yu LJ Wan W and Karton A
Journal Chemical Physics Letter 2017 675 27-34
DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017
Graphical TOC
67
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74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
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86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik
1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part
I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical
Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part
II Some results and discussion In Mathematical Proceedings of the Cambridge
Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson
Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced
electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991
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Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
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Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
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2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
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and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
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PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
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Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
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Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
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J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
61
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65
Chapter 3 Atmosphere chemistry application
66
322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Presentation of the article
Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Authors Sarrami F Yu LJ Wan W and Karton A
Journal Chemical Physics Letter 2017 675 27-34
DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017
Graphical TOC
67
68
69
70
71
72
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik
1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part
I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical
Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part
II Some results and discussion In Mathematical Proceedings of the Cambridge
Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson
Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced
electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991
95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
References
132
24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139
134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am
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Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
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2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
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Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
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and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
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Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
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Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
62
63
64
65
Chapter 3 Atmosphere chemistry application
66
322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Presentation of the article
Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Authors Sarrami F Yu LJ Wan W and Karton A
Journal Chemical Physics Letter 2017 675 27-34
DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017
Graphical TOC
67
68
69
70
71
72
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik
1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part
I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical
Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part
II Some results and discussion In Mathematical Proceedings of the Cambridge
Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson
Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced
electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991
95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
References
132
24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139
134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am
Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980
72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ
and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett
1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
Activity Relationship 2002 21 73
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Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
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Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
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Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
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Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
63
64
65
Chapter 3 Atmosphere chemistry application
66
322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Presentation of the article
Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Authors Sarrami F Yu LJ Wan W and Karton A
Journal Chemical Physics Letter 2017 675 27-34
DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017
Graphical TOC
67
68
69
70
71
72
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik
1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part
I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical
Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part
II Some results and discussion In Mathematical Proceedings of the Cambridge
Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson
Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced
electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991
95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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132
24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139
134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am
Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980
72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ
and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett
1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
Activity Relationship 2002 21 73
References
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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy
of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD
Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci
2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley
amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I
J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
2007 3(2) 407
References
134
69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
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Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
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Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000
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2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett
1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
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487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
64
65
Chapter 3 Atmosphere chemistry application
66
322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Presentation of the article
Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Authors Sarrami F Yu LJ Wan W and Karton A
Journal Chemical Physics Letter 2017 675 27-34
DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017
Graphical TOC
67
68
69
70
71
72
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik
1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part
I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical
Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part
II Some results and discussion In Mathematical Proceedings of the Cambridge
Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson
Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced
electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991
95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139
134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am
Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980
72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ
and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett
1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
Activity Relationship 2002 21 73
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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy
of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD
Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci
2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley
amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I
J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
2007 3(2) 407
References
134
69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys
Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J
Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G
Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem
Phys 1989 90 5622
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94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997
106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999
110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem
Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999
313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem
Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000
112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys
2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett
1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
2009 11 2899
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487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
65
Chapter 3 Atmosphere chemistry application
66
322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Presentation of the article
Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Authors Sarrami F Yu LJ Wan W and Karton A
Journal Chemical Physics Letter 2017 675 27-34
DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017
Graphical TOC
67
68
69
70
71
72
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part
I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical
Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part
II Some results and discussion In Mathematical Proceedings of the Cambridge
Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson
Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced
electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991
95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139
134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am
Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980
72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ
and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett
1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
Activity Relationship 2002 21 73
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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy
of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD
Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci
2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley
amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I
J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
2007 3(2) 407
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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys
Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem
Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem
Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J
Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G
Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem
Phys 1989 90 5622
References
136
115 Curtiss L A Raghavachari K Trucks G W Pople J A J Chem Phys 1991
94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997
106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999
110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem
Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999
313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem
Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000
112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys
2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett
1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
2009 11 2899
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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327
487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 3 Atmosphere chemistry application
66
322 Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Presentation of the article
Title Sulphuric acid-catalysed formation of hemiacetal from glyoxal and ethanol
Authors Sarrami F Yu LJ Wan W and Karton A
Journal Chemical Physics Letter 2017 675 27-34
DOI httpsdxdoiorg 101016jcplett201702084 Date of Publication March 2017
Graphical TOC
67
68
69
70
71
72
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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II Some results and discussion In Mathematical Proceedings of the Cambridge
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980
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and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett
1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci
2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley
amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I
J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys
Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem
Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem
Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J
Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G
Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem
Phys 1989 90 5622
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115 Curtiss L A Raghavachari K Trucks G W Pople J A J Chem Phys 1991
94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997
106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999
110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem
Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999
313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem
Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000
112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys
2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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131 Karton A Sylvetsky N and Martin JM W4‐17 J Comput Chem 2017 38
2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett
1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
2009 11 2899
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487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
67
68
69
70
71
72
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980
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and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett
1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci
2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys
Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
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Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G
Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem
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E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327
487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
References
140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
68
69
70
71
72
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
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140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
69
70
71
72
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
References
140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
70
71
72
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
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140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
71
72
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
References
140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
72
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
References
140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
73
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
References
140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
74
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
References
140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
75
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes 41 Introduction
Boron like carbon forms stable covalently bonded molecular frameworks
through self-bonding a typical example being polyhedral cluster structures
possessing a unique stereochemistry Polyhedral heteroboranes have been the subject
of intense research for over 55 years 231232233234235 A subset of this extensive class
of compounds is dicarba-closo-dodeca-boranes commonly referred to as carboranes
(an abbreviation of the IPUAC name carbaboranes) having the general formula
C2B10H12
Carborane clusters were first reported in the 1960s and since then this area has
experienced enormous growth Many new synthetic procedures have been
developed236237238239240241 The synthetic advances bonding theories of boron
clusters and more specifically icosahedral carborane derivatives have been utilized 242243 in such diverse areas244 as medicine (including boron neutron capture therapy
and drug delivery) catalysis nonlinear optical materials liquid crystals metal-ion
extraction super acid chemistry 245 conducting organic polymers coordination
polymers and others
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
References
140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
76
411 Introduction to Thermochemistry of icosahedral
closo-dicarboranes
Highest members of this class of compounds are dicarba-closo-dodecaboranes
commonly referred to as carboranes (an abbreviation of the IPUAC name carbaboranes)
having the general formula C2B10H12 Carboranes exist as (1) ortho meta (2) and (3)
para isomers which differ in the relative positions of the carbon atoms in the cluster
The structures of the three isomers for carborane are shown in Figure 41 The clusters
have nearly icosahedral geometry in which each of the carbon and boron atoms are
hexacoordinate
Figure 41 ortho (1) meta (2) and (3) para-Carborane
The synthesis of ortho-carborane was first reported in 1963 by two groups246247
Ortho-carboranes are prepared by the reaction of acetylenes including both mono and
substituted alkynes with B10H12L2 which is generated from decaborane (B10H14) and a
weak Lewis base (L= CH3CN RSR R3N) The meta and para-carborane isomers are
prepared by thermal isomerization of ortho-carborane under an inert atmosphere At
400ndash500 degC orthondashcarborane converts to the meta-isomer which in turn rearranges to
the para-isomer between 600ndash700degC The mechanism of isomerization has been the
subject of considerable interest248249250251252 The structural properties of such species
are still not clearly understood especially for systems comprising large clusters which
are not always amenable from direct structural investigations such as those utilizing X-
ray and electron diffraction techniques There have been only a small number of
correlated ab initio investigations of their thermochemical properties
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
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105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
77
One of the goals of the present paper was to re-evaluate the stability of the
icosahedral dicarborane isomers their ionization potentials (IPs) and the various CndashH
and BndashH BDEs by using the high-level ab initio W1ndashF12 thermochemical protocol
W1ndashF12 is a high-level composite theory that obtains the all-electron relativistic
CCSD(T)CBS energy (complete basis-set-limit coupled cluster with singles doubles
and quasi perturbative triple excitations) and achieves an accuracy in the sub-kcal molndash1
range for molecules that have wave functions dominated by dynamical correlation We
obtained heats of formation (
isomerization energies ionization potentials and CndashH and BndashH bond dissociation
energies for the carborane isomers using the high-level ab initio W1ndashF12
thermochemical protocol To the best of our knowledge the thermochemical properties
of the carboranes have not been previously studied at the CCSD(T)CBS level of theory
Thus this investigation provides the most accurate thermochemical values that are
presently available for these compounds Our best W1ndashF12 heats of formation
According to these W1ndashF12 values the meta isomer is less stable than the para isomer
by 269 kcal molndash1 whereas the ortho isomer is less stable than the para isomer by 1865
kcal molndash1 These isomerization energies are in reasonably good agreement with
previous theoretical values obtained at much lower levels of theory Finally we
evaluated the performance of a range of lower cost Gn and CBS composite ab initio
procedures We found that the G3(MP2)B3 procedure offers a stellar pricendashperformance
ratio with an overall RMSD of only 027 kcal molndash1
Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Chapter 4 Thermochemistry of icosahedral closo-dicarboranes
78
412 Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Presentation of the article
Title Thermochemistry of icosahedral closo-dicarboranes a composite ab initio quantum-chemical perspective
Authors Sarrami F Yu LJ and Karton A
Journal Canadian Journal of Chemistry 2016 94 1082-1089
DOI httpsdxdoiorg101139cjc-2016-0272 Date of Publication July 2016
79
80
82
83
84
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Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
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79
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik
1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part
I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical
Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part
II Some results and discussion In Mathematical Proceedings of the Cambridge
Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson
Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced
electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991
95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139
134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am
Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980
72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ
and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett
1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
Activity Relationship 2002 21 73
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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy
of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD
Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci
2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley
amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I
J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
2007 3(2) 407
References
134
69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys
Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
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2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J
Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G
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Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000
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2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
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Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
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487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
80
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci
2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
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Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
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Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G
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2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
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138
151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327
487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
References
139
173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
References
140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
82
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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II Some results and discussion In Mathematical Proceedings of the Cambridge
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
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DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
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Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
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Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
83
84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem
Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
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Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G
Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem
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2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
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84
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik
1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part
I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical
Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part
II Some results and discussion In Mathematical Proceedings of the Cambridge
Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson
Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced
electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991
95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
References
132
24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139
134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am
Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980
72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ
and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett
1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
Activity Relationship 2002 21 73
References
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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy
of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD
Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci
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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
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Phys
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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J
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Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000
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Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
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487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
85
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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II Some results and discussion In Mathematical Proceedings of the Cambridge
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980
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and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett
1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci
2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley
amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I
J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys
Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem
Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem
Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J
Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G
Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem
Phys 1989 90 5622
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115 Curtiss L A Raghavachari K Trucks G W Pople J A J Chem Phys 1991
94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997
106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999
110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem
Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999
313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem
Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000
112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys
2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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131 Karton A Sylvetsky N and Martin JM W4‐17 J Comput Chem 2017 38
2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett
1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
2009 11 2899
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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327
487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
References
139
173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
References
140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
86
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
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Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
87
Chapter 5 Summary and Conclusions
This thesis examined the applications of high-level computational methods for a
range of important thermochemical and kinetic properties in organic and
biochemistry The dissertation has covered various theoretical procedures (eg ab
initio methods DFT methods and composite methods) to study specific reaction
mechanism based on 1) antioxidant activity of carnosine and vitamin E and
designing more effective candidates 2) catalytic reaction related to the atmosphere
and 3) calculation of thermochemical and kinetic properties (eg different type of
data set for isomerization energies reaction energies and their barrier heights) This
combination of these approaches gives a more in-depth understanding of the
application of high-level computational methods in chemistry biochemistry and
atmospheric chemistry A brief summary for the research presented along is
provided
Computational anti-oxidant design based on carnosin was the first project we
investigated by studying the reaction of intramolecular Br+ shift in carnosine that
from the imidazole ring and primary amine moieties The Br+ transfer is found to be
the rate-determining step with a barrier of 972 kJ molndash1 relative to the minimum-
energy conformation of N-brominated carnosine Based on that results we started to
design new candidates by first) increasing the length of the β-alanyl-glycyl side-
chain for Br+ shifts (structural effect) and second) substitution of the imidazole ring
with some electron donator and acceptor groups for both the Cl+ and Br+ shifts
(electronic effect) In addition we showed that combination of structural and
electronic effects leads to the most effective candidate For example a derivative of
carnosine in which the length of the β-alanyl-glycyl side chain is increased by one
carbon and the imidazole ring situated with a strong electron-donating group results
in barriers of 414 and 278 kJ molndash1 respectively for the Cl+ and Br+ transfers
Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
2007 3(2) 407
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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem
Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem
Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
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Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G
Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem
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115 Curtiss L A Raghavachari K Trucks G W Pople J A J Chem Phys 1991
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E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
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Chapter 6 Appendices
88
In another project we investigated the mechanism for the intramolecular ring-
opening reaction of a-tocopherone (as a part of antioxidant activity mechanism of
vitamin E) using DHDFT method The uncatalysed reaction is associated with a
high activation enthalpy of 1599 kJ mol-1 Involvement of one and two water
catalysts in the TS reduce the reaction barrier height to 1273 and 1103 kJ molndash1
respectively This catalytic efficiency can be rationalised by (i) the reduction in
strain energy in the TSs in the order uncatalysed 1-water catalysed and 2-water
catalysed and (ii) improved trajectories for the proton transfers from the
hydroxyl group to the heterocyclic oxygen This catalytic effect can be
explained by reducing the strain energy from uncatalyst to 2-water catalysed
which improves the proton transfer from hydroxyl group to heterocyclic oxygen
Based on proposed mechanism we continued to explore new potential candidate
by reducing the size of heterocyclic ring and replacing the heterocyclic oxygen
by sulfur atom Our results showed that reducing the size of the heterocyclic ring
of the a-tocopherone to a four-membered ring not only reduces the barrier for
the ring-opening reaction but also significantly increases the thermodynamic
driving force for the overall reaction In particular for the four-membered ring
analogue of a-tocopherol we obtained reaction barrier heights of 892 and 873
kJ mol-1 for the reactions catalysed by one and two water molecules
respectively We hope that our computational investigation will inspire further
experimental investigations of the antioxidant activity of the proposed antioxidants
In the second part of this thesis we investigated the application of high-level
computational methods for two important catalytic atmospheric reaction mechanisms
including 1) sulphuric acid-catalysed 14-hydrogen transfer in higher Criegee
intermediates (CIs) and 2) sulphuric acid-catalysed formation of hemiacetal from
glyoxal and ethanol In the first project Using the high-level G4(MP2) composite ab
initio theoretical procedure sulphuric acid was found to effectively catalyse 14
hydrogen shift reactions in methyl CI and in isoprene derived and a-pinene derived
CIs These products formed through this channel are likely to directly contribute to
organic aerosol production Conversely water was found to exhibit only a minor
catalytic effect for these 14 H-shift reactions The reaction barrier heights for the
sulphuric acid-catalysed reactions are 164 (methyl CI) 245 (isoprene CI) and 84
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik
1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part
I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical
Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part
II Some results and discussion In Mathematical Proceedings of the Cambridge
Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson
Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced
electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991
95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
References
132
24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139
134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am
Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980
72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ
and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett
1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
Activity Relationship 2002 21 73
References
133
49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy
of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD
Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci
2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys
Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem
Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem
Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J
Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G
Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem
Phys 1989 90 5622
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110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem
Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999
313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem
Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000
112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys
2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett
1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
2009 11 2899
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138
151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327
487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
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139
173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
References
140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
89
(a-pinene CI) kJ molndash1 relative to the reactant complexes in comparing to the
uncatalyst reaction 722 (methyl CI) 805 (isoprene CI) and 662 (a-pinene CI) kJ
molndash1 of respectively Therefore the computational findings presented here suggest
the possibility of a facile bimolecular reaction of sulphuric acid with higher Criegee
intermediates containing a β-hydrogen resulting in the formation of vinyl
hydroperoxide Reaction with sulphuric acid is therefore likely an important
removal process for stabilized CIs in regions of high H2SO4 concentrations
In the second project of this chapter we used the high-level (G4(MP2)
composite ab initio procedure to investigate the uncatalysed water-catalysed
ethanol-catalysed HC(O)OH-catalysed and H2SO4-catalysed reactions of glyoxal
with two consecutive ethanol molecules to form a hemiacetal in the first step and a
dihemiacetal in the second step Introduction of a water molecule reduces the
reaction barrier for the first step by converting the strained 4-membered cyclic TS to
less strained 6-membered cyclic TS In particular we obtained an activation energy
of = 873 kJ molndash1 relative to the RC1 for water-catalysed reaction A formic acid
catalyst reduces the barrier for this reaction to 330 kJ molndash1 relative to RC1 This
significant reduction in the activation enthalpy is attributed to the conversion of the
6-membered ring TS to an 8-membered ring TS An H2SO4 catalyst further reduces
the barrier for this step to merely 163 kJ molndash1 relative to RC1 This reduction in the
activation enthalpy is attributed to the further reduction in strain energy associated
with moving from a first-row central atom to a larger second-row central atom in the
oxoacid This work shows that H2SO4 can also effectively catalyse an intermolecular
proton transfer that is coupled with the formation of a covalent CndashO bond These
findings may have significant consequences for atmospheric models since the
conversion of glyoxal to hemiacetal in the atmosphere may have important
consequences for secondary organic aerosol formation under atmospheric conditions
In the last part of my thesis we obtained heats of formation isomerization
energies ionization potentials and CndashH and BndashH bond dissociation energies for the
carborane isomers using the high-level W1ndashF12 thermochemical protocol To the
best of our knowledge the thermochemical properties of the carboranes have not
been previously studied at the CCSD(T)CBS level of theory Our best heats of
formation values are ndash5063 kcal molndash1(para-carborane) ndash4794 kcal molndash1
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
References
140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
90
(metacarborane) and ndash3197 kcal molndash1 (ortho-carborane) According to these W1ndash
F12 values the meta isomer is less stable than the para isomer by 269 kcal molndash1
whereas the ortho isomer is less stable than the para isomer by 1865 kcal molndash1
These isomerization energies are in reasonably good agreement with previous
theoretical values obtained at much lower levels of theory These values agree with
the experimental values adopted by the NIST Chemistry Web Book to within
overlapping uncertainties however they suggest that the experimental IPs represent
underestimations Finally we evaluated the performance of a range of lower cost Gn
and CBS composite ab initio procedures We found that the G3(MP2)B3 procedure
offers a stellar pricendashperformance ratio with an overall RMSD of only 027 kcal
molndash1 for the isomerization ionization and bond dissociation energies However the
more recent G4-type procedures provide relatively poor performance with RMSDs
of 369 kcal molndash1 (G4(MP2)) 204 kcal molndash1 (G4) and 125 kcal molndash1 (G4(MP2)ndash
6X)
Although the high-level computational methods in this thesis are highly accurate
there are some limitations that have to be mentioned
1) When modelling biological systems (Chapter 2) we use simplified models in
which solvent and pH effects are treated in an approximate way (for example
with a continuum solvent model) In future work it would be good to
perform extensive Molecular Dynamic (MD) simulation to model these
effects more accurately
2) In the atmospheric catalytic reactions considered in Chapter 3 the reaction
barrier heights and the catalytic enhancements are calculated using classical
transition state theory and tunneling effects are completely neglected In
future work it would be good to convert our accurate reaction barrier heights
into reaction rates using master equation and RRKM methods with explicit
account of tunneling effects
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am
Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980
72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ
and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett
1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
Activity Relationship 2002 21 73
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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy
of Sciences 20031006 235 50 Meier RJ Faraday Discuss 2003 124 405 51 Ramalho TC de Alencastro RB La-Scalea MA and Figueroa-Villar JD
Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci
2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley
amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I
J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
2007 3(2) 407
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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys
Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem
Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem
Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J
Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G
Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem
Phys 1989 90 5622
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115 Curtiss L A Raghavachari K Trucks G W Pople J A J Chem Phys 1991
94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997
106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999
110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem
Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999
313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem
Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000
112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys
2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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131 Karton A Sylvetsky N and Martin JM W4‐17 J Comput Chem 2017 38
2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett
1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
2009 11 2899
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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327
487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
91
Chapter 6 Appendices
61 Appendix A Online Supplementary Information for ldquo Thermochemistry of icosahedral closo-
dicarboranes a composite ab initio quantum-chemical perspectiverdquo by Sarrami F
Yu LJ and Karton A Canadian Journal of Chemistry 2016 94 1082-1089
62 Appendix B Online Supplementary Information for ldquo Sulphuric acid-catalysed formation of
hemiacetal from glyoxal and ethanolrdquo by Sarrami F Yu LJ Wan W and
Karton A Chemical Physics Letters 2017 675 27-34
63 Appendix C Online Supplementary Information for ldquo Computational design of bio-inspired
carnosine-based HOBr antioxidants ldquo by Sarrami F Yu LJ and Karton A
Journal of computer-aided molecular design 2017 31 905-913
64 Appendix D Online Supplementary Information for ldquo A computational investigation of the
sulphuric acid catalysed 1 4 hydrogen transfer in higher Criegee intermediatesrdquo by
Mackenzie Rae FA and Karton A International Journal of Quantum Chemistry
2018 118 25599
65 Appendix E Online Supplementary Information for ldquo Mechanistic insights into the water-
catalysed ring-opening reaction of vitamin E by means of double-hybrid density
functional theoryrdquo by Sarrami F Kroeger A A and Karton A Chemical
Physics Letters 2018 708 123
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980
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and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett
1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci
2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
2007 3(2) 407
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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys
Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
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Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G
Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem
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2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327
487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
References
139
173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
References
140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
92
66 Appendix F Online Supplementary Information for ldquo An assessment of theoretical procedures for
π-conjugation stabilisation energies in enonesrdquo by Yu LJ Sarrami F Karton A
and OrsquoReilly RJ Molecular Physics 2015113 1284-1296
67 Appendix G Online Supplementary Information for ldquo A Reaction barrier heights for
cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab
initio proceduresrdquo by Yu LJ Sarrami F OrsquoReilly RJ and Karton Chemical
Physics 2015 458 1-8
68 Appendix H Online Supplementary Information for ldquo Can DFT and ab initio methods describe all
aspects of the potential energy surface of cycloreversion reactions rdquo by Yu LJ
Sarrami F OReilly RJ and Karton A Molecular Physics 2016114 21-33
69 Appendix I Online Supplementary Information for ldquoSol-Gel auto-combustion synthesis and
physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen
storage performance and density functional theory ldquoSalehabadi A Salavati-Niasari
M Sarrami F and Karton A Renewable Energy 2017 114 1419-1426
610 Appendix J Online Supplementary Information for ldquo Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel
auto-combustion synthesis characterization and joint experimental and
computational structural analysis for electrochemical hydrogen storage
performancesrdquo by Salehabadi A Sarrami F Salavati-Niasari M Gholami T
Spagnoli D and Karton A Journal of Alloys and Compounds 2018 744 574-582
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
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GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys
Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem
Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
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2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
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502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
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Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
93
611 Appendix K Online Supplementary Information for ldquo Study of dual encapsulation possibility of
hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated
graphene oxide using density functional theory molecular dynamics simulation and
experimental methodsrdquo by Moradi S Taran M Mohajeri P Sadrjavadi K
Sarrami F Karton A Journal of Molecular Liquids 2018 262 204-217
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
References
140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
94
61 Appendix A Electronic Supplementary Information
Thermochemistry of icosahedral closo-
dicarboranes A composite ab initio quantum-
chemical perspective
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik
1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part
I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical
Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part
II Some results and discussion In Mathematical Proceedings of the Cambridge
Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson
Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced
electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991
95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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24 Schuumltz M Werner H-J J Chem Phys 2001 114 661 25 M Schuumltz H-J Werner Chem Phys Lett 2000 318 370 26 Riplinger C Neese F J Chem Phys 2013 138 034106 27 Riplinger C Sandhoefer B Hansen A Neese F J Chem Phys 2013 139
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Chapter 6 Appendices
95
Table S1 TAE[(T)] diagnostics for the importance of post-CCSD(T) correlation effects for the species considered in the present study (shown in Fig 1 of the main
text)a
aTAE[(T)] is the percentages of the valence CCSD(T) atomization energy accounted for by the (T) component (for
further details see refs 1 2 3) bTAE[(T)] values are obtained at the CCSD(T)6-31G(d) level of theory cTAE[(T)] values are obtained at the CBS limit from W1-F12 theory dXbull indicates on which B or C atom the radical is centered (see Figure 1)
TAE[(T)]b TAE[(T)]c 6-31G(d) W1-F12
para 15 19 C2B10H12 meta 15 19
ortho 16 20 para 18 22
C2B10H12+ meta 17 21
ortho 18 22 para Bbulld 16 20 para Cbulld 16 20 meta B2bulld 16 20 meta B4bulld 16 R meta B5bulld 16 20
C2B10H12bull meta B9bulld 16 20 meta Cbulld
16 20 ortho B3bulld 16 20 ortho B4bulld 16 R ortho B8bulld 16 20 ortho B9bulld 16 20 ortho Cbulld 17 21
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
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J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
96
Table S2 Deviations and overall error statistics from W1-F12 values of
isomerization ionization CndashH bond dissociation and BndashH bond dissociation energies
for carboranes obtained by standard ab initio methods (kcal molndash1)
QCISD(T)
CCSD(T) SCF SCF
6-31G(d) 6-31G(d) 6-31G(d) VTQZa
Isomerization meta 021 021 -030 -040
ortho 064 065 183 163
Ionization para -488 -445 -1748 -1484
meta -548 -577 -1938 -1790
ortho -522 -547 -1446 -1748
CndashH BDE para 020 032 -1602 -1590
meta 005 019 -1584 -1566
ortho 007 023 -1506 -1493
BndashH BDE para -058 -058 -1539 -1560
meta B2ndashHb -071 -071 -1541 -1555
meta B4ndashHb -064 -064 -1539 -1560
meta B5ndashHb -053 -053 -1535 -1561
meta B9ndashHb -056 -054 -1532 -1556
ortho B3ndashHb -072 -072 -1542 -1562
ortho B4ndashHb -060 -058 -1521 -1542
ortho B8ndashHb -054 -052 -1524 -1550
ortho B9ndashHb -048 -047 -1526 -1555
Error statisticsc RMSD 223 226 1484 1485
MAD 130 133 1402 1404
MSD -116 -114 -1380 -1385
LD -548 -577 -1938 -1790
aExtrapolated SCF component used in G4(MP2) theory bBxndashH indicates on which BndashH bond is being broken (see Figure 1) cThe error statistics are over all the chemical properties listed above RMSD = root- mean-square deviation MAD = mean-absolute deviation MSD = mean-signed deviation LD = largest deviation
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980
72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ
and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett
1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci
2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley
amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I
J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
2007 3(2) 407
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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys
Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem
Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem
Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J
Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G
Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem
Phys 1989 90 5622
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115 Curtiss L A Raghavachari K Trucks G W Pople J A J Chem Phys 1991
94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997
106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999
110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem
Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999
313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem
Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000
112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys
2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett
1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
2009 11 2899
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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327
487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
97
Table S3 Higher-level correction terms E(HLC) used in the G3(MP2) and G4(MP2)
procedures (kcal molndash1)
G3(MP2) G4(MP2)
Isomerization meta 0 0
ortho 0 0
Ionization para 302 -048
meta 302 -048
ortho 302 -048
CndashH BDE para 175 -180
meta 175 -180
ortho 175 -180
BndashH BDE para 175 -180
meta B2ndashHa 175 -180
meta B4ndashHa 175 -180
meta B5ndashHa 175 -180
meta B9ndashHa 175 -180
ortho B3ndashHa 175 -180
ortho B4ndashHa 175 -180
ortho B8ndashHa 175 -180
ortho B9ndashHa 175 -180
aBxndashH indicates on which BndashH bond is being broken (see Figure 1)
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik
1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part
I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical
Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part
II Some results and discussion In Mathematical Proceedings of the Cambridge
Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson
Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced
electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991
95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
98
Table S5 Full References for Molpro 2012 (ref 22) CFOUR (ref 41) and Gaussian 09 (ref 50) (22) MOLPRO version 20121 a package of ab initio programs Werner H-J Knowles P J Manby F R Schuumltz M Celani P Knizia G Korona T Lindh R Mitrushenkov A Rauhut G Adler T B Amos R D Bernhardsson A Berning A Cooper D L Deegan M J O Dobbyn A J Eckert F Goll E Hampel C Hesselmann A Hetzer G Hrenar T Jansen G Koumlppl C Liu Y Lloyd A W Mata R A May A J McNicholas S J Meyer W Mura M E Nicklaszlig A Palmieri P Pfluumlger K Pitzer R Reiher M Shiozaki T Stoll H Stone A J Tarroni R Thorsteinsson T Wang M See also httpwwwmolpronet (41) CFOUR a quantum chemical program package written by JF Stanton J Gauss ME Harding PG Szalay with contributions from AA Auer RJ Bartlett U Benedikt C Berger DE Bernholdt YJ Bomble L Cheng O Christiansen M Heckert O Heun C Huber T-C Jagau D Jonsson J Juseacutelius K Klein WJ Lauderdale F Lipparini DA Matthews T Metzroth LA Muumlck DP ONeill DR Price E Prochnow C Puzzarini K Ruud F Schiffmann W Schwalbach C Simmons S Stopkowicz A Tajti J Vaacutezquez F Wang JD Watts and the integral packages MOLECULE (J Almloumlf and PR Taylor) PROPS (PR Taylor) ABACUS (T Helgaker HJ Aa Jensen P Joslashrgensen and J Olsen) and ECP routines by A V Mitin and C van Wuumlllen For the current version see httpwwwcfourde (50) Gaussian 09 Revision D01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V Mennucci B Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
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2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley
amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I
J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem
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2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
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94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
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Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
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Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
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Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
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Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
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Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
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Chapter 6 Appendices
99
62 Appendix BElectronic Supplementary Information
Sulphuric acid-catalysed formation of hemiacetal
from glyoxal and ethanol Farzaneh Sarrami Li-Juan Yu Wenchao Wan and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
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DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
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Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
100
Table S1 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed reaction of glyoxal and two ethanol molecules and the reactions catalysed by water ethanol formic acid and sulphuric acid
Specie
Catalyst RC1 TS1 INT1 INT2 TS2 INT3 PROD
Uncatalysed 157 1726 -117 23 1591 NA -203
Water 455 1482 102 364 1273 56 -203
Ethanol 400 1350 89 165 1148 07 -203
Formic acid 74 574 -180 151 598 -140 -203
Sulphuric acid 86 386 -171 179 312 -173 -203
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
101
Table S3 Full reference for Gaussian 09 (ref 30) (30) Gaussian 09 Revision E01 Frisch M J Trucks G W Schlegel H B Scuseria G E Robb M A Cheeseman J R Scalmani G Barone V MennucciB Petersson G A Nakatsuji H Caricato M Li X Hratchian H P Izmaylov A F Bloino J Zheng G Sonnenberg J L Hada M Ehara M Toyota K Fukuda R Hasegawa J Ishida M Nakajima T Honda Y Kitao O Nakai H Vreven T Montgomery Jr J A Peralta J E Ogliaro F Bearpark M Heyd J J Brothers E Kudin K N Staroverov V N Kobayashi R Normand J Raghavachari K Rendell A Burant J C Iyengar S S Tomasi J Cossi M Rega N Millam N J Klene M Knox J E Cross J B Bakken V Adamo C Jaramillo J Gomperts R Stratmann R E Yazyev O Austin A J Cammi R Pomelli C Ochterski J W Martin R L Morokuma K Zakrzewski V G Voth G A Salvador P Dannenberg J J Dapprich S Daniels A D Farkas Ouml Foresman J B Ortiz J V Cioslowski J Fox D J Gaussian Inc Wallingford CT 2009
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327
487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
102
63 Appendix C Electronic Supplementary Information
Computational design of bio-inspired carnosine-
based HOBr antioxidants
Farzaneh Sarrami Li-Juan Yu and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009 Australia
Supplementary Data
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley
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J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
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2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem
Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J
Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G
Gauss J Stanton J F J Chem Phys 2006 125 064108114 Pople J A Head-Gordon M Fox D J Raghavachari K Curtiss L A J Chem
Phys 1989 90 5622
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110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem
Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999
313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem
Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000
112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys
2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
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Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
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502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
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Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
103
Figure S1 Atom numbers for the structure carnosine in REAC and INT2 used in
Table 1
Table S1 Atomic polar tensor (APT) charges on the imidazole ring and the halide
atom in the REAC and INT2 (see Figure S1 for atom numbering)
APT charges
REAC
Cl+ INT2
REAC
Br+ INT2
N1 ndash0691 ndash0725 ndash0709 ndash0734
N2 ndash0002 0008 ndash0122 ndash0114
C1 0291 0282 0300 0285
C2 0015 ndash0032 0017 ndash0035
C3 0135 0188 0135 0191
H1 0123 0204 0119 0198
H2 0150 0181 0148 0173
H3 Nil 0904 Nil 0919
Imidazole ringa 0019 1011 ndash0111 0882
X ndash0089 0011 0047 0147aSum of the APT charges on the atoms of the imidazole ring
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci
2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley
amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I
J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
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Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
144108 109 Ochterski JW Petersson GA and Montgomery Jr JA J Chem
Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 1999 110(6) 2822 111 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
Phys 2000 112(15) 6532 112 Harding M E Vazquez J Ruscic B Wilson A K Gauss J Stanton J F J
Chem Phys 2008 128 15 113 Bomble Y J Vazquez J Kallay M Michauk C Szalay P G Csaszar A G
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110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem
Phys Lett 1999 314 101119 Curtiss L A Redfern P C Raghavachari K Pople J A Chem Phys Lett 1999
313 600 120 Curtiss L A Redfern P C Raghavachari K Rassolov V Pople J A J Chem
Phys 1999 110 4703 121 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 2000
112 7374 122 Curtiss L A Redfern P C Rassolov V Kedziora G Pople J A J Chem Phys
2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
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Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
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502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
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Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
104
Table S2 Bond length of N2ndashX (Aring) (Figure 1) for TS2 in the intramolecular X+
transfer in the N-halogenated derivatives of carnosine shown in Figure 5 (X = Cl and
Br)
Cl+ Br+
Ra N2ndashX (Aring) N2ndashX (Aring)
NO2 (078) 1764 1875
CHO (042) 1782 1890
H (00) 1790b 1893
OH (ndash037) 1804 1896
NH2 (ndash066) 1816 1900 a
p constants are given in parenthesis b
Values taken from reference 37
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980
72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ
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1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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49 Reimers JR CAI ZL Bilić A and Hush NS Annals of the New York Academy
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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
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Phys
2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
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2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
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Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
105
Table S3 Sum of the atomic polar tensor (APT) charges on the N2 (Figure 1) and halide
atoms in TS2 for the intramolecular X+ transfer in the N-halogenated derivatives of
carnosine shown in Figure 5 of the main text (X = Cl and Br)
ap constants are given in parenthesis
Cl+ Br+
Ra N2bullbullbullX+ (au) N2bullbullbullX+ (au)
NO2 (078) +065 +063
CHO (042) +059 +055
H (00) +023 +021
OH (ndash037) ndash004 ndash006
NH2 (ndash066) ndash014 ndash016
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
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Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
106
64 Appendix D Electronic Supplementary Information
A computational investigation of sulphuric
acid-catalysed 14-hydrogen transfer in higher
Criegee intermediates
Farzaneh Sarrami FelixA Makenzie-Rae and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA 6009
Australia
Supplementary Data
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
107
Figure S1 Optimized transition structures for the uncatalysed water-catalysed and
sulphuric acid-catalysed 14 H-shift reactions in methyl CI
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
108
Figure S2 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed
(black line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line)
reactions for the 14 H-shifts of isoprene CI
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
109
Figure S3 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI1
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
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T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
110
Figure S4 Reaction profiles (G4(MP2) ΔG298 kJ molndash1) for the uncatalysed (black
line) water-catalysed (orange line) and sulphuric acid-catalysed (blue line) reactions
for the 14 H-shifts of α-pinene CI2 (CI2-I and CI2-II)
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
111
Table S2 Full details for reference 59 (Gaussian 09)
[59] MJ Frisch GW Trucks HB Schlegel GE Scuseria MA Robb JR Cheeseman G Scalmani V Barone B Mennucci GA Petersson H Nakatsuji M Caricato X Li HP Hratchian AF Izmaylov J Bloino G Zheng JL Sonnenberg M Hada M Ehara K Toyota R Fukuda J Hasegawa M Ishida T Nakajima Y Honda O Kitao H Nakai T Vreven JA Montgomery Jr JE Peralta F Ogliaro MJ Bearpark J Heyd EN Brothers KN Kudin VNStaroverov R Kobayashi J Normand K Raghavachari AP Rendell JC Burant SS Iyengar J Tomasi M Cossi N Rega NJ Millam M Klene JE Knox JB Cross V Bakken C Adamo J Jaramillo R Gomperts RE Stratmann O Yazyev AJ Austin R Cammi C Pomelli JW Ochterski RL Martin K Morokuma VG Zakrzewski GA Voth P Salvador JJ Dannenberg S Dapprich AD Daniels Ouml Farkas JB Foresman JV Ortiz J Cioslowski DJ Fox Gaussian09 Gaussian Inc Wallingford CT USA 2009
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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72(1) 650 40 Frisch MJ Pople JA and Binkley JS J Chem Phys 1984 80(7) 3265 41 Francl MM Pietro WJ Hehre WJ Binkley JS Gordon MS DeFrees DJ
and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett
1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
Activity Relationship 2002 21 73
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105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
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Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
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Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
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M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
112
65 Appendix E Electronic Supplementary Information
Mechanistic insights into the water-catalysed
ring-opening reaction of vitamin E by means of
double-hybrid density functional theory
Farzaneh Sarrami Asja A Krorger and Amir Karton
School of Molecular Sciences The University of Western Australia Perth WA
6009 Australia
Supplementary Data
Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
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Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci
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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley
amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I
J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
2007 3(2) 407
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105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
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Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
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Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
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J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
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L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
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Chapter 6 Appendices
113
Figure S1 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the uncatalysed rearrangement reaction of α-tocopherone to ATQ The bonds being broken and formed in the transition structures are represented by black dashed lines
Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
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A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
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Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
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2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
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J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
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Chapter 6 Appendices
114
Figure S2 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ mol ) for the rearrangement reaction of α-tocopherone to ATQ catalysed by one (red line) and two (blue line) water molecules Dashed lines in the transition structures represent bonds being broken and formed whilst in the RCs and PCs dashed lines represent hydrogen bonds
Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
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Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
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Chapter 6 Appendices
115
Figure S3 Reaction profile (∆G298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the uncatalysed (black line) H2O-catalysed (red line) and 2H2O-catalysed (blue line) rearrangement reaction in the proposed antioxidant candidate 1 (Scheme 1 of the main text) A schematic representation of the TSs is shown in which bonds being broken and formed are represented by dashed lines
Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
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PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
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Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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Chapter 6 Appendices
116
Figure S4 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1)
for the uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed
(blue line) rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
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A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
117
Figure S5 Reaction profile (∆H298 CPCM(water)-DSD-PBEP86 kJ molndash1) for the
uncatalysed (black line) 1H2O-catalysed (red line) and 2H2O-catalysed (blue line)
rearrangement reaction of candidate 2 to the related quinone
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
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J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
118
Table S1 Reaction Gibbs free energies (∆G298) calculated at the CPCM(water)-DSD- PBEP86 level for the four possible products (A B C and D) of the radical coupling reaction between the tocopheroxyl radical and HObull (Figure 2 of the main text) ∆G298 values in kJ mol
ndash1are given relative to the free reactants
Intermediate ∆G298
A ndash713 B ndash2317 C ndash2587 D ndash2283
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik
1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part
I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical
Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part
II Some results and discussion In Mathematical Proceedings of the Cambridge
Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson
Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced
electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991
95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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134101 28 Slater J C Phys Rev 36 (1930) 57 29 Boys S F Proc Roy Soc London Ser A 1950 200 542 30 Gordon M S Binkley J S Pople J A Pietro W J and Hehre W J J Am
Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980
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and Pople JA J Chem Phys 1982 77(7) 3654 42 K Raghavachari G W Trucks J A Pople and M Head- Gordon Chem Phys Lett
1989 157 479 43 Thomas L H Proc Cambridge Phil Soc 1927 23 542 44 Fermi E ZPhysik 1928 48 73 45 Hohenberg 1 P Kohn W Phys Rev 1964 136 B864 46 Lewars GE Computational Chemistry Springer 201647 Kohn W L Sham J Phys Rev 1965 140 A1133 48 Sulpizi M Folkers G Rothlisberger U Carloni P Scapozza L Quantitative Structure
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Biophys Chem 2004110 267 52 RAMALHO TC DA CUNHA EF and DE ALENCASTRO RB J Theo
Comput Chem 2004 3 1 53 Noslashrskov JK Bligaard T Rossmeisl J and Christensen CH Nature
Chemistry 2009 1 37 54 Noslashrskov JK Abild-Pedersen F Studt F and Bligaard T Proc Natl Acad Sci
2011 108 937 55 Hammer BJKN and Noslashrskov JK Surface Science 1995 343 211 56 Linic S Jankowiak J and Barteau MA J Catal 2004 224 489 57 Greeley J and Mavrikakis M Nature materials 2004 3 810 58 Greeley J Jaramillo TF Bonde J Chorkendorff IB and Noslashrskov JK A
Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley
amp Sons 2013 63 Ew J P Ruzsinszky A Tao J Staroverov V N Scuseria G E Csonka G I
J Chem Phys 2005 123 062201 64 Peverati R and Truhlar DG Phil Trans R Soc A 2014 372 20120476 65 Perdew JP and Schmidt K In AIP Conference Proceedings 2001 577 1 66 Mattsson AE Science 2002 298 759 67 Zhao Y and Truhlar DG Theor Chem Acc 2008 120(1-3) 21568 Riley KE Opt Holt BT and Merz KM 2007 J Chem Theor Comput
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69 Perdew JP Ruzsinszky A Tao J Staroverov VN Scuseria GE and Csonka
GI J Chem Phys 2005 123(6) 062201 70 Kurth S Perdew JP and Blaha P Int J Quantum chem 1999 75(4‐5) 889 71 Vosko SH Wilk L Nusair M Can J Phys 1980 581200 72 Perdew JP and Wang Y Phys Rev B 1986 33 8800 73 Perdew JP and Wang Y Phys Rev B 1992 45 13244 74 Perdew JP Burke K and Ernzerhof M Phys Rev Lett 1996 77 3865 75 Ernzerhof Burke K and Ernzerhof M Phys Rev Lett 1997 78 1396 76 Becke A D Phys Rev A 1988 38 3098 77 Lee C Yang W Parr R G Phys Rev B 1988 37 785 78 Hamprecht FA Cohen AJ Tozer DJ Handy NC J Chem Phys 1998 15 6264 79 Becke A D J Chem Phys 1996 104 1040 80 Kirkwood J G J Chem Phys 1935 3 300 81 Kurth S Perdew JP Blaha P Int J Quantum Chem 1999 75 889 82 Sousa SF Fernandes OA Ramos MJ J Phys Chem A 200711110439 83 Goumlorling A Levy M Phys Rev B 1993 47 13105 84 Goumlorling A Levy M Phys Rev A 1994 50 196 85 Eshuis H J Bates E Furche F Theor Chem Acc 2012 131 86 Grimme S J Chem Phys 2006 124 034108 87 Moslashller C and Plesset M S Phys Rev1934 46 618 88 Schwabe T and Grimme S Phys Chem Chem Phys 2007 9 3397 89 Grimme S and Schwabe T Phys Chem Chem Phys 2006 8 4398 90 Karton A Tarnopolsky A Lameacutere JF Schatz GC and Martin JM J Phys
Chem A 2008 112 12868 91 Tarnopolsky A Karton A Sertchook R Vuzman D and Martin JM J Phys
Chem A 2008 112 3-8 92 Kozuch S Gruzman D and Martin JM 2010 DSD-BLYP J Phys Chem
C 2010 114(48) 20801 93 Kozuch S and Martin JM 2011 DSD-PBEP86 Phys Chem Chem Phys 2011
13(45) 20104 94 Goerigk L and Grimme S J Chem Theor Comput 2011 7(10) 3272
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95 Kristyan S and Pulay P Chem Phys Lett 1994 229 175 96 Hobza P Sponer J and Reschel T J Comput Chem 1995 16 1315 97 Pe rez-Jorda J M and Becke A D Chem Phys Lett 1995 233 134 98 Grimme S WIREs Comput Mol Sci 2011 1 211 99 Klime-s J Michaelides A J Chem Phys 2012 137 120901 100 Burns L A V-azquez-Mayagoitia A B Sumpter G C Sherrill D J Chem
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2011 134 084107101 Becke A D Johnson E R J Chem Phys 2005 123 154101 102 Johnson E R Becke A D J Chem Phys 2005 123 24101 103 Grimme S Antony J Ehrlich S Krieg H J Chem Phys 2010 132 154104 104 Feller D Peterson K A Dixon D A J Chem Phys 2008 129 204105 105 Martin J M L de Oliveira G J Chem Phys 1999 111 1843 106 Parthiban S Martin J M L J Chem Phys 2001 114 6014 107 Boese A D Oren M Atasoylu O Martin J M L Kallay M Gauss J J Chem
Phys 2004 120 4129 108 Karton A Rabinovich E Martin J M L Ruscic B J Chem Phys 2006 125
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Phys 1996104(7) 2598 110 Montgomery Jr JA Frisch MJ Ochterski JW and Petersson GA J Chem
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Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
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Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
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Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
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Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
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11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
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2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
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Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
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J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
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Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
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Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
119
66 Appendix F Presentation of the article
Title An assessment of theoretical procedures for π -conjugation stabilisation energies in enones
Authors Yu LJ Sarrami F Karton A
Journal Molecular Physics 113(11) 1284-1296
DOI httpsdxdoiorg 101080002689762014986238 Date of Publication February 2015
120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik
1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part
I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical
Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part
II Some results and discussion In Mathematical Proceedings of the Cambridge
Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson
Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced
electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991
95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
References
132
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120
Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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Collection of Peer-Reviewed Research and Review Articles from Nature Publishing
Group 2011 (pp 280) 59 Hohenberg P Kohn W Phys Rev B 1964 136 864 60 Parr RG In Horizons of Quantum Chemistry Springer 1980 5-15 61 Kohn W and Sham LJ Phys Rev 1965 140 A1133 62 Cramer CJ Essentials of computational chemistry theories and models John Wiley
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Chapter 6 Appendices
121
67 Appendix G
Presentation of the article
Title A Reaction barrier heights for cycloreversion of heterocyclic rings An Achillesrsquo heel for DFT and standard ab initio proceduresrdquo
Authors Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal Chemical Physics 2015 458 1-8
DOI httpsdxdoiorg101016jchemphys201507005
Date of Publication September 2015
122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
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122
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
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Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
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metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
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729
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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
123
68 Appendix H
Presentation of the article
Title Can DFT and ab initio methods describe all aspects of the potential energy surface of cycloreversion reactions
Author
Yu LJ Sarrami F OrsquoReilly RJ and Karton A
Journal
Renewable Energy 2017 114 1419-1426
DOI httpsdxdoiorg1010800026897620151081418
Date of Publication
September 2015
124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
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124
Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik
1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part
I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical
Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part
II Some results and discussion In Mathematical Proceedings of the Cambridge
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Chapter 6 Appendices
125
69 Appendix I
Presentation of the article
Title
Sol-Gel auto-combustion synthesis and physicochemical properties of BaAl2O4 nanoparticles electrochemical hydrogen storage performance and density functional theory
AuthorsSalehabadi A Salavati-Niasari M Sarrami F and Karton A
Journal Renewable Energy 2017 114 1419-1426
DOI
httpsdxdoiorg101016jrenene201707119
Date of Publication
December 2017
126
Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
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Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
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Chapter 6 Appendices
127
610 Appendix J
Presentation of the article
Title
Dy3Al2(AlO4)3 ceramic nanogarnets sol-gel auto-combustion synthesis characterization and joint experimental and computational structural analysis for electrochemical hydrogen storage performances
AuthorsSalehabadi A Sarrami F Salavati-Niasari M Gholami T Spagnoli D and Karton
Journal Journal of Alloys and Compounds 2018 744 574-582
DOI
httpsdxdoiorg101016jjallcom201802117
Date of Publication
May 2018
128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
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2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
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2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
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J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
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Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
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M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
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128
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
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metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
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143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
Chapter 6 Appendices
129
611 Appendix K
Presentation of the article
Title
Study of dual encapsulation possibility of hydrophobic and hydrophilic drugs into a nanocarrier based on bio-polymer coated graphene oxide using density functional theory molecular dynamics simulation and experimental methods
Authors Moradi S Taran M Mohajeri P Sadrjavadi K Sarrami F Karton
Journal Journal of Molecular Liquids 2018 262 204-217
DOI
httpsdxdoiorg101016jmolliq201804089
Date of Publication
July 2018
130
References
131
References 1 Born M Oppenheimer R Zur quantentheorie der molekeln Annalen der Physik
1927 389 (20) 457-4842 Hartree DR The wave mechanics of an atom with a non-Coulomb central field Part
I Theory and methods In Mathematical Proceedings of the Cambridge Philosophical
Society Cambridge University Press 1928 24(1) 89-110 3 Hartree DR The wave mechanics of an atom with a non-coulomb central field Part
II Some results and discussion In Mathematical Proceedings of the Cambridge
Philosophical Society Cambridge University Press 1928 24(1) 111-132 4 Fock V Z physik Phys Rev 1930 35 p210 5 Leach A R Molecular Modelling Principles and Applications second ed Pearson
Education EMA UK 2001 6 Jensen F Introduction to computational chemistry John wiley amp sons 2013 7 Pilar FL Elementary quantum chemistry 1990 286 8 Szabo A Ostlund N S Modern quantum chemistry Introduction to advanced
electronic structure theory McGraw-Hill Inc New York NY 1989 9 Schinke R J Chem Phys 2011 134 064313 10 Brouard M Enriquez S P P A Say os R and Simons J P J Phys Chem 1991
95 8169 11 Levine IN Quantum chemistry Pearson Higher Ed 2013 12 Moslashller C Plesset M S Phys Rev 1934 46 618ndash622 13 Bartlett R J Musiał M Rev Mod Phys 2007 79 291 14 Čiacutežek J J Chem Phys 1966 45 425615 Coester F Nucl Phys 1958 7 421 16 Coester F Kuumlmmel H Nucl Phys 1960 17 477 17 HiraoK Int J Quantum Chem 1992 517 18 Nakano H J Chem Phys 1993 99 7983 19 Coester F Nucl Phys 1958 7 421 20 Coester F and Kuumlmmel H Nucl Phys 1960 17 477 21 Nakano H Chem Phys Lett1993 207 372 22 Balabanov N B Peterson K A J Chem Phys 2005123 23 Watts J D Bartlett R J Int J Quant Chem 1993 51
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Chem Soc 1928 104 2797 31 Binkley J S Pople J A and Hehre W J J Am Chem Soc 1980 102 939 32 Frish M J Pople J A and Binkley J S J Chem Phys 1984 50 3265 33 Hariharan P C and Popel J A Theor Chim Acta 1973 28 213 34 Dunning Jr T H J Chem Phys 1989 90 1007 35 Kendall R A Dunning Jr T H and Harrison R J J Chem Phys 1992 96 6769 36 Hehre WJ Stewart RF and Pople JA J Chem Phys 1969 51(6) 2657 37 Hehre WJ Ditchfield R and Pople JA J Chem Phys 1972 56(5) 2257 38 Binkley JS Pople JA and Hehre WJ J Am Chem Soc 1980 102(3) 939 39 Krishnan RBJS Binkley JS Seeger R and Pople JA J Chem Phys 1980
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111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
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115 Curtiss L A Raghavachari K Trucks G W Pople J A J Chem Phys 1991
94 7221 116 Curtiss L A Raghavachari K Redfern P C Pople J A J Chem Phys 1997
106 1063 117 Baboul A G Curtiss L A Redfern P C Raghavachari K J Chem Phys 1999
110 7650 118 Curtiss L A Raghavachari K Redfern P C Baboul A G Pople J A Chem
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2001 114 9287 123 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2005 123 124107 124 Raghavachari K Curtiss L A Clifford E D Gernot F Kwang S K Gustavo
E S In Theory and Applications of Computational Chemistry Elsevier Amsterdam
2005 785 125 G1 Pople JA Head-Gordon M Fox DJ Raghavachari K Curtiss LA J Chem
Phys 1989 90 5622 126 G2 Curtiss LA Raghavachari K Trucks GW Pople JA J Chem Phys 1991
94 7221 127 G3 Curtiss LA Raghavachari K Redfern PC Rassolov V Pople JA J Chem
Phys 1998 109 7764 128 G4 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007 126 084108 129 Curtiss LA Redfern PC Raghavachari K J Chem Phys 2007127 124105130 Kesharwani MK Karton A Sylvetsky N and Martin JM Aus J Chem
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131 Karton A Sylvetsky N and Martin JM W4‐17 J Comput Chem 2017 38
2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett
1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
Gharagozloo P and Aitken RJ Basic science of reproductive medicine 2015 21(6)
502 143 Wong WH Lee WX Ramanan RN Tee LH Kong KW Galanakis CM
Sun J and Prasad KN Ind Crops Prod 2015 63 238 144 Kelly J F Occup and Environ Med 2003 60 612 145 Gulevitsch V Amiradgibi S Ber Dtsch Chem Ges 1900 33 15504 146 Boldyrev AA and Severin SE Advan in Enzyme Regul 1990 30 175 147 Hipkiss A R Adv Food Nutr Res 2009 57 87 148 Hipkiss A R Worthington V C Himsworth D T J Herwig W Biochim
Biophys Acta 1998 1380 46 149 Pattison D I Davies M J Biochem 2006 45 8152 150 Van der Veen BS de Winther MP and Heeringa P Antioxid Redox Signal
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151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327
487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
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131 Karton A Sylvetsky N and Martin JM W4‐17 J Comput Chem 2017 38
2063 132 Kesharwani MK Karton A and Martin JM J Chem Theo Comput 2015 444 133 L A Curtiss K Raghavachari P C Redfern and J A Pople Chem Phys Lett
1997 270 419 134 Karton A and Martin JM J Chem Phys 2012 136(12) 124114 135 Waris G and Ahsan H J carcinogenesis 2006 5 14 136 Giunta B Fernandez F Nikolic WV Obregon D Rrapo E Town T and Tan
J J neuroinflammation 2008 5(1) 51 137 Bedard K and Krause KH Physiological Rev 2007 87(1) 245 138 Sosa V Molineacute T Somoza R Paciucci R Kondoh H and L Leonart ME
Ageing Res Rev 2013 12(1) 376 139 Sivanandham V Pharmacol Onl 2011 1 1062 140 Lanzafame FM La Vignera S Vicari E and Calogero AE Reprod Biomed
Online 2009 19(5) 638 141 Ross C Morriss A Khairy M Khalaf Y Braude P Coomarasamy A and El-
Toukhy T Reprod Biomed Online 2010 20(6) 711 142 Moazamian R Polhemus A Connaughton H Fraser B Whiting S
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Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
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173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
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193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
References
138
151 Klebanoff SJ J Leukocyte Biol 2005 77 598 152 Van Dalen C Whitehouse M Winterbourn C Kettle A Biochem J 1997 327
487 153 Slungaard A Mahoney J R J Biol Chem 1991 266 (8) 4903 154 Thomas E L Fishman M J Biol Chem 1986 261 (21) 9694 155 Klebanoff S J J Leukocyte Biol 2005 77 598 156 Vander Veen B S de Winther M P J Heeringa P Antioxid Redox Signal 2009
11 2899157 Davies M J Hawkins C L Pattison D I Rees M D Antioxid Redox Signal
2008 10 1199 158 Nicholls S J Hazen S L Arterioscler Thromb Vasc Biol 2005 25 1102 159 Ohshima H Tatemichi M Sawa T Arch Biochem Biophys 2003 417 3 160 Pattison D I Davies M J Biochem 2006 45 8152 161 Pattison D I Davies M J Chem Res Toxicol 2001 14 1453 162 Pattison D I Davies M J Biochemistry 2004 43 (16) 4799 163 Curtiss L A Redfern P C Raghavachari K J Chem Phys 2007 127 124105 164 Curtiss L A Redfern P C Raghavachari K WIREs Comput Mol Sci 2011 1
810 165 Barclay LRC Can J Chem 1993 71(1) 1 166 Barclay LRC Baskin KA Dakin KA Locke SJ and Vinqvist MR 1990
Can J Chem 1990 68(12) 2258 167 YAMAUCHI Ryo Food Sci Technol Int Tokyo 1997 34 301 168 Erben-Russ M Bors W and Saran M Int J Radiat Biol Relat Stud Phys
Chem Med 1987 52(3) 393 169 Haagen-Smit A J Ind Eng Chem 1952 44 1342 170 Haagen-SmitAJ Fox MM J Air Pollut Control Assoc1954 4 105 171 Brasseur G P Orlando J J Tyndall G S Eds Atmos Chem Glob Change
1999 172 Kanakidou M Seinfeld JH Pandis SN Barnes I Dentener FJ Facchini
MC Dingenen RV Ervens B Nenes ANCJSE Nielsen CJ and Swietlicki E
Atmos Chem Phys 2005 5(4) 1053
References
139
173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
References
140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
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228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
References
139
173 Blando JD Turpin BJ Atmos Environ 2000 34 1623 174 Warneck P Atmos Environ 2003 37 2423 175 Ervens B Feingold G Frost GJ Kreidenweis SM J Geophys Res 2004 109 176 Crahan KK Hegg D Covert DS Jonsson H Atmos Environ 2004 23 3757 177 Gelencser A Varga Z Atmos Chem Phys 2005 5 2823 178 Lim H-J Carlton AG Turpin BJ Environ Science Tech 2005 39 4441 179 Carlton AG Lim H-J Altieri K Seitinger S Turpin BJ Geophys Res Lett
2006 33180 Altieri KE Carlton AG Lim HJ Turpin BJ Seitzinger S Environ Science
Tech 2006 40 4956 181 De Gouw JA Middlebrook AM Warneke C Goldan PD Kuster WC
Roberts JM Fehsenfeld FC Worsnop DR Canagaratna MR Pszenny AAP
and Keene J Geophys Res Atmos 2006 110(D16) 182 Volkamer R Jimenez JL San Martini F Dzepina K Zhang Q Salcedo D
Molina LT Worsnop DR and Molina MJ Geophys Res Lett 2006 33(17) 183 Bahreini R Ervens B Middlebrook AM Warneke C De Gouw JA DeCarlo
PF Jimenez JL Brock CA Neuman JA Ryerson TB and Stark H J Geophys
Res Atmos 2009 114(D7) 184 Criegee R Angew Chem Int Ed Engl 1975 14 745 185 Johnson D Marston G Chem Soc Rev 2008 37 699 186 Vereecken L Science 2013 340 154 187 Taatjes C A Shallcross D E Percival C J Phys Chem ChemPhys 2014 16
1704 188 Donahue N M Drozd G T Epstein S A Presto A A Kroll J H Phys Chem
Chem Phys 2011 13 10848 189 Kugel RW Ault B S J Phys Chem A 2015 119 312 190 Barnes I Calvert J G Atkinson R J Kerr A Madronich S Moortgat G K
Wallington T J Yarwood G J Atmos Chem 2001 39 328191 Ainson R Arey J Atmos Environ 2003 37 197 192 Liu F Beames J M Petit A S McCoy A B Lester M I Science 2014 345
1596
References
140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
References
141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
References
140
193 Womack C C Martin-Drumel M A Brown G G Field R W McCarthy M C
Sci Adv 2015 1 e1400105 194 Ahrens J Carlsson P Hertl N Olzmann M Pfeifle M Wolf T Zeuch Angew
Chem Int Ed 2014 53 715 195 Sakamoto Y Inomata S Hirokawa J J Phys Chem A 2013 117 12912minus12921 196 Heaton K J Sleighter R L Hatcher P G Hall W A IV Johnston M V
Environ Sci Technol 2009 43 7797 197 Kroll J H Clarke J S Donahue N M Anderson J G J Phys Chem A 2001
105 1554 198 Kroll J H Sahay S R Anderson J G Demerjian K L Donahue N M J Phys
Chem A 2001 105 4446 199 Mauldin Iii R L Berndt T Sipila M Paasonen P Petaja T Kim S Kurten
T Stratmann F Kerminen V M Kulmala M Nature 2012 488 193 200 Boy M Mogensen D Smolander S Zhou L Nieminen T PaasonenP Plass
DuumllmerC SipilaM PetaȷaT MauldinL Berresheim H Kulmala M Atmos Chem
Phys 2013 13 3865 201 Percival C J Welz O Eskola A J Savee J D Osborn D L Topping D O
Lowe D Utembe S R Bacak A McFiggans G Cooke M C Xiao P Archibald
A T Jenkin M E Derwent R G Riipinen I Mok D W K Lee E P F Dyke J
M Taatjes C A Shallcross D E Faraday Discuss 2013 165 45 202 L Vereecken D R Glowacki M J Pilling Chem Rev 2015 115 4063 203 M Kumar D H Busch B Subramaniam W H Thompson Phys Chem Chem
Phys 2014 16 22968 204 J M Anglada J Gonzalez M Torrent-Sucarrat Phys Chem Chem Phys 2011 13
13034 205 L Jiang Y S Xu A Z Ding Int J Mol Sci 2013 14 5784 206 L A Curtiss P C Redfern K Raghavachari J Chem Phys 2007 127 124105 207 Goldstein A H Galbally I E Environ Sci Technol 2007 41 1514 208 Volkamer R Jimenez J L San Martini F Dzepina K Zhang Q Salcedo D
Molina L T Worsnop D R Molina M J Geophys Res Lett 2006 33 L17811
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G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
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Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
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metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
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251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
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141
209 Heald C L Jacob D J Park R J Russell L M Huebert B J Seinfeld J H
Liao H Weber R J Geophys Res Lett 2005 32 L18809 210 Munger J W Jacob D J Daube B C Horowitz L W Keene W C Heikes B
G J Geophys Res 1995 100 9325 211 Grosjean E Grosjean D Fraser M P Cass G R Environ SciTechnol 1996 30
2687 212 Wittrock F Richter A Oetjen H Burrows J P Kanakidou M
Myriokefalitakis S Volkamer R Beirle S Platt U Wagner T Geophys Res Lett
2006 33 L16804 213 Ervens B and Volkamer R Atmos Chem Phys 2010 10(17) 8219 214 Silva GD Phys Chem Chem Phys 2010 12(25) 6698 215 Silva GD The Journal of Physical Chemistry A 2010 115(3) 291 216 Silva GD Graham C and Wang ZF 2009 Environ Science amp tech 44(1) 250 217 Volkamer R San Martini F Molina LT Salcedo D Jimenez JL Molina
MJ Geophys Res Lett 2007 34 L19807 218 TM Fu DJ Jacob F Wittrock JP Burrows M Vrekoussis DK Henze
J Geophys Res Atmos 2008 113 D15303 219 Zhang Q Jimenez JL Canagaratna MR Allan JD Coe H I Ulbrich
MRAlfarra Takami A Middlebrook AM Sun YL Geophys Res Lett 2007 34
L13801 220 Hazra MK Francisco JS Sinha A J Phys Chem A 2007 118 4095 221 Liggio J Li SM McLaren R Environ Sci Tech 2005 39 1532 222 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 223 Hastings WP Koehler CA Bailey EL De Haan DO Environ Sci Tech
2005 39 8728 224 Haan DOD Corrigan AL Smith KW Stroik DR Turley JJ Lee FE
Tolbert MA Jimenez JL Cordova KE Ferrell GR Environ Sci Tech 2009 43
818225 Corrigan AL Hanley SW De Haan DO Environ Sci Tech 2008 42 4428 226 Gomez ME Lin Y Guo S Zhang R J Phys Chem A 2014 119 4457 227 Jang M Kamens RM Environ Sci Tech 2001 35 4758
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
References
142
228 Buszek RJ Sinha A Francisco JS J Am Chem Soc 2011 133 2013 229 Karton A Chem Phys Lett 2014 592 330 230 Lin CR Yu L-J Li S Karton A Chem Phys Lett 2016 659 100 231 Cotton AF Wilkinson G Bochmann M Murillo CA Adv Inorg Chem 1999 232 Liebman J F and Arthur G Wiley-VCH 1988 233 Abel E W Francis G Albert S and Geoffrey W eds Heteronuclear metal-
metal bonds 1995 10 234 Siebert W International Meeting on Boron Chemistry Royal Society of Chemistry
Information Services 1997 235 King R Bruce Chem Rev 2001 101 1119 236 Štiacutebr B Chem Rev 1992 92 225 237 Saxena A K Hosmane N S Chem Rev 1993 93 1081 238 Sivaev I B Bregadze V I Sjoberg S Chem Commun 2002 67 679 239 Deng L Xie Z W Chem Rev 2007 251 2452 240 Grimes R N Academic Press 2011 241 Olid D Nuntildeez R Vintildeas C Teixidor F Chem Soc Rev 2013 42 3318 242 Plešek J Chem Rev 1992 92 269 243 Farra s P Juaacuterez-Peacuterez E J Lepšik M Luque R Nuacutentildeez R Teixidor F Chem
Soc Rev 2012 41 3445 244 In Boron Science New Technologies and Applications Hosmane N S Ed CRC
Press Boca Raton FL 2011 245 Reed C A Chem Commun 2005 1669 246 Heying TL Ager JW SL Clark Jr Mangold DJ Goldstein HL Hillman
M Polak RJ Szymanski JW Inorg Chem 1963 2 1089 247 Fein MM Bobinski J N Mayes N Schwartz MS Cohen Inorg Chem 1963 2
111 248Hoffmann R Lipscomb WN Inorg Chem 1963 2 231 249 Kaesz HD Bau R Beall HA Lipscomb WN J Am Chem Soc 1967 89
4218 250 Kaczmarczyk A Dobrott RD Lipscomb WN Proc Natl Acad Sci 1962 48
729
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218
References
143
251 Grafstein D Dvorak J Inorg Chem 1963 2 1128 252 Kaesz HD Bau R Beall H Lipscomb WN J Am ChemSoc 1967 89 4218