15th conference on current trends in computational...

OOrrggaanniizziinngg CCoommmmiitttteeee Delbert Bagwell U.S. Army ERDC

Jaroslav Burda Charles University in Prague

Cary F. Chabalowski U.S. Army Research Laboratory

Glake Hill Jackson State University

William A. Lester, Jr. University of California at Berkeley

Jerzy Leszczynski (Chairman) Jackson State University

David Magers Mississippi College

Alan L. Middleton U.S. Army ERDC

W. Andrzej Sokalski Wroclaw University of Technology

SSttaaffff Shonda Allen Hill Jackson State University

Olexandr Isayev Jackson State University

Debra Jackson Jackson State University

Ami Mehta Jackson State University

Yevgeniy Podolyan Jackson State University

SSuuppppoorrtt

National Science Foundation (CREST Program)

U.S. Army Engineer Research and Development Center

Department of Defense (Chemical Materials and Computational Modeling (CMCM) Project) through ERDC

US Department of Commerce (Atmospheric Dispersion Project)

Army High Performance Computing Research Center

National Institutes of Health (RCMI Program)

Department of Defense (Computational Design of Novel Materials Project)

Office of Vice President for Research and Strategic Initiatives, JSU

Parallel Quantum Solutions

Conference on Current Trends in Computational Chemistry 2006 November 3-4, 2006

Jackson, Miss.


Jackson, Miss.

Schedule of Events Conference on Current Trends in Computational Chemistry 2006

5

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7:30 – 9:00 Continental Breakfast

8:00 – 12:00 Registration

9:00 – 9:30 Opening Ceremony

9:30 – 10:30 1st Session (S1) Schaefer Lecture

10:30 – 10:40 Group photo

10:40 – 11:10 Coffee Break

11:10 – 12:40 2nd Session (S2) 2 Talks

12:40 – 2:15 Lunch

2:15 – 4:30 3rd Session (S3) 3 Talks


5:00 – 7:00 First Poster Session (P1)

7:00 – 10:00 Dinner

SSaattuurrddaayy,, NNoovveemmbbeerr 44

8:00 – 9:00 Continental Breakfast

8:30 – 11:00 Registration

9:00 – 10:30 4th Session (S4) 2 Talks


11:00 – 1:00 Second Poster Session (P2)

1:00 – 2:00 Lunch




5:30 – 7:30 Third Poster Session (P3)

7:30 – 8:00 Cocktails

8:00 – 11:00 Noble Lecture Banquet Best Student Poster Award Presentation

Noble Lecture Speaker: Dr. Lucjan Piela, Warsaw University

Invited Presentations Conference on Current Trends in Computational Chemistry 2006

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SScchhaaeeffeerr LLeeccttuurree Session Chairman: Gregory Tschumper University of Mississippi

Henry F. Schaefer III University of Georgia

Benzyne and Combustion Chemistry

22nndd SSeessssiioonn Session Chairman: Morgan Ponder Samford University

Russell J. Boyd Dalhousie University

The Electron Density as an Interpretive Tool in Chemistry

Peter Pulay University of Arkansas

The Role of Parallel Computation in Quantum Chemistry

33rrdd SSeessssiioonn Session Chairman: Janusz Rak University of Gdansk

Mikhail Basilevsky Karpov Institute of Physical Chemistry

Molecular Level Simulations of Solvent Reorganization Energies in Electron Transfer Reactions and Charge Transfer Spectra

W. Andrzej Sokalski Wroclaw University of Technology

Predicting Catalytic Activity of the Molecular Environment from the Knowledge of Reactant and Transition State Structures Only

Harold A. Scheraga Cornell University

The Two Aspects of the Protein Folding Problem

44tthh SSeessssiioonn Session Chairman: Xavier Assfeld Université Henri Poincaré

Mostafa A. El-Sayed Georgia Institute of Technology

The Strong Enhanced Scattering and Photothermal Properties of Gold Nanoparticles of Different Shapes and Their Applications in Nanophotonics, Nanomotors and Nanomedicine

Kenneth M. Merz, Jr. University of Florida

The Role of Quantum Mechanics in Structure-Based Drug Design

55tthh SSeessssiioonn Session Chairman: Jesse Edwards Florida A&M University

Magdolna Hargittai Eötvös University

Changing Relationship between Computation and Experiment: Metal Halide Molecular Structures

N. Yngve Öhrn University of Florida

Nonadiabatic, Time-Dependent, Direct Dynamics of Molecular Reactive Processes

66tthh SSeessssiioonn Session Chairman: Lawrence Pratt Fisk University

Jean-Luc Brédas Georgia Institute of Technology

Charge and Energy Transport in Organic Semiconductors

Bobby G. Sumpter Oak Ridge National Laboratory

Computational Studies of Nanoscale Self-Assembly: A New Class of Supramolecular Wires


Jackson, Miss.

Contents for Abstracts Conference on Current Trends in Computational Chemistry 2006

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Session† Presentation Page

P1 Benchmark Computations on New Models for π-Type Interactions between Adenine and Aromatic Aminio Acid Side Chains Julie A. Anderson and Gregory S. Tshumper

19

P1 Theoretical Investigation of Excitation Energies of Methoxy and Amine Derivatized Polyphenylene-vinylene for Organic Photovoltaics Applications Anu Bamgbelu and Suely M. Black

20

S3 Molecular Level Simulations of Solvent Reorganization Energies in Electron Transfer Reactions and Charge Transfer Spectra M.V. Basilevsky

21

P1 The Performance of the New 6-31G## Basis Set: Nuclear Spin–Spin Coupling Constants in the First-Row Hydrides V.I. Bolshakov, V.V. Rossikhin, E.O. Voronkov, S.I. Okovytyy, and J. Leszczynski

22

P1 The Correction of Basis Sets Inadequacy in DFT Calculations of NMR Shielding: Transition Metal-Containing Complexes V.I. Bolshakov, V.V. Rossikhin, E.O. Voronkov, S.I. Okovytyy, and J. Leszczynski

24

P1 Effect of Central Metal ions on First Hyperpolarizability of Unsymmetrical Metal Porphyrins P. Bonifassi, Paresh .C. Ray and J. Leszczynski

27

S2 The Electron Density as an Interpretive Tool in Chemistry Russell J. Boyd

28

S6 Charge and Energy Transport in Organic Semiconductors Jean-Luc Brédas

29

P1 Conformations of Cyclodecyl 4-Nitrophenylacetate Judge Brown, Diwakar M. Pawar, Frank Fronczek and Eric A. Noe

30

P1 The Influence of the Solvent Environment on the Reactivity of Organometallic Complexes Jaroslav V. Burda and Jerzy Leszczynski

31

P1 Conventional Strain Energy in Isomers of Dimethylcyclobutadiene Qianyi Cheng and David H. Magers

32

P1 Analysis of Charge Distribution in Excited States of Substituted Benzenes Sheritta M. Cooks and Tracy Hamilton

33

P1 Interaction of DNA Bases with Amino Acids by ab Initio Calculations P.C. Thompson, W. Kolodziejczyk, G.A. Hill, J. Leszczynski, B. Crews, M.S. de Vries

34

P1 Interaction-induced Electric Properties in Hydrogen-Bonded Systems V. Crockett, B. Skwara, A. Kaczmarek, J. Leszczynski, G. Hill, Jr.

35

P1 Density Functional Theory Methods for Dispersion Interactions in Proteins Jessica Cross, Meghan Hofto, Andrew-Godfrey-Kittle, Karina van Sickle, Lori Culberson, and Mauricio Cafiero

36

P1 Is the Acidity of the N1 Proton in Spiroquinazolinones Important for PDE7 Inhibitory Activity? Pankaj R. Daga, Robert J. Doerksen

37

P1 Size Dependent Optical Properties of DNA Coated Gold Nanoparticles Gopala K. Darbha, Angela Fortner, Jelani Griffin and Paresh Chandra Ray

39

Conference on Current Trends in Computational Chemistry 2006 Contents for Abstracts

12

P1 Chemisorption of Spillover Hydrogen Atoms on the External Surface of Small Diameter Armchair Single-Walled Carbon Nanotubes T. C. Dinadayalane, Anna Kaczmarek, Jerzy Łukaszewicz, and Jerzy Leszczynski

40

P1 Absolute Configuration of 4-Arylflavan-3-ols: Theoretical Calculation of Electronic Circular Dichroic Characteristics Yuanqing Ding, Xing-Cong Li and Daneel Ferreira

43

P1 Electron Propagator Studies of Vertical Electron Detachment Energies and Isomerism in Purinic Deoxyribonucleotides O. Dolgounitcheva , V.V. Zakjevskii, V.G. Zakrzewski, and J. V. Ortiz

44

P1 Theoretical Studies (Quantum Mechanical) of Furan-, Pyrrole-, and Thiophene-Based Organic Semiconductors Courtney E Dula, Gilda K. Sibedwo, Dawn E. Scott and Edmund Moses N. Ndip

46

S6 The Strong Enhanced Scattering and Photothermal Properties of Gold Nanoparticles of Different Shapes and Their Applications in Nanophotonics, Nanomotors and Nanomedicine Mostafa A. El-Sayed

49

P1 Obtaining Reliable Structures for the Accurate Calculation of Energetics in Delocalized π···π Complexes: Cyanogen Dimer and Diacetylene Dimer Adel M. ElSohly, Brian W. Hopkins, and Gregory S. Tschumper

50

P1 Prediction of Excited States for Carbon, Nitrogen and Oxygen Systems Using Quantum Monte Carlo Theory Floyd Fayton Jr, Ainsley Gibson, William A. Hercules, and John A.W. Harkless

51

P1 Designing Bioactive Molecules Using Virtual Screening James I. Fells, Sr., Ryoko Tsukahara, Abby L. Parrill, and Gabor Tigyi

52

P1 Conformational Analysis of 3 Separate Qualitative Biologically Active Enantiomers of α-Hydroxy Phosphonates Jason Ford-Green, Devashis Majumdar, Jerzy Lesczcynski

53

P1 Relative Reactivity in a Series of Fumarates Ryan Fortenberry, David H. Magers, Wujian Miao, and Charles E. Hoyle

54

P1 Theoretical Study of the Cycloaddition of Aminoisocyanocarbenes to Alkenes Fillmore Freeman and Dung Judy Ann Pham

56

P1 Relative Energies of Conformers and Conformational Interconversion Mechanisms of Tetraoxacyclohexanes Fillmore Freeman, Chansa Cha, Elika Derek, Chinh Do, Jung Hwan Hwang, Lisa Phung, Quyen Tu Phung, Travis Picorelli, and Tina Wang

57

P1 The Guanine-Zn-Cytosine Base-Pair in M-DNA Miguel Fuentes-Cabrera, Bobby G. Sumpter, Judit E. Šponer, Jiří Šponer, Leon Petit, and Jack C. Wells

58

P1 An ab Initio Quantum Mechanical Study of Hydrogen-Bonded Complexes Al’ona Furmanchuk, Olexandr Isayev, Leonid Gorb, and Jerzy Leszczynski

59

P1 Hydration of Urea and Trimethylamine-N-oxide Earl Chauncey Garrett, G. Reid Bishop, and David H. Magers

60

P1 Computational Study of Electronic Structure Properties: Ionization Potentials and Electron Affinities of the First Row Transition Metals Using Various ab Initio, DFT and QMC Methods Ainsley A. Gibson, Floyd A. Fayton, William A. Hercules and John A. W. Harkless

62


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P1 Alterations of DNA Bases Tautomeric State and Their Role in UV Mutagenesis H. A. Grebneva

63

P1 LEE Induced DNA Damage: Cytosine in Double Helix Jiande Gu, Jing Wang, Janusz Rak, and Jerzy Leszczynski

67

P1 Hydrogen Tunneling and Protein Motion in Enzyme Reactions Sharon Hammes-Schiffer

68

P1 Purine Moiety as an Excess Electron Trap in the Watson-Crick AT Pair Solvated with Formic Acid. A Computational and Photoelectron Spectroscopy Study Maciej Haranczyk, Kamil Mazurkiewicz, Maciej Gutowski, Janusz Rak, Dunja Radisic, Soren Eustis, Di Wang, and Kit H. Bowen

69

S5 Changing Relationship between Computation and Experiment: Metal Halide Molecular Structures Magdolna Hargittai

72

P1 Effect of Ring Annelation on Li+-Benzene Interaction: A Theoretical Study Ayorinde Hassan, T. C. Dinadayalane and Jerzy Leszczynski

74

P1 Study of the Optimised STO-nG Expansion and its Derivatives Philip E Hoggan

76

P1 Quantum Chemical Study of the Effects of π–π Stacking of the Fullerene C20 with DNA Bases Tiffani M. Holmes, Dinadayalane Tandabany, Glake A. Hill, Jerzy Leszczynski

77

P1 Electronic Structure and Bonding of {Fe(PhNO2)}6 Complexes: A Density Functional Theory Study Olexandr Isayev, Leonid Gorb, Igor Zilberberg, Jerzy Leszczynski

78

P1 The Calculation of Electrostatic Potentials and Forces Using a Modified De Wette–Nijboer Method Harsh Jain and Elijah Johnson

79

P1 A Cluster Based Approach for Conformational Sampling of Solvated Biomolecules Samuel Keasler, Ricky B Nellas, and Bin Chen

80

P2 Ab Initio Free Energy of Vacancy Formation in Photocatalytic Titanium Dioxide J. Brandon Keith, Hao Wang, and James P. Lewis

81

P2 A Theoretical Study of n-BuLi/ Li-aminoalkoxide Compounds: Aggregation vs. Reactivity Hassan K. Khartabil, Manuel F. Ruiz López, Yves Fort and Philippe Gros

83

P2 Ab Initio Prediction of Explosives Physicochemical Properties Yana Kholod, Leonid Gorb, Mohammad Qasim, Herbert Fredrickson and Jerzy Leszczynski

84

P2 The Quantum Chemical Foundations for the CL-20 Photolysis Product Identification Yana Kholod, Sergiy Okovytyy, Leonid Gorb, Mohammad Qasim, and Jerzy Leszczynski

85

P2 Computing Configurational Entropy from Molecular Dynamics Simulations Using ACCENT-MM Benjamin J. Killian and Michael K. Gilson

86

P2 Theoretocal Conformational Studies on DFP to Probe the Role of Its Low-Energy Conformers on Biological Activity Wojciech. Kolodziejczyk, D. Majumdar, Szczepan Roszak and Jerzy Leszczynski

87


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P2 Resonance-Enhanced Two-Photon Ionization Technique: Computer Simulation Dmytro Kosenkov, Leonid Gorb, and Jerzy Leszczynski

88

P2 The Stable 1:1 and 1:2 Complexes of Pyridoxale-5'-phosphate Methylamine Shiff Base with Water: DFT Study of Structure and Vibrational Spectra G.M. Kuramshina, S.A. Sharapova,D.A. Sharapov, Yu.A. Pentin, H.Takahashi

90

P3 A Comparison of Methods for Modeling Quantitative Structure–Activity Relationships. Acetylcholinesterase Inhibitors V.E. Kuz’min, A.G.Artemenko, E.N. Muratov

94

P3 The Hierarchical QSAR Technology for Effective Virtual Screening and Molecular Design of Potential Pharmaceutical Agents V.E. Kuz’min, A.G.Artemenko, E.N. Muratov, L.N. Ognichenko, A.I. Hromov, A.V. Liahovskij, P.G. Polischuk

98

P2 Interaction of Metal Porphyrins with Fullerene C60: A New Insight Meng-Sheng Liao, John D. Watts, and Ming-Ju Huang

101

P2 Electronic Structure, Absorption Spectra, and Hyperpolarizabilities of Some Novel Push-Pull Zinc Porphyrins. A DFT/TDDFT Study Meng-Sheng Liao, P. Bonifassi, J. D. Watts, M.-J. Huang, and J. Leszczynski

102

P2 Extending the Hückel 4n+2 rule to Metallofullerenes: The Txample of M2@C84 (M=Sc, Y) Dan Liu and Frank Hagelberg

104

P2 Self-Consistent Strictly Localized Bond Orbital within the Local Self-Consistent Field Method Pierre-François Loos and Xavier Assfeld

105

P2 Conventional Strain Energy in Boracycloproane, Diboracyclopropane, Boracyclobutane and Diboracyclobutane Brandon Magers, Harley McAlexander, and David H. Magers

107

P2 Conventional Strain Energy and Sigma Delocalization in Small Heterocycles of Carbon and Silicon Harley McAlexander, Brandon Magers, Crystal B. Coghlan, and David H. Magers

108

P2 An ab Initio Molecular Dynamics Investigation of the Various Decarboxylation Mechanisms Involved in Fatty Acid Synthesis Matthew McKenzie and Bin Chen

109

S4 The Role of Quantum Mechanics in Structure-Based Drug Design Kenneth M. Merz, Jr.

110

P2 ONIOM and PCM Computational Study of the Hydration of α-L-Fucopyranose S. Moussi, O. Ouamerali

111

P2 Coordination and Hydrogen Bonding in [M(H2O)n]+ (n=1,2,3,4,5,6), M=Li, Na, K Species Jamshid Najafpour, Gholam Hossein Shafiee, Abdolreza Sadjadi, Shant Shahbazian, Ng Seik Weng

112

P2 A Coupled–Cluster Study of Isomers of the SO2Cl Radical and SO2Cl– Anion Brian Napolion and John D. Watts

113

P2 Metalation of DNA Bases Adria Neely, Glake Hill

114


15

P3 Application of Basis Set 6-31G** to Quantum-Chemical Calculations of Conjugated Organic Molecules Sergey E. Nefediev

115

P2 Probing the Vapor – Liquid Nucleation Mechanisms of Multicomponent Mixtures Using Atomistic Simulations Ricky B Nellas and Bin Chen

117

S5 Nonadiabatic, Time-Dependent, Direct Dynamics of Molecular Reactive Processes Yngve Öhrn

118

P2 Theoretical Study of the Adsorption of Dimethyl Methylphosphonate on Calcium Oxide Y. Paukku, A. Michalkova, and J. Leszczynski

119

P2 Conformational Isomerism in N-Triphenylmethylformamide Diwakar M. Pawar, Dalephine Cain-Davis, Frank R. Fronczek, and Eric A. Noe

121

P2 Conformations of Cyclopentadecane and Related Compounds: A Study by Computational Methods, Dynamic NMR Spectroscopy and X-ray Crystallography. Diwakar M. Pawar, Frank Fronczek and Eric A. Noe

122

P2 Conformational Analysis of trans-Cyclodecene Using Calculated (GIAO) Chemical Shifts Diwakar M. Pawar and Eric A. Noe

123

P2 Ab Initio Study of the Epoxyendic Imide Alkaline Hydrolysis in Gas Phase and Solution T. Petrova, S. Okovytyy, L. Gorb, J. Leszczynski

124

P2 Basis Set and Electron Correlation Effects on Lithium Carbenoid Dimerization Energies Lawrence M. Pratt, Diêp Hương Trần Phan, Phuong Thảo Thi Trần, Ngân Văn Nguỹên

126

S2 The Role of Parallel Computation in Quantum Chemistry Peter Pulay and Jon Baker

129

P2 Progressive Derivation of Most Likely Transformations of CL-20 and Investigation of Most Likely Bond-Breaking Sites Mo Qasim, Brett Moore, L. Gorb and J. Leszczynski

130

P2 Proton and Metal Ion Affinities of α,ω-Diamines and Heterocyclic Amines J. Srinivasa Rao and G. Narahari Sastry

133

P2 Multiple Linear Regression Analysis and Optimal Descriptors: Predicting the Cholesteryl Ester Transfer Protein Inhibition Activity Bakhtiyor F. Rasulev Andrey A. Toropov, Ashton Hamme and Jerzy Leszczynski

136

P2 Predicting the Flavonoids Inhibition Activity towards Na,K-ATP-ase: A Computational Study Using Molecular Modeling and QSAR GA-MLRA Analysis B.F. Rasulev, Z.A. Khushbaktova and J. Leszczynski

137

P2 SH/π Interactions: Quantum Mechanical Potential Energy Surfaces of the H2S-Benzene Complex and Protein Databank Mining Experiments Ashley L. Ringer, Anastasia Asenenko, and C. David Sherrill

138

P2 Docking and Molecular Simulations of a Series of Estradiol Derivative Selective Estrogen Modulators Jamar Robinson, John S. Cooperwood, Musiliyu Musa, Reginald Parker, Jesse Edwards

139

P2 Theoretical Study of Adsorption of Selected Nucleic Acids on Dickite T. L. Robinson, A. Michalkova, L. Gorb, and J. Leszczynski

140


16

P2 Theoretical Studies of Symmetric Five-Membered Heterocycle Derivatives of Carbasole and Fluorene – Precursors of Conducting Polymers Szczepan Roszak, Jacek Doskocz, Marek Doskocz, Jadwiga Soloducho, and Jerzy Leszczynski

142

P2 Molecular Dynamic Studies of Several HIV-1 Protease Modified Peptide Inhibitors: Shape and Size Specificity Christina Russell, Debra Bryan, John West, Ben Dunn, Reginald Parker, Jesse Edwards

143

P2 Role of Intermolecular Interaction on Nonlinear Optical Properties and Two Photon Absorption Cross-Section of Molecular Aggregates Zuhail Sainudeen and Paresh Chandra Ra

144

P2 An ONIOM Study of Catalytic Site of the Phosphodiesterases E. Alan Salter and Andrzej Wierzbicki

145

S4 The Two Aspects of the Protein Folding Problem Harold A. Scheraga

146

P2 A Theoretical Investigation of Ionization Potentials and Spectral Origins of Guanine Tautomers M.K. Shukla and Jerzy Leszczynski

147

P2 Ionization Potential and Electron Affinity of Some Carbon Nanostructures: A Density Functional Theory Investigation M.K. Shukla and Jerzy Leszczynski

150

P3 Hydrogen-Bonded Interactions between Guanine and Amino Acid Side-Chain in Aqueous Solution: A DFT Study Indu Shukla, Jing Wang, Jerzy Leszczynski

151

P3 A Theoretical Study on the Interactions of Li+ with Defect-Free and Stone-Wales Defect Armchair (6,6) Single-Walled Carbon Nanotube Tomekia Simeon, T. C. Dinadayalane and Jerzy Leszczynski

152

P3 DFT Studies on Structurally Diverse Farnesyltransferase Inhibitors: Multivariate Analysis of Correlation between Physicochemical Properties and Antimalarial Activity Prasanna Sivaprakasam, Aihua Xie, Robert J. Doerksen

154

S3 Predicting Catalytic Activity of the Molecular Environment from the Knowledge of Reactant and Transition State Structures Only Andrzej Sokalski, Borys Szewczyk, Edyta Dyguda-Kazimierowicz, Jerzy Leszczynski

156

P3 A DFT Study on The Mono-Reduction of 2,4-Dinitrotoluene (DNT) by Titanium(3+) Ions in the Presence of Iron(2+) Ions Vitaly Solkan and Jerzy Leszczynski

157

P3 The Singlet Oxygen Activation by Unique Transition-Metal Ion Structures in Fe(2+)/ZSM-5 , Co(2+)/ZSM-5 , and Zn(2+)/ZSM-5 Zeolites: Formation of the Adduct between Activated Oxygen and Ethene Vitaly Solkan and Jerzy Leszczynski

160

P3 DFT Study of Nitrous Oxide Decomposition Catalysed by Ga+ Ion Vitaly Solkan

163

P3 DFT Study of Ethane Decomposition over Zn-ZSM-5 Vitaly Solkan

166


17

P3 DFT Study on the Carbon Monoxide Interaction with Small Metal Cluster Co4, Rh4, Pt4, Co3Pt, Rh3Pt Supported on Co(II)/Rh(II)-ZSM-5 and Cluster Pt4

Supported on Co(I)/Ni(I)-ZSM-5 Vitaly Solkan

168

P3 Singlet Oxygen Activation by Unique Metal Ion Structures in Zn(2+)/ZSM-5 Zeolites: Formation of a Complex between Singlet Oxygen and Metyl-Zn-Z Vitaly Solkan

171

P3 Modeling Excess Electrons Bound to Water Clusters Thomas Sommerfeld, Kenneth D. Jordan, and Albert DeFusco

173

P3 Enthalpies of Formation of TNT Derivatives by Homodesmotic Reactions Amika Sood, Patricia Honea, and David H. Magers

175

P3 Effect of Axial Ligation on Metalloporphyrin and Phthalocyanine Geometry and Spectra Nicole Strauss, Erica Baldwin, and William A. Parkinson

176

S3 Computational Studies of Nanoscale Self-Assembly: A New Class of Supramolecular Wires Bobby G. Sumpter

177

P3 Conventional Strain Energy and Sigma Delocalization in Small Heterocycles of Carbon and Germanium Lyssa A. Taylor and David H. Magers

178

P3 A Self–Consistent Coupled–Cluster Solvent Reaction Field Method Kanchana S. Thanthiriwatte and Steven R. Gwaltney

179

P3 Molecular Wrapping and Mechanical Strength in Lignin-CNT-Epoxy Composites D. Thomas, J. Edwards, D. Bryan and R. Parker

180

P3 Interaction of DNA Bases with Amino Acids by ab Initio Calculations Patrina C. Thompson, Glake A. Hill, Jerzy Leszczynski

182

P3 Correlated Transition State for the Reaction of Phenol with Formaldehyde Julaunica Tigner, Erica King, and Melissa S. Reeves

183

P3 QSAR Modeling of Toxicity for Nitrobenzene Derivatives towards Rats: Comparative Analysis by MLRA and Optimal Descriptors A.A. Toropov, B.F. Rasulev and J. Leszczynski

184

P3 Multicentered Integrated QM:QM Methods for Weakly Bound Clusters: An Efficient and Accurate 2-Body:Many-Body Treatment of Hydrogen Bonding and Van Der Waals Interactions Gregory S. Tschumper

185

P3 Heterocomplexes of DyBr3 with Alkali Halides: A Computational Study of Their Structures and Relative Stabilities Zoltán Varga and Magdolna Hargittai

186

P3 Theoretical Study on the Radical-Radical Reaction of CH3S with ClO Wenliang Wang, Yan Liu, Weina Wang

188

P3 Theoretical Study and Rate Constant Calculation on the Hydrogen Abstraction Reaction of C2H3 with CH3F Wenliang Wang, Lixia Feng, Weina Wang

191

P3 Catalytic Phosphonylation Mechanisms of Sarin and Acetylcholinesterase: A Density Functional Study Jing Wang, Jiande Gu, and Jerzy Leszczynski

193


18

P3 Ground and Electronically Excited States of Methyl Hydroperoxide. Comparison with Hydrogen Peroxide John D. Watts and Joseph S. Francisco

194

P3 Quantum Chemical Calculations on Aliphatic Nitrate-Based Explosives. Prediction of New Conformers David J. Watts, Ming-Ju Huang, and John D. Watts

195

P3 Energetics of Oxaspirocycle Prototypes: 1,7-Dioxaspiro[5.5]undecane and 1,7,9-Trioxadispiro[5.1.5.3]hexadecane Abby Jones Weldon and Gregory S. Tschumper

196

P3 Theoretical Study of 1- Methylcytosine and Its Tatomer with Tetrahedral Edge Clay Minerals Fragments A. Wilson, A. Michalkova, and J. Leszczynski

199

P3 Ethylene Production in the Collision Induced Dissociation of Metal Dication – Acetonen Complexes Jianhua Wu, Frank Hagelberg and Alexandre A. Shvartsburg

201

P3 3D Quantitative Structure–Farnesyltransferase Inhibition Analysis for Some Diaminobenzophenones Aihua Xie,Shawna R. Clark, Robert J. Doerksen

202

P3 Computer Simulation Studies of Water Borne Two-Component Polyurethane Film Formation Shihai Yang, Ras Pandey, Marek Urban

204

P3 Quantum Transport in Porphirin: Interaction with Metals Ilya Yanov, Yana Kholod and Jerzy Leszczynski

205

P3 Electron Propagator Calculations on the C60 Photoelectron Spectrum V.G. Zakrzewski, O. Dolgounitcheva, and J.V.Ortiz

206

P3 A Fast and Reliable Method for Predicting pKa Values Shuming Zhang, Jon Baker and Peter Pulay

207

P3 The Most Stable Structure of Fullerene[20] and Its Derivatives C20(C2H2)n and C20(C2H4)n (n=1−4): A Theoretical Study Congjie Zhang, Wenxiu Sun, Zexing Cao

208

P3 Do Methanethiol Adsorbates on The Au(III) Surface Dissociate? Jian-Ge Zhou and Frank Hagelberg

209

P3 Comprehensive Conformational Analysis of 2'-Deoxynucleosides: Nonempirical Quantum-Mechanical Study Roman Zhurakivsky, Dmytro Hovorun

210

†S* – Oral presentation (* denotes session number); P* – Poster presentation (* denotes poster session number)

Conference on Current Trends in Computational Chemistry 2006

19

Benchmark Computations on New Models for π-Type Interactions between Adenine and Aromatic Aminio Acid Side Chains

Julie A. Anderson and Gregory S. Tshumper

Department of Chemistry and Biochemistry University of Mississippi, University, Mississippi 38677-1848 USA

Both the cyanogen/diacetylene dimer (Figure 1) and the triazene/benzene dimer (Figure 2) have been used to model the interaction between adenine and aromatic amino acid side chains. The MP2 complete basis set limits of the interaction energies of these model systems have been determined by extrapolation techniques with correlation consistent basis sets and by explicitly correlated MP2-R12 methods. Because of the well known tendency of second-order Möller-Plesset perturbation theory to overestimate the stability of stacked configurations of π-π complexes, higher order correlation effects have been examined with the CCSD(T) method.

Figure1 Figure 2


20

Theoretical Investigation of Excitation Energies of Methoxy and Amine Derivatized Polyphenylene-vinylene for Organic

Photovoltaics Applications

Anu Bamgbelu* and Suely M. Black*

*Center for Materials Research, Norfolk State University, Norfolk, VA 23504 CCMSI, Jackson State University, Jackson, MS 39217

*Department of Chemistry, Norfolk State University, Norfolk, VA 23504

Electronics and photonics technologies have opened their materials base to organics, in particular Π-conjugated polymers. The goal with organic-based devices is primarily to benefit from a unique set of characteristics combining the electrical properties of semiconductors with the typical properties of plastics. Geometries and band gaps of Alkoxy and amine derivatized Poly- [phenylvinylene] (PPV) oligomers of up to four units have been systematically studied using both ZINDO and B3LYP Density Functional Theory (DFT) methods. On the basis of the fully optimized DFT geometries of neutral forms of PPV oligomers, excitation energies were obtained at the DFT and ZINDO levels, and extrapolated to the excitation energy value of the infinite chain. Both the ZINDO//B3LYP/6-31G* band gap (2.7eV) and the DFT//B3LYP/6-31G* band gap (2.0eV) obtained from extrapolation of the oligomers’ calculated values are in qualitative agreement with the experimental value (2.5eV) for the methoxy-derivatized PPV. The amine-derivatized PPV yielded a larger band gap (2.4eV). This difference most likely results from the spiral conformation of this system, as opposed to the planar form of all PPV (OMe) oligomers studied. The influence of the phenyl ring substituent, choice of basis set, theoretical method on the structures, highest occupied and lowest unoccupied molecular orbitals, as well as the extrapolated first excitation energy of the polymers are discussed.


21

Molecular Level Simulations of Solvent Reorganization Energies in Electron Transfer Reactions and Charge Transfer Spectra

M.V. Basilevsky

Photochemistry Center of Russian Academy of Sciences (Moscow) and Karpov Institute of Physical Chemistry (Moscow)

The original computational algorithm for studying solvent reorganization energies accompanying charge transfer processes in polar and non-polar solvents is elaborated. It treats electrostatic polarization of a solvent in terms of a usual non-polarizable MD procedure supplemented by scaling the average response field and the corresponding reorganization energy at the final stage of a computation. The underlying physical model invokes a continuum approach for fast inertialess component of solvent polarization but retains explicit molecular level treatment for its inertial component associated with slow nuclear motion of solvent particles. Such methodology provides a physically relevant background for separating inertialess and inertial responses in terms of a single parameter, the optical dielectric permittivity of a solvent.

The results of computations for real chemical electron transfer systems in solvents of different polarity (water, acetonitrile, dichloroethane, tetrahydrofurane, benzene, supercritical CO2) are presented and discussed. The extension of this methodology for evaluation of Stokes shifts in absorption/emission electronic spectra of organic chromofore molecules is also considered.


22

The Performance of the New 6-31G## Basis Set: Nuclear Spin–Spin Coupling Constants in the First-Row Hydrides

Vladimir. I. Bolshakov1, Vladimir V. Rossikhin1, Eugene O. Voronkov2, Sergiy I. Okovytyy3,4, and Jerzy Leszczynski4

1Pridneprovs’ka State Academy of Civil Engineering and Architecture, 49635, Ukraine, 2Dnepropetrovsk National Technical University, Dnepropetrovsk, 49010, Ukraine,

3Dnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine, 4Computational Center for Molecular Structure and Interactions, Department of Chemistry,

Jackson State University, Jackson, Mississippi 39217 USA

The performance of the newly developed 6-31G## basis set for calculating the nuclear spin-spin coupling constants of first-row hydrides has been studied at the HF and DFT levels of theory. The 6-31G## basis set has been constructed by augmentation of the 6-31G basis set by diffuse and polarization functions which are generated from the corresponding 6-31G basis AOs response functions obtained in the frame of propagator approach, what gives a possibility to describe correctly the changes in molecular electronic density under the perturbation influence [1]. All calculations have been carried out with the Gaussian 03 package [2]. The obtained results are collected in Tables 1, 2 and compared with other available theoretical and experimental results. The predicted values of nuclear spin-spin coupling constants for the first-row hydrides are in good agreement with the experimental data.

Table 1. The CHF and DFT nuclear spin-spin coupling constants( Hz) of first-row hydrides

CHF BP86 B3LYP PBE1PBE Mole-cule Coupling 6-31G## CHF3 Expt.3

J2(H1, H1) -27.3 (54)* -12.8 -13.3 -14.7 -26.6 (162)* -12.6 CH4 J1(H1,C13) 169.3 (54) 142.1 149.6 146.5 155.1 (162) 125.3 J2(H1, H1) -23.3 (46) -10.6 -11.3 -12.2 -23.9 (138) -10.4 J1(H1, N14) 58.2 (46) 43.8 49.0 47.4 54.4 (138) 43.6 NH3 J1(H1, N15) -81.7 (46) -61.5 -68.8 -66.5 - -61.1 J2(H1, H1) -20.3 (38) -8.3 -9.4 -10.0 -20.9 (110) -7.2 H2O J1(H1, O17) -114.7 (38) -74.8 -86.9 -85.2 -99.8 (110) -79

HF J1( H1 ,F19) 822.9 (30) 490.0 438.8 442.2 654.4 (129) 530 *Basis set size given in parentheses.

Table 2. The nuclear spin-spin coupling constants (Hz) in the water monomer

BP86 RAS4SCF4 CASSCF4 Molecule Coupling 6-31G## (38) HIII (54) HIIIa (72) CCSD4 Expt. 3,5

J2(H1, H1) -8.3 -12.6 -9.3 -10.8 -7.2 H2O in gas-phase J1(H1, O17) -74.8 -77.12 -75.2 -74.9 -79.0

J2(H1, H1) -8.6 (CH3NO2) - - -7.3 H2O

in solvents J1(H1, O17) -79.1 (H2O) -76.4 (C6H12) -79.0 (CH3NO2)

- - - -

-78.7 -80.6

*Basis set size given in round parentheses.


23

References 1. Okovytyy S.I., Rossikhin V.V., Kasyan L.I., Voronkov E.O., Umrikhina L.K., Leszczynski J. J. Phys. Chem. A 2002,106,No 16, 4176. 2. M. J. Frisch, G. W. Trucks, H. B. Schlegel, et al., Gaussian, Inc., Wallingford CT, 2004. 3. A. Soncini and P. Lazzeretti. J. Chem. Phys., 118, No. 16, 7165, 2003. 4. M. Pecul, J. Sadlej, Chem. Phys. Lett. , 308, 486,1999. 5. I. Alkorta J. Elguero,. Int. J. Mol. Sci., 4, 64, 2003.


24

The Correction of Basis Sets Inadequacy in DFT Calculations of NMR Shielding: Transition Metal-Containing Complexes

Vladimir. I. Bolshakov,1 Vladimir V. Rossikhin,1 Eugene O. Voronkov,2 Sergiy I. Okovytyy,3,4 and Jerzy Leszczynski4

1Pridneprovs’ka State Academy of Civil Engineering and Architecture, 49635, Ukraine, 2Dnepropetrovsk National Technical University, Dnepropetrovsk, 49010, Ukraine,

3Dnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine, 4Computational Center for Molecular Structure and Interactions, Department of Chemistry,

Jackson State University, Jackson, Mississippi 39217 USA

The DFT methods are presently routinely and successfully applied to the study wide-ranging problems of chemical interest. An important aspect of many of these studies is the calculation of the electric, magnetic, and optical properties associated with the responses of a molecular electronic system to perturbations such as externally applied weak electromagnetic fields. It is well known that DFT methods suggest a significant improvement of above-mentioned problems, yielding results comparable or even better than MP2 for significantly less computational cost. In terms of basis sets, the correction of theirs inadequacy by physically justified procedure proposed by us in [1, 2] may be useful and seems to offer good price/performance ratio.

The optimization of molecule geometry is important preliminary procedure in calculations of NMR magnetic shielding constants. The data of Table 1 show that proposed 6-31G## basis set allow us to obtain geometrical parameters of selected complexes close to experimental values. So, it may be used in subsequent calculations of NMR constants for such complexes for which the experimental geometry has not been obtained. In Tables 2-4 the results of magnetic shielding constants calculations of metal-containing compounds are shown. Calculations have been performed using 6-31G##, 3-21G## and CEP-31G## basis sets in the frame of non-hybrid and hybrid functionals. Obtained results compared with data of other authors, which received in larger basis sets size and experimental values. One can see that using of hybrid functionals for 3d-metals is more preferably. At the same time, for 4d-metals better results for nuclear shielding are obtained by exchange functionals.

Table 1. Optimized and experimental geometry (Å) for selected Me-containing complexes

BP86 B3lYP PBE1PBE Complex Bond

distance 6-31G##/6-31Ga) Expt.3

RuO4 (Td) RRu-O 1.715 1.697 1.682 1.706 OsO4 (Td) ROs-O 1.721 1.705 1.692 1.712

6-31G/6-31G## b) RFe-C 2.044 2.065 2.036 2.064 RC-C 1.438 1.426 1.423 1.440

Fe(Cp)2 (D5h)

RC-H 1.091 1.081 1.082 1.104 a) Numerator – basis set on Me atom, denominator – basis set on O atoms. b) Numerator – basis set on Me and H atoms, denominator – basis set on C atoms.


25

Table 2. Calculated absolute 17O NMR chemical shifts (ppm) in transition metal oxo complexes BP86 B3LYP PBE1PBE Expt.4

CEP-31G##/6-31G a) BS I4 CEP-31G##/6-

31G a) BS I4 BS II5 CEP-31G##/6-31G a) BS II5

Complex CSGT GIAO GIAO CSGT GIAO GIAO GIAO CSGT GIAO GIAO

WO −24 -110 -108 -157 -126 -126 -183 -108 -115 -112 -102 -129

MoO −24 -212 -228 -251 -240 -259 -289 -201 -222 -238 -193 -239

CrO −24 -500 -439 -508 -605 -534 -640 -480 -591 -515 -479 -544

ReO −4 -280 -268 -282 -317 -306 -339 - -299 -286 - -278

TcO −4 -415 -405 -421 -482 -474 -518 - -458 -447 - -458

MnO −4 -901 -792 -832 -1014 -895 -1149 - -1005 -880 - -939

OsO4 -498 -484 -517 -592 -579 -657 - -567 -552 - -505

RuO4 -826 -817 -765 -981 -962 -1037 - -952 -931 - -820

FeO4 -1235 -1109 -1224 -1798 -1640 -1957 - -1827 -1661 - - a) Numerator – basis set on Me atom, denominator – basis set on O atoms.

Table 3. Calculated absolute 17O NMR chemical shifts (ppm) in transition metal oxo complexes

BP86 B3LYP PBE1PBE 6-31G##/6-31G

a) BS I4 6-31G##/6-31G

a) BS I4 6-31G##/6-31G a) BS II5 Complex

CSGT GIAO GIAO CSGT GIAO GIAO CSGT GIAO GIAO

Expt.4

CrO −24 -442 -458 -508 -541 -559 -640 -516 -531 -479 -544

MnO −4 -786 -789 -832 -933 -917 -1149 -911 -894 - -939

FeO4 -1134 -1118 -1224 -1706 -1682 -1957 -1728 -1703 - - a) Numerator – basis set on Me atom, denominator – basis set on O atoms.

Table 4. NMR parameters (ppm) in Me-cene, computed with different DFT-functionals

BP86 B3LYP PBE1PBE B3LYP BPW91Complex Property

CSGT GIAO CSGT GIAO CSGT GIAO GIAO GIAO

6-31G/6-31G## b) II6 II6

Expt.6

Fe(Cp)2 σ 57Fe -2131 -2081 -4485 -4420 -4175 -4093 -4388 -2603 -

Fe(CO)5 σ 57Fe -1702 -1648 -3020 -2684 -2525 -2448 -2903 -1946 - δ 57Fe 445 433 1465 1737 1650 1645 1485 657 1532

3-21G/3-21G## b) - Rh(Cp)2]+ σ 103Rh 997 1259 518 795 915 1207 915 1201 -

b) Numerator – basis set on Me and H atoms, denominator – basis set on C atoms. All calculations have been carried out with the Gaussian 03 package [7].


26

References 1.Rossikhin V.V., Kuz'menko V.V., Voronkov E.O., Zaslavskaya L.I., J. Phys. Chem., 1996, 100, No 51,19801. 2.Okovytyy S.I., Rossikhin V.V., Kasyan L.I., Voronkov E.O., Umrikhina L.K., Leszczynski J. J. Phys. Chem. A 2002,106,No 16, 4176 3. David R. Lide, ed., CRC Handbook of Chemistry and Physics, CRC Press, Boca Raton, FL, 2005. 4. Kaupp, M., Malkina, O. L., Malkin, V. G., J. Chem. Phys., 1997, 106, 9201. 5. Adamo, C., Barone, V., Chem. Phys. Lett., 1998, 298, 113. 6. Biihl M., Chem. Phys. Lett., 1997,267, 251. 7. Frisch M. J., Trucks G. W., Schlegel H. B., et al., Gaussian, Inc., Wallingford CT, 2004.


27

Effect of Central Metal ions on First Hyperpolarizability of Unsymmetrical Metal Porphyrins

P. Bonifassi, Paresh .C. Ray and J. Leszczynski

Department of Chemistry, Jackson State University, Jackson, MS, 39217, USA

We present a quantum-chemical analysis of the central metal ions effect on first hyperpolarizabilities of a series of push-pull porphyrins whose synthesis and NLO properties has been reported earlier (J. Am. Chem. Soc. 127, 9710, 2005). The effect of the donor-acceptor strengths and conjugation path lengths has been evaluated to demonstrate the engineering guidelines for enhancing molecular optical non-linearity. The molecular geometries are obtained via B3LYP/6-31G (d,p) level optimization including SCRF/PCM approach, while the dynamic NLO properties are calculated with the ZINDO/CV method including solvent effects. It has been observed that the first hyperpolarizabilities can be greatly enhanced by changing the central metal ions and increasing the strengths of the electron donor/acceptor. It is found that the CT transition between the metal ion’s d orbital and the macrocycle π orbital plays an important role on first hyperpolarizability of metal porphyrins. Our data suggest a new approach to enhance nonlinear optical properties of porphyrin materials. Importance of our results on the design of electro-optic materials will be discussed.


28

The Electron Density as an Interpretive Tool in Chemistry

Russell J. Boyd

Department of Chemistry, Dalhousie University Halifax, Nova Scotia, Canada, B3H 4J3

Some recent applications of the analysis of the topological properties of the electron density to a variety of topics in chemistry will be summarized. The examples will be taken from our recent work on a variety of inorganic, organic and biochemical systems. In particular, our recent investigations on the solvated electron and our search for non-nuclear attractors in anionic water clusters will be summarized. Non-nuclear attractors have been located only in highly symmetric systems in which the water molecules are hydrogen bonded to one another in a plane and the dangling hydrogen atoms are all oriented in the same direction. Furthermore, we have shown that the solvated electron is largely localized within the cavity formed between the planes of the water molecules. An example of a non-nuclear attractor in the tetrameric species [H2O]4

− is shown below: ↓

Fluorine-fluorine bonding interactions in aromatic compounds1 and the first example of a

cage critical point in a single ring2 will be described. If time permits, other systems,3,4 including our recent analysis5 of extended weak interactions in DNA will be summarized. 1 C.F. Matta, N. Castillo and R.J. Boyd, J. Phys. Chem. A, 109, 3669 (2005). 2 N. Castillo, C.F. Matta and R.J. Boyd, Chem. Phys. Letters 409, 265 (2005). 3 N. Castillo and R.J. Boyd, Chem. Phys. Letters 416, 70 (2005). 4 N. Castillo and R.J. Boyd, J. Chem. Theory Comput. 2, 271 (2006). 5 C.F. Matta, N. Castillo and R.J. Boyd, J. Phys. Chem. B, 110, 563 (2006).


29

Charge and Energy Transport in Organic Semiconductors

Jean-Luc Brédas

School of Chemistry and Biochemistry and Center for Organic Photonics and Electronics

Georgia Institute of Technology Atlanta, Georgia 30332-0400

Conjugated organic oligomer and polymer materials are being increasingly exploited as the active semiconductor elements in devices such as light-emitting diodes, photovoltaic cells, or field-effects transistors. In the operation of such devices, electron-transfer and energy-transfer processes play a key role, for instance in the form of charge transport, energy transport, charge separation, or charge recombination.

In this lecture, we will first provide a brief introduction to the basic operation of some of the devices into which conjugated oligomers or polymers are incorporated. We will then give a theoretical description of the charge-transport phenomena based on Marcus electron-transfer theory and full quantum-mechanical extensions thereof. Such a description is useful to generate a molecular, chemically-oriented understanding [1]. In particular, we will discuss the parameters that impact the mobility of charge carriers, that is the electronic coupling within chains and between adjacent chains and the reorganization energy of the chains upon ionization. Materials under study include conjugated oligomers such as oligoacenes and oligoarylenes.

[1] J.L. Brédas, D. Beljonne, V. Coropceanu, and J. Cornil, “Charge-Transfer and Energy-Transfer Processes in π-Conjugated Oligomers and Polymers”, Chemical Reviews 2004, 104, 4971-5004.


30

Conformations of Cyclodecyl 4-Nitrophenylacetate

Judge Brown, b Diwakar M. Pawar,b Frank Fronczek a and Eric A. Noeb

aDepartment of Chemistry, Louisiana State University, Baton Rouge, LA 70803. bDepartment of Chemistry, Jackson State University, 1400 J. R. Lynch Street

Jackson, MS 39217-0510

A conformational study of cyclodecyl 4-nitrophenylacetate, C18H25NO4, (1), in the solid state is described. The colorless crystals grown by slow evaporation of ethyl acetate solvent occur in the monoclinic system in space group P21/c. No disorder was found. The ring exists in the expected diamond-lattice boat-chair-boat [2323] conformation with the substituent p-nitrophenylacetoxy group in the BCB IIIe position. Based on this finding, the major conformation of chlorocyclodecane and cyclodecyl acetate at low temperatures were also assigned to BCB IIIe. The geometry obtained by molecular mechanics (MM4) force field for 1 is compared with the crystal structure.

This work was supported by NSF-CREST (Grant No. HRD-9805465).


31

The Influence of the Solvent Environment on the Reactivity of Organometallic Complexes

Jaroslav V. Burdaa and Jerzy Leszczynskib

aDepartment of Chemical Physics and Optics Charles University in Prague 121 16 Prague 2,Czech Republic

bDepartment of Chemistry, Jackson State University, 1325 J. R. Lynch Street, Jackson, Mississippi 39217-0510, USA

Pt(II) complexes Cisplatin (diammine-dichloro-platinum(II) complex) and its analogues are known for their

high activity in the anticancer treatment. In the first part of our poster we concentrated on the physical background of the activation of these drugs in the hydration process of replacing chloro-ligands by water molecules. Thermodynamic and kinetic parameters were determined for this hydration reaction using in vacuo and continuous-solvent-distribution approaches. Comparing with experimental data it can be seen very good agreement in EH-CSD method. The process of cisplatin activation in cellular environment can be understand purely on the thermodynamical footings as formation of less stable Pt-complexes under the LeChatelier-Braun-van Hoff’s principle of chemical equilibrium.

Ru(II)-piano-stool complexes Detachment of the chloro-ligand in [Ruthenium(II)(Arene)(en)Cl]+ was studied in

connection with cisplatin activation. Similarly, transition state for process of the water replacement was searched and both thermodynamical and kinetical data for activation and interactions with DNA bases were estimated. Very good agreement of determined parameters with experimental measurements was obtained when COSMO technique applied.


32

Conventional Strain Energy in Isomers of Dimethylcyclobutadiene

Qianyi Cheng and David H. Magers

Computational Chemistry Group Department of Chemistry & Biochemistry, Mississippi College

The conventional strain energies for 1,3-dimethylcyclobutadiene (Figure 1.), 1,2-dimethylcyclobutadiene (Figure 2.), and 1,4-dimethylcyclobutadiene (Figure 3.), are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models to see if reduction of strain might correlate with the stabilizing effect these different dimethyl substitutions have on cyclobutadiene. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory (MP2), and density functional theory. The DFT functional employed is Becke’s three-parameter hybrid functional using the LYP correlation functional. Two basis sets, both of triple zeta quality on valence electrons, are employed: 6-311G(d,p) and 6-311+G(2df,2pd). Finally, computed bond angles are also examined for correlation with the relative stability and the relative strain energies of the different isomers. We gratefully acknowledge support from the Mississippi College Catalysts, the alumni support group of the Department of Chemistry & Biochemistry.

Figure 1: 1,3-dimethylcyclobutadiene Figure 2: 1,2-dimethylcyclobutadiene

Figure 3: 1,4-dimethylcyclobutadiene


33

Analysis of Charge Distribution in Excited States of Substituted Benzenes

Sheritta M. Cooks and Tracy Hamilton

University of Alabama in Birmingham

In this work, we have studied the effects of various activating and deactivating groups on the charge distribution of di-substituted benzenes in its ground and first excited states via computational chemistry. When a substituent group is added to benzene it causes a polarization of charge density around the ring, primarily through the π system. There is also an effect that originates between the bond dipole in neighboring groups. Substituents with electronegativity higher than an aromatic carbon (π acceptors) will place a net positive charge on the substituted carbon atom, while substituents that are less electronegative will have the opposite effect (π donors). The purpose of this work was to determine how these rules (which derive from many experiments on the ground state) apply to excited states. We investigate the push-pull character in di-substituted benzenes with special emphasis on substituted phenols. The Mulliken charges were obtained at the CIS/6-31G*//B3LYP OPT/6-31G* theoretical level for the CIS ground and first excited state and plotted against substituent constants σm and σp to obtain free energy relationships.

In this work, we have studied the effects of various activating and deactivating groups on the charge distribution of di-substituted benzenes in its ground and first excited states via computational chemistry. Previous work for mono-substituted benzenes provided that deactivating groups, such as –CN and -COOH, decreases electron density in the pi system of the benzene ring making the ring more positive. In contrast, activating groups, such as –OH and –NH2, increase the electron density in the pi system of the benzene ring making the ring more negative. The Mullekin charges were obtained at the CIS/6-31G*//B3LYP OPT/6-31G* theoretical level for the CIS ground and first excited state and plot against substituent constants σm and σp to obtain free energy relationships.

There are some groups, which when attached to one of the ring carbons of Benzene that will activate the ring toward further substitution. Electrons in the atoms “p” orbitals lend to the Pi system of the benzene ring. They do this by increasing the negative electron density in the ring thus making the ring more attractive to the approaching electron seeking electrophile.

Activating groups: -OH, -NH2, NO2 (direct ortho and para positions) The extreme electronegativity deactivating groups such as –Cl, -F pull electrons from the

ring leaving the ring more postitive, and therefore, less attractive to the incoming electrophile. However, the three lone pairs of non-bonding electrons found on the halogen atom will provide increased electron density at the ortho and para positions due to the resonance effect of the lone pairs. Other deactivating groups are meta directors. These deactivators reduce the negative electron density of the ring by sucking it out of the ring either by resonance or inductive effect. This is because when the electron density is diminished in the ring, it occurs more at the ortho and para positions leaving the meta directors. This is because when the electron density is diminished in the ring, it occurs more at the ortho and para positions leaving the meta positions relatively more negative. Therefore, if the electrophile does manage to be attracted to the deactivated ring, it will find the meta position.

Deactivation groups: -CN, -COOH, (direct ortho and para positions)


34

Interaction of DNA Bases with Amino Acids by ab Initio Calculations

Patrina C. Thompson, Wojciech Kolodziejczyk, Glake A. Hill*, Jerzy Leszczynski*

Jackson State University

Bridgit Crews**, Mattanjah S. de Vries**

University of California Santa Barbara

Potential structures guanine and aspartic acid complexes have been calculated to establish optimal hydrogen bonding patterns between nucleotide bases and amino acids. All complexes have been fully optimized at Density Functional Theory (B3LYP) and Moller-Plesset Perturbation Theory (MP2) levels using different basis sets. The structures were calculated at the DFT and MP2 levels in 6-31+G(d) and 6-31++G(d,p) basis sets. The infrared (IR) spectra was calculated and compared with experimental data. The energetically favored structure will be discussed.


35

Interaction-induced Electric Properties in Hydrogen-Bonded Systems

Victoria Crockett,1 Bartłomiej Skwara,1,2 Anna Kaczmarek,1,3 Jerzy Leszczynski,1

Glake Hill, Jr.1

1 Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, MS 39217

2 Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, 27 Wybrzeże Wyspiańskiego, 50-370 Wrocław, Poland

3 Faculty of Chemistry, Nicolaus Copernicus University 7 Gagarin St., 87-100 Toruń, Poland

The design of novel materials with the desirable nonlinear optical properties requires the detailed knowledge about the investigated systems at the molecular level [1,2]. The intermolecular interactions in the bulk have been proven to significantly influence the macroscopic properties of the material [3-5]. Thus, thorough analysis of the intermolecular interactions in the microscopic scale is necessary for the explanation of the modifications of the properties in the presence of interactions between molecules.

The objective of the present study is the investigation of the dipole moment μ, polarizability

α and hyperpolarizability β of the hydrogen-bonded systems. The contributions to the electric properties arising from the mutual interactions between substystems are analyzed. The interaction-induced electric properties ΔP are calculated according to the supermolecular approximation as

ΔP=P(AB)-P(A)-P(B), where P(X) denotes the property of the system X (X=A, B, AB). In order to eliminate the basis set superposition error, the Boys and Bernardi counterpoise procedure is applied.

References: [1] Kanis, D.R.; Ratner, M.A.; Marks, T.J., Chem. Rev., 1994, 94, 195. [2] Bredas, J.L.; Adant, C.; Tacx, P.; Persoons, A., Chem. Rev., 1994, 94, 243. [3] Wang, B.-Q., Li, R.-Z., Wu, D., Hao, X.-Y., LI, R.-J., Sun, C.-C., J. Chem. Phys. A., 2004, 108, 2646-2468. [4] Moliner, V., Escribano, P., Peris, E., New J. Chem., 1998, 22, 387-392. [5] Maroulis, G., J. Chem. Phys., 2000, 113, 1813-1820.


36

Density Functional Theory Methods for Dispersion Interactions in Proteins

Jessica Cross, Meghan Hofto, Andrew-Godfrey-Kittle, Karina van Sickle, Lori Culberson, and Mauricio Cafiero

Rhodes College, Department of Chemistry

Recent work in our group has focused on the ability of Density Functional Theory methods to predict electronic interaction energies between proteins and ligands, with the longer term goal of producing accurate DFT-based binding free-energies. We have taken two approaches to this end: examining model systems with current DFT methods and examining actual protein/ligand interactions using protein crystal structures. We present here some results on aromatic model systems (benzene-benzene and benzene-indol) and the interactions of Phenylalanine hydroxylase and Tyrosine Hydroxylase with various substrates. Our electronic-interaction-only approach is used to predict degrees of protein function when point mutations occur in the enzyme structures.


37

Is the Acidity of the N1 Proton in Spiroquinazolinones Important for PDE7 Inhibitory Activity?

Pankaj R. Daga,a Robert J. Doerksena,b

aDepartment of Medicinal Chemistry and bResearch Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, USA

Phosphodiesterases (PDEs) are an important class of enzymes which play an essential role in various biological processes. These enzymes carry out hydrolysis of key secondary messengers adenosine and guanosine 3’, 5’-cyclic monophosphates into corresponding 5’-monophosphate nucleotides.1,2 Among the eleven different PDE isoforms reported in the literature, PDE7 has been shown to be important in the pathogenesis of T-cell related diseases, autoimmune diseases, airway diseases and fertility disorders.3-5 Recently Lorthiois and his associates, from Pfizer, reported a series of substituted spiroquinazolinones, for example 1, as PDE7 inhibitors.6 In the report, these researchers showed that substitution on the quinazoline nucleus had a large impact on the inhibitory activity against PDE7 and specificity over other PDEs. Lorthiois et al.6 found it difficult to explain the structure-activity relationship (SAR) for, e.g., substitution at the 8-position. To understand the SAR better, we decided to study various properties including the molecular electrostatic potential (MESP) of these inhibitors using Hartree-Fock calculations as well as Density Functional Theory with Becke’s three-parameter exchange potential and the Lee–Yang–Parr correlation functional. The activities of the inhibitors were found to be in good correlation with the acidity of the proton attached to N1 as well as the electrostatic potential at N1. The binding conformation of this type of inhibitor is not known. Our preliminary docking studies show that this proton on N1 is involved in an H-bonding interaction with an amide side-chain of the active site Glutamine residue. Figure 1 shows the MESP plotted on the density surfaces for the most active (left) and the least active inhibitor (right). The most positive region of the MESP, shown by the deepest blue near N1 of the inhibitors, shifts from N1 to N3 as the activity decreases. The hydrogen bonding ability and nucleophilic nature of N1 of the spiroquinazolinone ring appear to be important features governing the interaction with PDE7.

NH

NH

O

Cl

Cl1 2

34

56

78

1


38

Figure 1. Molecular electrostatic potential surface plotted on the density surface of two inhibitors.

References

1. Bender, A. T.; Beavo, J. A. Cyclic nucleotide phosphodiesterases: Molecular regulation to clinical use. Pharmacolog. Rev. 2006, 58, 488-520.

2. Jeon, Y. H.; Heo, Y. S.; Kim, C. M.; Hyun, Y. L.; Lee, T. G.; Ro, S.; Cho, J. M. Phosphodiesterase: overview of protein structures, potential therapeutic applications and recent progress in drug development. Cell. Mol. Life Sci. 2005, 62, 1198-1220.

3. Li, L.; Yee, C.; Beavo, J. A. CD3- and CD28-dependent induction of PDE7 required for T cell activation. Science 1999, 283, 848-851.

4. Vergne, F.; Bernardelli, P.; Chevalier, E. PDE7 inhibitors: Chemistry and potential therapeutic utilites. Ann. Rep. Med. Chem. 2005, 40, 227-241.

5. Giembycz, M. A.; Smith, S. J. Phosphodiesterase 7A: A New Therapeutic Target for Alleviating Chronic Inflammation? Curr. Pharm. Design 2006, 12, 3207-3220.

6. Lorthiois, E.; Bernardelli, P.; Vergne, F.; Oliveira, C.; Mafroud, A.-K.; Proust, E.; Heuze, L.; Moreau, F.; Idrissi, M.; Tertre, A.; Bertin, B.; Coupe, M.; Wrigglesworth, R.; Descours, A.; Soulard, P.; Berna, P. Spiroquinazolinones as novel, potent, and selective PDE7 inhibitors. Part 1. Bioorg. & Med. Chem. Lett. 2004, 14, 4623-4626.


39

Size Dependent Optical Properties of DNA Coated Gold Nanoparticles

Gopala K. Darbha, Angela Fortner, Jelani Griffin and Paresh Chandra Ray

Department of Chemistry, Jackson State University, 1400 J.R. Lynch Street, Jackson, MS 39217, USA

We present theoretical and experimental results on dye fluorescence quenching induced by gold nanoparticles having different particle sizes. Distance and size dependent optical properties have been described using extended Mie calculations and compared with the experimental findings. The fluorescence of ss-DNA increases by a factor of 100 when it binds to a complimentary DNA while the addition of single-base mismatch DNA had no effect on the fluorescence efficiency. The mechanism of distant dependence fluorescence quenching has been discussed and our experimental results match reasonably well with the theoretical findings obtained using fluorescence quenching model by Gersten and Nitzan. Fluorescence spectra clearly show that the quenching efficiency decreases with increasing size of the gold nanoparticles and increasing the distance between dye and nanoparticles.


40

Chemisorption of Spillover Hydrogen Atoms on the External Surface of Small Diameter Armchair Single-Walled Carbon

Nanotubes

T. C. Dinadayalane,a Anna Kaczmarek,a,b Jerzy Łukaszewicz,b and Jerzy Leszczynskia,*

aComputational Center for Molecular Structure and Interactions, Department of Chemistry, PO Box 17910, Jackson State University, Jackson, Mississippi 39217

bDepartment of General Chemistry, Nicolaus Copernicus University, 7, Gagarin Street, 87-100 Toruń, Poland

Single-walled carbon nanotubes (SWNTs) have attracted considerable attention due to their phenomenal electronic and mechanical properties, and the variety of potential applications from chemistry, material science to biomedicine.1-3 Due to the shape and unique properties of SWNTs, researchers consider carbon nanotubes as one of the attractive substrates for storage of hydrogen, to achieve 6.5 wt % target set by the US Department of Energy. Hydrogen can interact with carbon nanotubes by two different ways; physisorption and chemisorption.4 In the physisorption process, H2 retains in its molecular entity when it interacts with carbon nanotubes whereas atomic hydrogens, generated by dissociation of H2 molecules, bind with carbon atoms of nanotubes leading to strong C−H bonds in the chemisorption process. Covalent binding of atomic hydrogen on the sidewalls of SWNTs results in the disruption of bonding network by changing carbon atom hybridization from sp2 to sp3.

Hybrid density functional theory calculations have been performed to examine the chemisorptions of one and two hydrogen atoms on the outer surface of (3,3) and (4,4) armchair single-walled carbon nanotubes. The (3,3) and (4,4) SWNTs of different lengths considered in this study are depicted in Scheme 1. One hydrogen atom has been attached at C1 in all the structures. In the processes of chemisorptions of two hydrogen atoms, the first H has been attached at C1 and the second H has been bound at other carbon atom positions indicated (Scheme 1). The addition of H atoms on the outer wall of SWNT (exohedral addition) has only been taken here because this has been reported to be more favorable than the addition on the inner wall of SWNT (endohedral addition).5 The hydrogen atom chemisorptions on the external walls of these SWNTs are exothermic processes. Our results clearly indicate that two hydrogen atoms prefer to bind at adjacent positions rather than at alternate carbon sites. This is in contrast to the results reported recently on zigzag nanotubes.5 Exothermicity of hydrogen atom chemisorptions decreases while increasing the diameter of armchair nanotubes, which is contradictory to zigzag model.5 Thus, our results do not support the reason of “crowding effect” given by Yang et al. for lower binding energy of 1,2- than 1,3-addition of two hydrogen atoms.5 The site preference for the chemisorption of two hydrogen atoms varies for armchair and zigzag nanotubes. However, in the case of binding of two NO2 groups on the tube sidewalls, ortho (1,2) addition is more favorable compared to meta (1,3) and para (1,4) for both armchair and zigzag nanotubes.6


41

Scheme 1

The circumferential C−C bond breaking upon chemisorptions of two hydrogen atoms at adjacent positions leads to high deformation for the shortest nanotubes taken here. The 1,3-H-chemisorbed armchair nanotubes are kinetically and thermodynamically less stable compared to 1,2-, 1-2’- and 1,4-H-chemisorbed SWNTs. The deformation energy data reveals that the chemisorption of two hydrogen atoms results in extremely high distortion to the SWNTs than single hydrogen binding. Changing the length of the nanotube affects the energy of hydrogen chemisorption and the band gap values.

Acknowledgements: This research was supported by ONR grant # N00014-03-1-0116 and the grant from the US

Army Engineer Research and Development Center, grant # W912HZ-05-C-0051. Mississippi Center for Supercomputing Research (MCSR) and Army High Performance Computing Research Center (AHPCRC) are acknowledged for computational facilities.


42

References:

(1) Dinadayalane, T. C.; Leszczynski, J. “Toward nanomaterials: Structural, Energetic and

Reactivity Aspects of Single-walled Carbon Nanotubes.” In Nanomaterials: Design and

Simulation, (Eds.) Balbuena, P. B.; Seminario, J. M. 2006, pp 167-199.

(2) Baughman, R. H.; Zakhidov, A. A.; de Heer, W. A. Science 2002, 297, 787.

(3) Tasis, D.; Tagmatarchis, N.; Bianco, A.; Prato, M. Chem. Rev. 2006, 106, 1105.

(4) Barone, V.; Heyd, J.; Scuseria, S. E. J. Chem. Phys. 2004, 120, 7169.

(5) Yang, F. H.; Lachawiec, Jr. A. J.; Yang, R. T. J. Phys. Chem. B 2006, 110, 6236.

(6) Seo, K.; Park, K. Ah.; Kim, C.; Han, S.; Kim, B.; Lee, Y. H. J. Am. Chem. Soc. 2005, 127,

15724.


43

Absolute Configuration of 4-Arylflavan-3-ols: Theoretical Calculation of Electronic Circular Dichroic Characteristics

Yuanqing Ding, Xing-Cong Li and Daneel Ferreira

National Center for Natural Products Research and Department of Pharmacognosy, Research Institute of Pharmaceutical Sciences, School of Pharmacy, The University of Mississippi,

University, Mississippi 38677

Condensed tannins are globally abundant in plants; their biological and industrial application depends on an understanding of their composition, configuration and conformational behaviour. Owing to the ramification of such polymers, essential features of the dynamic behaviour of the heterocycles are reliant on projections from features of monomers and oligomers, which have mainly been restricted to derivatives of examples, but with limited structural variety. Ref

A unique range of model 4-arylflavan-3-ols and analogs had been synthesized for appraisal of selected structural and conformational qualities by 1H, 13C NMR and circular dichroism data. Assignment of absolute configuration at chiral C-4 is key to definition of their absolute configuration. Electronic circular dichroism spectra represent a powerful method to assign absolute configuration of flavonoids.

Theoretical calculation of electronic circular dichrosim has been performed to assign the absolute configuration at chiral C-4 of 4-arylflavan-3-ols and their methyl ether acetates, using time dependent density functional theory (TDDFT) with 6-31G* basis set. Crucial Cotton effects between 220-240nm have been found to assign the absolute configuration at C-4.

References. (a) L. J. Porter, R. Y. Wong, M. Benson, B. G. Chan, V. N. Vishwanadhan, R. D. Gandour

and W. L. Mattice, J. Chem. Res. (S) 86; (M) 830 (1986). (b) F. R. Fronczek, G. Grannuch, F. L. Tobiason, J. L. Broeker, R. W. Hemingway and W. L. Mattice, J. Chem. Soc., Perkin Trans. 2 1661 (1984). (c) E. Haslam, The Flavonoids, Advances in Research, edited by J. B. Harborne and T. J. Mabry, p. 417. Chapman and Hall, London (1980). (d) L. J. Porter, R. Y. Wong, B. G. Chan, J. Chem. Soc., Perkin Trans. 1 1413 (1985). (e) J. P. Steynberg, E. V. Brandt and D. Ferreira, J. Chem. Soc., Perkin Trans. 2 1569 (1991).


44

Electron Propagator Studies of Vertical Electron Detachment Energies and Isomerism in Purinic Deoxyribonucleotides

O. Dolgounitcheva , V.V. Zakjevskii, V.G. Zakrzewski, and J. V. Ortiz

Department of Chemistry and Biochemistry, Auburn University Auburn, AL 36849

Electron transfer phenomena in DNA and RNA are extremely important in such biological events as mutations, carcinogenesis, radiation induced free radical formation and others. These phenomena might be directly connected to electron detachments from and electron attachments to fragments of DNA and RNA, such as nucleotides or just nucleobases. While ionization events in nucleobases (NAB) are fairly well studied both experimentally with the ultraviolet photoelectron spectroscopy (UV PES) [1] and theoretically with the state-of-the-art ab initio methods [2], the same cannot be said about larger units, such as oligo- or mononucleotides. Experimental studies of ionizations from larger DNA/RNA fragments are complicated by the instability of nucleotides in the gas phase. Even nucleobases are subject to decomposition under conditions of PES. The well established phenomenon of NAB tautomerism further complicates the picture [3].

Direct experimental studies of ionization phenomena in isolated, deprotonated mononucleotides became possible only recently with the development of electrospray photodetachment PES [4]. The most attractive feature of this technique is the possibility of using relatively low temperatures (50-100o) [4] at which no decomposition of substrates occurs. Photodetachment photoelectron spectroscopy was applied to anionic mononucleotides just recently [5]. The spectra were in most cases poorly resolved. The spectrum of deoxyguanidine monophosphate (dGMP-) contained a low-energy feature which was absent in the spectra of other mononucleotide anions.

The goal of the current study was to perform the most precise, electron propagator calculations of the vertical electron detachment energies (VEDE) for two anionic purinic mononucleotides and to compare these VEDEs with the published photodetachment photoelectron spectra of Ref. [5].

Nucleotide anions display a huge variety of possibilities for structural isomerism. In the current study we accounted for rotational isomerism only. β-N-glycosides were studied. All calculations were performed with the Gaussian-03 suite of programs [6]. Geometry optimizations of several dGMP- and deoxyriboadenosine monophosphate (dAMP-) structures were done with the B3LYP method and 6-311++G** basis. Vibrational frequencies analysis confirmed minima for all stationary points obtained. Ionization energies of mononucleotides were calculated within the Partial Third Order Electron Propagator method (P3) [7] and the same basis. No reduction of the active space of orbitals was done.

Five low-lying rotational isomers of dAMP- and three of dGMP- were found in B3LYP optimizations. Of these, only one of each is supposedly found under experimental conditions of photodetachment photoelectron spectroscopy of Ref. [5]. Both dAMP- and dGMP- structures contain intramolecular hydrogen bonds. However, these H-bonds are of completely different nature. While in the dAMP- the phosphate oxygen forms a H-bond with the 3’ hydroxy hydrogen of deoxyribose, in the dGMP- the phosphate oxygen binds with the hydrogen of the amino group of guanine.


45

Experimental photodetachment PES of dAMP- and dGMP- of Ref. [5] were assigned on the basis of our P3 electron propagator calculations. The distinctive feature at ~5 eV in the PES of dGMP- is assigned to electron detachment from the π1 of guanine. Our P3 value of 5.01 eV practically coinsides with the experimental VEDE (5.05±0.10 eV). The offset of ionizations at ~6.1 eV in the PES of dAMP- is caused by two almost degenerate events: electron detachment from the phosphate group and electron detachment from the π1 MO of adenine. In both cases, the first VEDEs of the phosphate group are essentially of the same energy.

Predictions were made for the VEDEs and molecular orbital structures of minor conformational isomers of dAMP- and dGMP-.

References 1. Kim, N.S.; Zhu, Q.; LeBreton, P.R. J.Am.Chem.Soc. 1999, 111, 11516 and references therein. 2. Dolgounitcheva, O.; Zakrzewski, V.G.; Ortiz, J.V. in Fundamental World of Quantum

Chemistry, Braedas, E.J.; Kryachko, E.S.; eds.; (Kluwer, Dordrecht, 2003). Vol. II, 525-555 and references therein.

3. Sponer, J.; Hobza, P.; Leszczynski, J. in Computational Molecular Biology (Elsvier, Amsterdam, 1999). Vol.8, 85.

4. Wang, L.-S.; Ding, C.F.; Wang, H.B.; Barlow, S.E. Res.Sci.Instrum. 1999, 70,1957. 5. Yang, X.; Wang, X.-B.; Vorpagel, E.R.; Wang, L.-S. Proc.Nat.Acad.Sci.USA

2004,101,17588. 6. Gaussian 03 (Revision C02): Gaussian, Inc. Wallingford, CT, 2004. 7. Ortiz, J.V. J.Chem.Phys. 1996, 104, 7599.


46

Theoretical Studies (Quantum Mechanical) of Furan-, Pyrrole-, and Thiophene-Based Organic Semiconductors

Courtney E Dula, Gilda K. Sibedwo, Dawn E. Scott and Edmund Moses N. Ndip

Chemistry Department, School of Science, Hampton University, Hampton, VA 23668

In the ever expanding field of molecular electronics, experimental data suggests that single molecules or a finite set of self-assembled molecules is capable of performing all the basic functions of conventional devices such as diodes and wires [1]. Research by Metzger et. al [2] has shown that small conjugated molecules (usually phenylene-based derivatives) act as conducting wires either when inserted into a metallic junction [3] or when anchored on a metallic surface and contacted by an STM tip [4]. Semiconductor device physics has experienced increased growth in applications since the discovery of negative differential resistance (NDR) Two kinds of molecular units exhibit NDR behavior [Figure 1]

Z

X

Y

X = N O 2 , C H 2 - C H 3

Y = H , N H 2 , N O 2

Z = S H , S C O C H 3

R

R 2

R 1

R

X

X

R 2

R 1

R = C H 2 , C H 2 - C H 2

X = R 1 = R 2 = H Figure 1: Chemical structures for which NDR behavior has been observed experimentally [5]

There are very few measurements in the open literature that deal with voltage dependence on electronic structure. Despite conflicting views about the existence of the NDR phenomenon in molecules, there are several theoretical studies in the open literature based on both semi empirical and ab initio methods that correlate the existence of NDR and molecular / electronic structure. The present study is: 1) an attempt to determine the molecular descriptors that can be used to ascertain NDR behavior; 2) to elucidate the mechanism that leads to NDR behavior. To this end we have initiated a study of furan-, pyrrole-, and thiophene-based molecules.


47

XY Y

YY

N N

Z

Z

Z

Z

X = O (furan); N (pyrrole); S (thiophene) Y = Y: HC=CH (ethylene); N=N (azo) Z = CH3, CH2CH3, C6H5, cyclopentyl

Figure 2: General Structures of furan-, pyrrole-, and thiophene-based conductors studied.

Optimized geometries have been obtained for at least 28 of the 30 molecular structures being investigated using the semi-empirical Hartree-Fock Austin model 1 (AM1) method, the Parameterized model 3 (PM3), and the Hartree-Fock minimum neglect of differential overlap (MNDO) method contained in the MOPAC semi-empirical program. AM1 [6], PM3 [7], and MNDO [8] methods are all parameterized methods that yield accurate geometries for organic molecules in their ground state. In addition to optimized geometries, dipole moments, electron densities / electrostatic potentials, HOMO-LUMO gaps, and polarizabilities have been determined for each molecule in the study. Conformational analysis calculations have also been carried out. Structures for at least three of the lowest energy conformations for each molecule have been determined.

BBST

BBST Calculations AM1 PM3

Ionization Potential 7.582 eV 7.824 eV Dipole 1.499 Debye 0.460 Debye

HOMO -7.583 eV -7.825 eV LUMO -0.736 eV -1.011 eV

Enthalpy 451.840 kJ 408.424 kJ

BEST


48

BEST Calculations AM1 PM3

Ionization Potential 7.711 eV 7.934 eV Dipole 2.837 Debye 2.262 Debye

HOMO -7.712 eV -7.934 eV LUMO -0.828 eV -1.100 eV


BMST

BMST Property AM1 PM3

Ionization Potential 7.603 eV 7.911 eV Dipole 1.503 Debye 0.0318 Debye HOMO -7.604 eV -7.912 eV LUMO -0.746 eV -1.068 eV


The results obtained for the systems studied here are comparable to results for other small systems where NDR has been observed. We are using the more refined ab initio methods (HF, MP2) and density functional theory (DFT – B3LYP) to further probe the consistency of these model compounds. We have chosen the more moderate size basis set, 6-311G with and without polarization functions for these calculations. We are using the US GAMESS (Iowa State), GAUSSIAN (Gaussian, Inc.) suite of programs for calculations and MOLDEN (freeware) for visualization along with TITAN (Wavefunction Inc.) for both calculations and visualization.

We acknowledge support from NSF-CCLI DUE -0511394 and NSF EEC NUE #0532472.

References Cited: 1. Packam, P.A., Science, (2000), 288, 319 2. Metzger, R.M. et al., J. Am. Chem. Soc., (1997), 119, 10445 3. Reed, M.A., Zhou, C., Muller, C.J., Burgin, T.P., and Tour, J.M., Science (1997), 278,

252 4. Andres, R.P., Bein, T., Dorogi, M., Feng, S., Henderson, J.I., Kubiak, C.P., Mahoney,

W., Oscifchin, R.G., and Reifenberger, R., Science, (1996), 272, 1323. 5. Karzazi, Y., Cornil, J., Bredas, J.L., Nanotechnology, (2002), 13, 336 6. Dewar, M.J.S., Zoebisch, E.G., Healy, E.F., and Stewart, J.J.P, J. Am. Chem. Soc.,

(1995), 107, 3702. 7. Stewart, J. J. P. , J. Comp. Chem. 10, 209 (1989); Stewart, J. J. P. , J. Comp. Chem. 10,

221 (1989). 8. Zerner, M.C., Loew, G.H., Kirchner, R.F., and Mueller-Westerhoff, U.T., J. Am. Chem.

Soc., (1980), 102, 589


49

The Strong Enhanced Scattering and Photothermal Properties of Gold Nanoparticles of Different Shapes and Their Applications in

Nanophotonics, Nanomotors and Nanomedicine

Mostafa A. El-Sayed

Laser Dynamics Laboratory, Georgia Institute of Technology Atlanta, GA, USA

Many new fields such as optoelectronics, sensors, nanocatalysis, nanomotors and NANOMEDICINE use the new exciting properties 1-3 of gold and silver nanoparticles. They absorb and scatter light orders of magnitudes stronger than other materials. This is due to the coherent surface plasmon oscillation of the free electrons in their conduction band.

The strong scattering properties can be used in imaging and sensitive detection of cancer

cells4. The strong absorbed photon energy is rapidly converted into heat. This localized heating of the gold nanoparticles can lead to: its melting, its coherent lattice oscillation5 (can be used in nanophotonics), it can lead to rapid sublimation of its atoms (leading to its propulsion and flying6 away with jet velocities) or it can heat and melts attached cancer cells leading to their destruction and thus used in cancer therapy7,8.

References: 1. Stephan Link and Mostafa A. El-Sayed, “Spectral Properties and Relaxation Dynamics of

Surface Plasmon Electronic Oscillations in Gold and Silver Nanodots and Nanorods”, JPhysChemB, 103 (40), 8410-8426 (1999) (Feature Article).

2. Mostafa A. El-Sayed "Some Interesting Properties of Metals Confined in Time and Nanometer Space of Different Shapes", Acc. Chem. Research, 34, (4), 257-264 (2001). Invited

3. Stephan Link, Mostafa A. El-Sayed, “Optical Properties and Ultrafast Dynamics of Metallic Nanocrystals”, Annual Review Phys. Chem., 54:331-66, (2003) Invited.

4. El-Sayed, Ivan; Huang, Xiaohua; El-Sayed, Mostafa A., “Surface Plasmon Resonance Scattering and Absorption of anti-EGFR Antibody Conjugated Gold Nanoparticles in Cancer Diagnostics; Applications in Oral Cancer,” Nano Letters 4(5), 829-834, (2005).

5. Wenyu Huang; Wei Qian; Mostafa A. El-Sayed, “Coherent Vibrational Oscillation in Gold Prismatic Monolayer Periodic Nanoparticle Arrays”, Nano Lett, 4, (9), 1741-1747, (2004).

6. Huang, W.Y.; Qian, W.; El-Sayed, M.A. Gold Nanoparticles Propulsion from Surface Fueled by Absorption of Femtosecond Laser Pulse at Their Surface Plasmon Resonanceî J. Am. Chem. Soc. :Communication, ASAP.

7. El-Sayed, Ivan; Huang, Xiaohua; El-Sayed, Mostafa A., “Selective Laser Photo-Thermal Therapy of Epithelial Carcinoma Using Anti-EGFR Antibody Conjugated Gold Nanoparticles”, Cancer Letters, (2006, 239, Issue 1, P. 129)(2005).

8. Huang, X; El-Sayed, M; J. Am. Chem. Soc.; 2006, 125(6), 1215-1220.


50

Obtaining Reliable Structures for the Accurate Calculation of Energetics in Delocalized π···π Complexes: Cyanogen Dimer and

Diacetylene Dimer

Adel M. ElSohly, Brian W. Hopkins, and Gregory S. Tschumper

Department of Chemistry and Biochemistry University of Mississippi, University, MS 38677-1848, USA

We introduce two new prototype delocalized π···π systems: the dimers of cyanogen and diacetylene (see Figure 1). Optimizations on the parallel-slipped and T-shaped configurations of these dimers with MP2 and CCSD(T) electronic structure methods and basis sets of double-, triple-, and quadruple-zeta quality have been performed. The thrust of this work focuses on the effect of the optimization procedures (method, basis set, cp-correction, and rigid monomer approximation) on the structure and energetics of each of the dimers. Estimates of the CCSD(T)/CBS interaction energy for each of the optimized geometries are reported. Due to error cancellation, interaction energies obtained with MP2 optimized structures are within 0.2 kcal/mol of values obtained with CCSD(T) optimized structures.

Figure 1. Parallel-slipped and T-shaped configurations of diacetylene dimer.


51

Prediction of Excited States for Carbon, Nitrogen and Oxygen Systems Using Quantum Monte Carlo Theory

Floyd Fayton Jr a, Ainsley Gibson a, William A. Hercules b, and John A.W. Harkless a

a Department of Chemistry, Howard University, Washington, DC 20059 b Department of Physics and Astronomy, Howard University, Washington, DC 20059

Quantum Monte Carlo (QMC) refers to a class of ab initio methods that use a stochastic simulation to solve the many-body Schrödinger equation. QMC differs from post-Hartree Fock methods in that it includes electron correlation explicitly. Diffusion Monte Carlo (DMC) and Variational Monte Carlo (VMC) are applied to elucidate the thermodynamic and electronic properties of reactions of nitrogen plasma with carbon in an oxygenated environment. In order to reach that goal, excited states of the atomic and binary compounds of carbon, nitrogen, and oxygen were estimated in order to illustrate the ability to accurately describe the range of reactions that may occur. Selected excited states of the constituent elements were calculated in order to show the accuracy of various electronic structure techniques. These techniques include DMC, VMC, CASSCF/cc-pVTZ and CISD/cc-pVTZ, all values were compared against experiment.


52

Designing Bioactive Molecules Using Virtual Screening

James I. Fells, Sr.1, Ryoko Tsukahara2, Abby L. Parrill1, and Gabor Tigyi2

1Department of Chemistry and Computational Research on Materials Institute, The University of Memphis, Memphis, TN 38152

2Department of Physiology, University of Tennessee Health Science Center, Memphis, TN 38163

Virtual screening is one of the main lead discovery tools employed by many pharmaceutical companies. This use is triggered by the demand to rapidly identify lead compounds due to the expanding numbers of potential drug targets resulting from genomic efforts. In our research, we are currently interested in studying the role of lysophosphatidic acid(LPA) and its receptors LPA1, LPA2, and LPA3. LPA has been linked to various diseases including breast cancer, cardiovascular disease, and prostate cancer. Virtual screening uses multiple approaches for lead identification and optimization. Our research currently utilizes docking, pharmacophore modeling, database mining, QSAR, and similarity searching in efforts to identify potential sub-type specific LPA receptor antagonists. We have developed a pharmacophore to mine the NCI database for leads. Seven hits identified by virtual screening have been confirmed to be LPA3 antagonists through biological assays. One of these antagonists is selective for LPA3 over LPA1 and LPA2. These leads have been further optimized by employing similarity searching for further database mining and QSAR modeling as a second in silico screening tool.


53

Conformational Analysis of 3 Separate Qualitative Biologically Active Enantiomers of α-Hydroxy Phosphonates

Jason Ford-Green1, Devashis Majumdar1, Jerzy Lesczcynski1

1Jackson State University, Department of Chemistry, Jackson, MS 39217

Many attempts have been carried out in the exhaustive effort to further understand the inhibition pathways of certain medicinal enzymes. Within these sets of understandings the central theme is to assess the relative geometrical orientation of the inhibitor in its cellular environment, and its conformational changes once inside the active site. Using the analysis from recently published literature (Samanta et al., 2006) we selected 3 separate derivatives (shown below) of a qualitative yet synthetically practical inhibitor with high binding affinities and inhibitory propensities to medicinal enzymes such as Renin, and HIV Protease/Polymerase. Their antiviral, and anticancer activities have also been reported. These α-hydroxy phosphonates were selected with respect to the highest values between their % yield and % enantiomeric excess. These values rate the relative level of practicality for quantity of compound synthesized, and measure of the biologically active enantiomer obtained in a non-racemic mixture.

Utilizing the Gaussian03 package thermochemical and geometrical analysis are provided which may show the nature of rotational transition from one conformation of the inhibitor to another once in the gas phase and aqueous phase of the molecular framework. Density Functional Theory calculations at the B3LYP/6-31G(d,p) level will be further calibrated against the higher level Second Order Moller-Plesset Pertubative Theory. The water solubility of the inhibitor is resolved through the CPCM (COSMO) model which uses the United Atom in Hartree Fock (UAHF) method while creating a polarized continuum around the built molecular cavity.

It is also of biological importance to understand the relative areas of reactivity about these α-hydroxy phosphonates to elucidate substrate-amino acid interaction. Molecular Electrostatic Potential surfaces are generated for the purpose of illustrating areas on an isodensity surface that show areas of high and low electronic density. Lastly, comparison of equivalent torsional angles between existing crystal structures of phosphonate compounds in the E+S complex and our low-energy conformer(s) will be done to possibly give insight into predicting the inhibitory properties of various α-hydroxy phosphonates that are readily synthesized at a high yield and quality.

Derivative 1: R2= Et R1= p-Br-C6H4 66%yield ≈99% enantiomeric excess Derivative 2: R2= Et R1= Me 91%yield 97% enantiomeric excess Derivative 3: R2= Et R1= CH2Ph 86%yield 92% enantiomeric excess


54

Relative Reactivity in a Series of Fumarates

Ryan Fortenberry1, David H. Magers1, Wujian Miao2, and Charles E. Hoyle2

1Computational Chemistry Group Department of Chemistry & Biochemistry, Mississippi College

2School of Polymers and High Performance Materials University of Southern Mississippi

Electrochemically obtained reduction potentials for diethyl fumarate (Figure 1.), ethyl vinyl fumarate (Figure 2.), and divinyl fumarate (Figure 3.) indicate that the presence of the vinyl ester group effects the reduction potential for the fumarate. Further studies, such as rates of dimerization and rates of oxidation, including additional systems with terminal vinyl groups such as 2-ethoxyethyl vinyl ether (Figure 4.), triethyleneglycoldivinyl ether (Figure 5.), and vinyl decanoate (Figure 6.) indicate varying degrees of reactivity of the molecules at this terminal vinyl group. Thus, we initiated computational studies of these systems to explain their experimental behavior. Population analysis of the electron density, LUMO energies, and electron affinities all correlate well with the observed experimental reactivity trends. We gratefully acknowledge support from the Mississippi College Catalysts, the alumni support group of the Department of Chemistry & Biochemistry.

O

O

O

O

Figure 1. diethyl fumarate

O

O

O

O

Figure 2. ethyl vinyl fumarate


55

O

O

O

O

Figure 3. divinyl fumarate

OO

Figure 4. 2-ethoxyethyl vinyl ether

OO

OO

Figure 5. triethyleneglycoldivinyl ether

O

OFigure 6. vinyl decanoate


56

Theoretical Study of the Cycloaddition of Aminoisocyanocarbenes to Alkenes

Fillmore Freeman* and Dung Judy Ann Pham

Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025

The singlet-triplet gaps (S—T, ΔEST) and the mechanisms of the cycloaddition of aminoisocyanocarbenes [C≡NCNH2, C≡NCN(CH3)2, C≡NCN(CF3)2] to alkenes to afford substituted cyclopropanes have been studied using B3LYP, B3PW91, CCSD(T), and QCSID(T) with the 6-31+G(d,p), 6-311+G(d,p), 6-311+G(3d,2p), cc-pVDZ, and cc-pVTZ basis sets. A range of alkenes with electron attracting groups and electron withdrawing groups were selected in order to determine the philicity of aminoisocyanocarbene (1). The correlation of ionization potentials and HOMO energies of the alkenes versus the activation energies of cycloaddition will be presented. The three aminoisocyanocarbenes have singlet ground states and CCSD/cc-pVTZ and QCISD/cc-pVTZ predict the singlet state of aminoisocyanocarbene (S-1) to be 38.18 and 38.23 kcal/mol, respectively, lower in energy than the triplet form (T-1). Substitution of methyl groups for hydrogens at nitrogen increases the ΔEST whereas substitution of trifluoromethyl groups lowers the ΔEST.


57

Relative Energies of Conformers and Conformational Interconversion Mechanisms of Tetraoxacyclohexanes

Fillmore Freeman,* Chansa Cha, Elika Derek, Chinh Do, Jung Hwan Hwang, Lisa Phung, Quyen Tu Phung, Travis Picorelli, and Tina Wang

Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025

Ab initio molecular orbital theory (HF), density functional theory (B3LYP), coupled cluster theory [CCD, CCSD(T)], quadratic configuration interaction theory [QCISD(T)], and Complete Basis Set models (CBS-4M, CBS-LQ, CBS-Q, CBS-QB3) have been used to calculate the relative energies, relative thermodynamic parameters, structural parameters, vibrational frequencies, and conformational interconversion mechanisms of 1,2,3,4-tetraoxacyclohexane (1), 1,2,3,5-tetraoxacyclohexane (2), 1,2,4,5-tetraoxacyclohexane (3), and 3,3,6,6-tetramethyl-1,2,4,5-tetraoxacyclohexane (4). CBS, CCSD, and QCISD predicted the relative energies of 1,2,3,4-tetraoxacyclohexane (1), 1,2,3,5-tetraoxacyclohexane (2), and 1,2,4,5-tetraoxacyclo-hexane (3) to be 50 : 1 : 4. CCSD/cc-pVDZ(T) predicted the barrier for the chair-chair interconversion of 1 to be 14.26 kcal/mol. CCSD/cc-pVDZ(T) and QCISD/cc-pVDZ(T) predicted the barrier for the chair-chair interconversion of 3 to be 19.29 and 19.35 kcal/mol, respectively. The barrier for the interconversion of the 3,6-twist enantiomers of 3 via a 3,6-boat transition state is predicted to be a relatively high 19.02 kcal/mol.


58

The Guanine-Zn-Cytosine Base-Pair in M-DNA

Miguel Fuentes-Cabrera, Bobby G. Sumpter, Judit E. Šponer, Jiří Šponer, Leon Petit, and Jack C. Wells

Oak Ridge National Laboratory, Oak Ridge, TN

M-DNA is a type of metalated-DNA that forms at high pH and in the presence of Zn, Ni, and Co, with the metals placed in between each base-pair, as in G-Zn-C. Experiments have found that M-DNA could be a promising candidate for a variety of nanotechnological applications, for it is speculated that the metal d-states enhance the conductivity, but controversy still clouds these findings. Here, we carry out a comprehensive ab initio study of eight G-Zn-C models in gas-phase to help discern the structure and electronic properties of Zn-DNA. Specifically, we study whether a model prefers to be planar and has electronic properties that correlate with Zn-DNA having a metallic-like conductivity. Out of all studied models there is only one that preserves its planarity upon full geometry optimization. Nevertheless, starting from this model one can deduce a parallel Zn-DNA architecture only. This duplex would contain the imino proton, in contrast to what has been proposed experimentally. Among the non-planar models there is one that requires less than 8 kcal/mol to flatten (both in gas- and solvent-conditions) and we propose that it is a plausible model for building an anti-parallel duplex. In this duplex Zn would replace the imino proton, in accordance with experimental models. Neither planar nor non-planar models have electronic properties that correlate with Zn-DNA having a metallic-like conductivity due to Zn d-states. To understand whether Density Functional Theory (DFT) can describe appropriately the electronic properties of M-DNAs, we have investigated the electronic properties of G-Co-C base-pairs. We have found that when self-interaction corrections (SIC) are not included, the HOMO state contains Co d-levels, whereas these levels are moved below the HOMO state when SIC are considered. This result indicates that caution should be exercised when studying the electronic properties of M-DNAs with functionals that do not account for strong electronic correlations.


59

An ab Initio Quantum Mechanical Study of Hydrogen-Bonded Complexes

Al’ona Furmanchuk, Olexandr Isayev, Leonid Gorb, and Jerzy Leszczynski

Computational Center for Molecular Structure and interactions, Jackson State University, Jackson, MS 39217, USA

Hydrogen bonds play a critical role in many chemical and biochemical processes. They not only dominate the influence of the aqueous environment on molecular structure, but also play a key role in determining the structure and function of biomolecules, such as proteins and nucleic acids [1, 2]. It is therefore critical to accurately determine the energies of hydrogen-bonded systems in order to reliably quantitative their impact on biological systems.

The present study focused on examination of typical hydrogen-bonded complexes via the density functional theory (DFT) using B3LYP and MPW1B95 functionals, and second-order Moller-Plesset perturbation (MP2) theory.

Interaction Gibbs Free Energies of intermolecular complexes are systematically analyzed and results are compared with data obtained from the basis set extrapolation procedure. The most reliable and economical procedure for accurately determining the hydrogen-bonding energies is discussed among considered approximations. 1 Jeffrey, G. A. An introduction to Hydrogen Bonding; Oxford University Press: New York, 1997. 2 Scheiner, S. Hydrogen Bonding; Oxford University Press: New York, 1997.


60

Hydration of Urea and Trimethylamine-N-oxide

Earl Chauncey Garrett, G. Reid Bishop, and David H. Magers


Both urea and trimethylamine-N-oxide (TMAO) (Figure 1.) are small molecules with large dipole moments, and both are easily dissolved in water. Urea is commonly used to denature biological macromolecules such as proteins and DNA. In contrast, TMAO is known to induce structure in these same molecules. Each of these small polar molecules is thought to interact differentially with water. Water also plays a role in stabilizing macromolecular structure. Here results are presented investigating the theoretical water binding properties of urea and TMAO to understand their differential activities. Specifically, the binding energies of both systems with three and with six water molecules are investigated. The complex with three water molecules and TMAO is shown in Figure 2, and the TMAO and six-water complex is presented in Figure 3.

Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies for all complexes are computed using SCF theory and density functional theory. The DFT functional employed is Becke’s three-parameter hybrid functional using the LYP correlation functional. We gratefully acknowledge support from the Mississippi College Catalysts, the alumni support group of the Department of Chemistry & Biochemistry.

Figure 1. Trimethylamine-N-oxide

Figure 2. Complex of trimethylamine-N-oxide and three water molecules


61

Figure 3. Complex of trimethylamine-N-oxide and six water molecules


62

Computational Study of Electronic Structure Properties: Ionization Potentials and Electron Affinities of the First Row Transition Metals

Using Various ab Initio, DFT and QMC Methods

Ainsley A. Gibson, Floyd A. Fayton, William A. Hercules1 and John A. W. Harkless

Department of Chemistry, Howard University, Washington DC 20059 1Department of Physics and Astronomy, Howard University, Washington DC 20059

This work presents a comparative study of the performance of various ab initio, DFT and quantum Monte Carlo methods in the determination of the ionization potentials and electron affinities of the first row transition metals. The primary objective is to demonstrate that Variational Monte Carlo (VMC) and fixed-node Diffusion Monte Carlo (DMC) are sufficient in a simplified, single-determinant application to be used in the determination of transition metal IP and EA as compared to experiment. Earlier studies have indicated that QMC is a suitable method for difficult systems and can be applied to the first row transition metals. These results are anticipated to be applicable to systems of interest in materials chemistry such as nano-materials, biological species that contain transition metals as well as catalytic systems.


63

Alterations of DNA Bases Tautomeric State and Their Role in UV Mutagenesis

H. A. Grebneva

Donetsk Physics and Technology Institute of the NAS of Ukraine 83114 Donetsk, Ukraine

UV radiation produces photoproducts in DNA. As indicated above, both cyclobutane pyrimidine dimers and (6-4) adducts are formed. Incorrect bases can be inserted when DNA containing photoproducts acts as the template for SOS-replication, repair, or transcription. The mutations that result from these incorrect bases are often targeted; that is, they occur at the same position as the photoproduct. Sometimes mutations are formed in the vicinity of the damage, a process that is termed untargeted mutagenesis. (6-4) adducts and cyclobutane dimers cause transitions, transversions, frameshifts, and complex mutations. Mutations occur very frequently at particular sites in DNA, the so-called hot spots of UV-mutagenesis. Other sites, where mutations rarely are found, are referred to as cold spots [1]. The irradiation of DNA molecule with ultraviolet light promotes the formation of cyclobutane pyrimidine dimers and (6-4) adducts. In replication or reparation processes they can result in mutations.

The generally accepted theory of the UV-mutagenesis rests upon the hypothesis that mutations are exceptionally due to accidental errors of DNA polymerases, while there is no difference in dimers resulting in mutations and nonmutational dimers. The view that polymerase fidelity drives mutagenesis is now commonly held [1-7], and is part of models for spontaneous mutagenesis [2, 4, 6] and UV-induced mutagenesis [6], as well as models of spontaneous untargeted mutagenesis [2, 3]. These models are based on the fact that both E. coli polymerases IV and V have relatively low synthesis fidelity [7]. It is assumed that sites of a specific nucleotide composition are repaired better (or worse) than others, and so on [5].

Mutations may also result from noninstructive sites. To know which of the bases will be incorporated by the polymerase, the use is made of the A rule [5]. It is shown that the adenine is most frequently incorporated in front of the noninstructive sits [5]. It is easy to see that such approaches are very restricted. They contradict several experimental facts and can’t explain many phenomena of the UV mutagenesis.

In a number of papers, I have attempted to construct a model of UV-mutagenesis that is based on the accumulated facts [8-22]. It was assumed that the tautomeric state of the constituent bases may change during the formation of dimers. A mechanism for changes in the tautomeric state of base pairs has been proposed for the radiationless deexcitation of the UV quantum from the triplet energy level [8, 14, 16]. It is shown that such changes in tautomeric states may result under dimer formation too [10, 14, 16]. The mechanism rests upon properties of triplet energy levels, hydrogen bonds, upon character and lifetime of atomic vibrations in paired bases of DNA [23, 24], of the surface of potential energies in DNA [23-27], character of changes in potential curves of hydrogen bonds upon noticeable change of H-bond length [28], typical lifetimes of the excited H-bond in DNA [29], upon the model of semiopen metastable states of DNA bases [30], etc [8, 14, 16].

It is shown five new tautomeric states of thymine and adenine [14, 16] and seven ones of guanine and cytosine [10, 19] may form. Within the terms of the organic chemistry such states are named salts and acids. Within the quantum chemistry terms these are rare tautomeric forms [21]. We shall use second meaning. It is shown that due to bending of the DNA strand such rare tautomeric forms of bases will be stable if the bases are in a small vicinity of the dimer or they


64

are forming the dimer. They are stable in the active centres of enzymes because there are no water molecules. They are stable in one-stranded DNA during the synthesis, because the synthesis is so fast that the bases can’t, as a rule, change their tautomeric state because of the contact with water molecules [21].

They may arise for the case when DNA is UV-irradiated and dimers are formed. New rare tautomeric conformations of A:T base pairs are proposed that are capable of influencing the character of base pairing [10, 14, 16, 19], and may result in transitions or transversions when the SOS system processes DNA containing thymine dimers [9, 11, 13, 15, 17, 22].

Several mechanisms for untargeted mutagenesis also have been developed [13, 15, 17]. It is proposed that premutations occur as a result of the formation of cytosine dimers [10, 19] and result in specific transitions and transversions upon SOS-repair and replication [11]. The model forms a basis for explaining the occurrence of hot and cold spot for UV mutagenesis [20] and free radical-induced mutagenesis [12].

Mutations can be viewed as occurring in several stages [16]. The first stage involves the formation of potentially mutagenic DNA damage (potential mutations). With UV-irradiation, the damage is frequently in the form of pyrimidine dimmers, and their formation requires only 10-6 second [16]. Some dimers are made up of bases in canonical conformations; others may contain one base or both bases in a rare tautomeric form. In the second stage, the damage may be removed by repair mechanisms (e.g., excision repair). Those dimers that are not removed can result in mutations through a combination of DNA synthesis and SOS repair [9, 22] The rare tautomeric forms that are found in dimers are relatively long-lived [16], and the process of transforming DNA damage (potential mutations) into actual transitions, transversions, frameshifts, and complex mutations requires seconds [6, 7, 4, 2]. Therefore these processes can be studied separately.

In papers [9, 15] I assumed that the DNA polymerase incorporates canonical bases that are capable of forming H-bonds with the template bases in preference to incorporating bases that are in rare tautomeric forms. Unfortunately, this assumption was poorly grounded and a hypothesis was developed which states that, under conditions where the SOS system is induced, the proofreading activity of the DNA polymerase becomes lower and the polymerase does not discriminate between bases in the canonical and rare tautomeric forms. In paper [22] presents the experimental observations that support the hypothesis. Usually in this case A rule is used. It has been shown that under SOS synthesis the DNA polymerase incorporates, as a rule, such canonical bases which are capable of forming hydrogen bonds with bases of the template DNA [22]. In [22] the following analysis considers mechanisms for targeted base substitution mutation when the template DNA contains cis-syn thymine cyclobutane dimers.

It has been shown that upon dimerization there may be changes in the tautomeric state of constituent bases. The mutagenous are dimers in which the tautomeric state of constituent bases has changed [22]. Such dimers may give transitions or transversions under SOS-replication and post-replication SOS-reparation [9, 22].

Structural analysis indicates that one type of dimer containing a single tautomeric base (TT*1, with the ‘*’ indicating a rare tautomeric base and the subscript referring to the particular conformation) can cause A:T→G:C transition or homologous A:T→T:A transversion, while other dimers (TT*2) can cause a one-nucleotide gap. The dimers containing T*4 result in A:T→C:G transversion, while TT*5 dimers can cause A:T→C:G transversion or homologous A:T→T:A transversion. If both bases in the dimer are in a rare tautomeric form, then tandem mutations or double-nucleotide gaps can be formed. The dimers containing the rare tautomeric forms T*’1, T*’2, T*’3, T*’4 and T*’5 may not result in mutations. The question of whether dimers containing T*4 and T*5 result in mutations requires further investigation.

The study was supported by the Ukrainian State Fund for Fundamental Research (Grant No Ф7-208/2004).


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1. K.A. Canella, M.M. Seidman, Mutation spectra in supF: approaches to elucidating sequence context effects. Mutat. Res. 450 (2000) 61-73.

2. M. Tang, P. Pham, X. Shen, J.-S. Taylor, M. O’Donnell, R. Woodgate, M. Goodman, Roles of Escherichia coli DNA polymerase IV and V in lesion-targeted and untargeted SOS mutagenesis. Nature 404(2000) 1014-1018.

3. A. Maor-Shoshani, N. B. Reuven, G. Tomer, Z. Livneh, Highly mutagenic replication by polymerase V (UmuC) provides a mechanism for SOS untargeted mutagenesis. Proc. Natl. Acad. Sci. USA 97 (2000) 565-570.

4. J.-S. Taylor, New structural and mechanistic insight into the A-rule and the instructional and non-instructional behavior of DNA photoproducts and other lesions. Mutat. Res. 510 (2002) 55-70.

5. P. Pham, J.G. Bertram, M. O’Donnell, R. Woodgate, M.F. Goodman, A model for SOS-lesion-targeted mutations in Escherichia coli. Nature 408 (2001) 366-370.

6. M. Ruiz-Rubio, B.A. Bridges, Mutagenic DNA repair in Escherichia coli 14. Influence of two DNA polymerase III mutator alleles on spontaneous and UV mutagenesis. Mol. Gen. Genet. 208 (1987) 542-548.

7. M. Tang, X. Shen, E.G. Frank, M. O’Donnell, R. Woodgate, M.F. Goodman, UmuD’(2)C is an error-prone DNA polymerase. Escherichia coli pol V. Proc. Natl. Acad. Sci. USA 96 (1999) 8919-8924.

8. H.A. Grebneva, The irradiation of DNA by ultraviolet light: potential alterations and mutations. Molecular Biolog. 28 (1994) 805-812.

9. H.A. Grebneva, The molecular mechanisms derivation of mutation bases alteration after a postreplication SOS-reparation a DNA containing thymine dimers. Biopolymers Cell 17 (2001) 487-500.

10. H.A. Grebneva, Mechanisms of formation of potential mutations under cytosine dimers formation in result irradiation double-stranded DNA by ultraviolet light. Review NAS Ukraine 7 (2001) 165-169.

11. H.A. Grebneva, Targeted mutagenesis caused by cytosine dimers and mechanism substitution mutation formation under SOS-replication after irradiation double-stranded DNA by ultraviolet light. Review NAS Ukraine 8 (2001) 183-189.

12. H.A. Grebneva, Possible nature of mutagenesis under activity of free radicals. Theses of reports on 10th Conference on Current Trends in Computational Chemistry. (Vicksburg, MS, USA, November 3-4. 2001). Jackson State University (2001) 89-92.

13. H.A. Grebneva, M.O. Ivanov, The possible molecular mechanisms of untargeted type mutation under SOS replication of double-stranded DNA. Biopolymers Cell 17 (2001) 388-395.

14. H.A. Grebneva, The nature and possible mechanisms of potential mutations formation due to the appearance of thymine dimers after irradiating double-stranded DNA by ultra-violet light. Biopolymers Cell 18 (2002) 205-218.

15. H.A. Grebneva, Possible molecular mechanisms of untargeted mutagenesis upon a post-replication SOS-reparation after irradiating double-stranded DNA by ultraviolet light. Biopolymers Cell 18 (2002) 394-400.

16. H.A. Grebneva, Nature and possible mechanisms formation of potential mutations arising at emerging of thymine dimers after irradiation of double-stranded DNA by ultraviolet light. J Mol Struct 645 (2003) 133-143.

17. H.A. Grebneva, DNA bases in rare tautomeric forms, that are not the components of dimers or modified bases, as one of the reason of an untargeted mutagenesis. Theses of reports on 13th Conference on Computational Chemistry, (Vicksburg, MS, USA, November 1-3. 2001). Jackson State University (2004) 62-65.


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18. H.A. Grebneva, DNA bases in rare tautomeric forms, that are not the components of dimers or modified bases, as one of the reasons of an untargeted mutagenesis. Theses of reports on 13th Conference on Current Trends in Computational Chemistry, November 1-2, Vicksburg, Mississippi, USA. Jackson State University (2004) 62-65.

19. H.A. Grebneva, Mechanism of alteration of DNA bases tautomer state under cis-syn cytosine dimers formation. Theses of reports on 5th Southern School in Computational Chemistry, April 8-9, Vicksburg, Mississippi, USA. Jackson State University (2005) 28-32.

20. H.A. Grebneva, A possible nature of hot and cold spots of UV-mutagenesis. Theses of reports on 14th Conference on Current Trends in Computational Chemistry, November 1-2, Vicksburg, Mississippi, USA. Jackson State (2005) 78-81.

21. H.A. Grebneva, Causes of rare tautomer forms stabilization of bases are in single- and double-stranded DNA under dimers formation. Theses of reports on 6th Southern School on Computational Chemistry, April 8-9, Vicksburg, Mississippi, USA. Jackson State University (2006) 33-36.

22. H. A. Grebneva, A model for targeted substitution mutagenesis during SOS replication of double-stranded DNA containing cis-syn cyclobutane dimers. Environmental and Molecular Mutagenesis 47 (2006) (in Press).

23. K.B. Tolpygo, H.A. Grebneva, Effect of the state of h-b-1 hydrogen bond of the character of some atom vibrations in guanine-cytosine pair of the DNA molecule. Int. J. Quant. Chem. 57 (1996) 219-227.

24. H.A. Grebneva, K.B. Tolpygo, Crystalline and local vibrations of paired bases in poly (dG)-poly (dC) interacting with the h-b-1 hydrogen bond. Int. J Quant. Chem. 62 (1997) 115-124.

25. L. Gorb, J. Leszczynski, Intramolecular proton transfer in mono- and dihydrated tautomers of guanine: an ab initio post Hartree-Fock study. J. Am. Chem. Soc. 120 (1998) 5024-5032.

26. L. Gorb, Y. Podolyan, J. Leszczynski, A theoretical investigation of tautomeric equilibrium and proton transfer in isolated and monohydrated cytosine and isocytosine molecules. J. Mol. Struct. (Theochem.) 487 (1999) 47-23.

27. L. Gorb, Y. Podolyan, J. Leszczynski, W. Siebrand, A. Fernandez-Ramos, Z. Smedarchina, A quantum-dynamics study of the prototropic tautomerism of guanine and its contribution to spontaneous point mutations in E. coli. Biopolymers (Nucl. Acid. Sci.) 61 (2002) 77-91.

28. H.A. Grebneva, Proton potential for broad spectrum of hydrogen bond length in water dimer. Zh. Struckt. Khim. 38 (1997) 422-430.

29. H.A. Grebneva, K.B. Tolpygo, The heat deexcitation of hydrogen bond protons in paired bases of DNA molecules. Studia Biophysica 135 (1990) 115-120.

30. D.M. Govorun, A structural-dynamic model on spontaneous semiopen states in DNA. Biopolymers Cell 13 (1997) 39-45.


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LEE Induced DNA Damage: Cytosine in Double Helix

Jiande Gu,a, b* Jing Wang,b Janusz Rak,c and Jerzy Leszczynski b*

aShanghai Institute of Materia Medica, CAS, Shanghai 201203 P. R. China bComputational Center for Molecular Structure and Interactions,

Department of Chemistry, Jackson State University, Jackson, MS 39217 U. S. A. cFaculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland

DNA strand breaks induced by low energy electrons (LEE) are of crucial importance because such electrons are produced in significant amounts during the interaction of ionizing radiation with genetic material in a cell. Both experimental investigations and theoretical studies have demonstrated that at very low energies, electrons may induce strand breaks in DNA via dissociative electron attachment. The electron attachment usually occurs at pyrimidine bases due to their relatively large electron affinity, causing bond breaking in DNA single strand. In double stranded DNA the negative charge on the electron-attached cytosine might be easily neutralized by proton transfer between G and C, forming a relatively stable neutral radical (5′-d(C-H)MP; see the scheme below).

In this report, we illustrate that a second electron attachment to the neutral radical of 5′-d(C-

H)MP, which might result in a very reactive anion (see the structure below). Intramolecular proton transfer from the C2′ of deoxyribose to the C6 of cytosine within the 5′-d(C-H)MP anion is predicted to have an activation energy barrier of only about 13 kcal/mol. The intramolecular proton transfer leads to an anionic structure of c. 3 kcal/mol lower in energy than the original 5′-d(C-H)MP anion. The geometrical features of the resulted proton transferred 5′-d(C-H)MP anion suggest that the N-C glycosidic bond is greatly weakened due to proton transfer and therefore the abasic site might be formed.

OPO

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5′-d(C-H)MP Radical 5′-d(C-H)MP Anion Proton transferd 5′-d(C-H)MP Anion


68

Hydrogen Tunneling and Protein Motion in Enzyme Reactions

Sharon Hammes-Schiffer

Department of Chemistry, 104 Chemistry Building, Pennsylvania State University, University Park, Pennsylvania, 16802

Theoretical studies of proton, hydride, and proton-coupled electron transfer reactions in enzymes will be presented. We have developed a theoretical formulation for proton-coupled electron transfer reactions. The quantum mechanical effects of the active electrons, transferring proton, and donor-acceptor mode are included in this formulation, and analytical nonadiabatic rate expressions have been derived in various limits. The application of this approach to proton-coupled electron transfer in the enzyme lipoxygenase will be discussed. The experimentally measured deuterium kinetic isotope effect of 80 at room temperature is found to arise from the small overlap of the reactant and product proton vibrational wavefunctions. Our calculations illustrate that the proton donor-acceptor vibrational motion plays a vital role in the proton-coupled electron transfer reaction. We have also developed a hybrid quantum/classical molecular dynamics approach that includes electronic and nuclear quantum effects, as well as the motion of the entire solvated enzyme. The application of this approach to hydride transfer in the enzyme dihydrofolate reductase will be discussed. An analysis of the simulations leads to the identification and characterization of a network of coupled motions that extends throughout the enzyme and represents conformational changes that facilitate the charge transfer process. Mutations distal to the active site are shown to significantly impact the catalytic rate by altering the conformational motions of the entire enzyme and thereby changing the probability of sampling conformations conducive to the catalyzed reaction. References: E. Hatcher, A. V. Soudackov, and S. Hammes-Schiffer, “Proton-coupled electron transfer in soybean lipoxygenase,” J. Am. Chem. Soc. 126, 5763-5775 (2004). S. Hammes-Schiffer, “Hydrogen tunneling and protein motion in enzyme reactions,” Acc. Chem. Res. 39, 93-100 (2006). S. Hammes-Schiffer and S. J. Benkovic, “Relating protein motion to catalysis,” Annual Reviews of Biochemistry 75, 519-541 (2006).


69

Purine Moiety as an Excess Electron Trap in the Watson-Crick AT Pair Solvated with Formic Acid. A Computational and

Photoelectron Spectroscopy Study

Maciej Haranczyk,a Kamil Mazurkiewicz,a Maciej Gutowski,a,b Janusz Rak,a Dunja Radisic,c Soren Eustis,c Di Wang,c and Kit H. Bowenc

aDepartment of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland bChemistry-School of Engineering and Physical Sciencs, Heriot-Watt University, Edinburgh

EH14 4AS, UK cDepartment of Chemistry, Johns Hopkins University, Baltimore, MD 21218, USA

Low-energy electrons (LEE) are formed as the dominant secondary species during water radiolysis [1]. The seminal work of Sanche et al.[2] proved unequivocally that LEE induce formation of single- and double-strand breaks in DNA. Among the DNA constituents the most susceptible to electron attachment are nucleobases (NBs). Having conjugated π-electron systems they possess unoccupied orbitals of low energy capable of capturing an excess electron. So far only pyrimidine bases were considered to be directly involved in the DNA damage induced by low-energy electrons [3-6]. The assumption was based on an electron affinity sequence assumed for isolated NBs: T≈C>A>G [7]. This sequence suggests that thymine and cytosine molecules should be primary targets for the formation of anions of NBs in DNA. One should, however, realize that in contrast to pyrimidine bases, purine molecules possess proton-donor and -acceptor centres that are not involved, or only partially involved, in the Watson-Crick pairing scheme, and may therefore form additional hydrogen bonds. The intermolecular interactions that develop through the above-mentioned proton-donor and -acceptor centers of purines may contribute to the stability of valence anions and alter the ordering of electron affinities observed in isolated NBs. Indeed, the interaction between anionic purines and amino acids or amino acid side chains (e.g. via the Hoogsteen scheme) might counterbalance the larger AEA's of isolated pyrimidines. If so then both types of NBs could play a significant role in DNA damage induced by low-energy electrons. In the cellular environment adenine may interact for example with the side chain of arginine, which at the physiological pH is protonated. Indeed the analysis of the AANT database of proteins-nucleic acids complexes [8] indicates that the Hoogsteen type interactions between adenine and charged arginine account for the majority of adenine-amino acid side chain contacts. Attachment of an electron to adenine (as well as to guanine) complexed with charged arginine might induce barrier-free proton transfer (BFPT; similar to the BFPT predicted in the numerous anionic complexes of nucleobases with proton donors [9-17]) and the reactive neutral AH. radical might initiate a sequence of processes leading to a single strand break.

In the current report a computational and experimental study of the anionic 9-methyladenine-1-methylthymine-formic acid trimer, MAMTFA-, is presented with the main purpose being to understand how the presence of FA affects the excess electron binding by the MAMT pair. A systematic search through the conformational space of the complex coupled with the examination of possible proton transfer reactions resulted in 16 anions that were characterized at the B3LYP/6-31+G** level.


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Figure 1. Electron binding to the Watson-Crick MAMT base pair solvated by formic acid at the Hoogsteen site (I). In consequence of intermolecular proton transfers the radicals MAH. (III) and MAH2

.+ (IV) are formed and the unpaired electron becomes localized on 9-methyladenine. Both initial electron attachment and two following intermolecular proton transfers are thermodynamically favourable and the accompanying changes of B3LYP electronic energies (kcal/mol) are given below arrows.

The complex in which the Watson-Crick MAMT pair forms a cyclic hydrogen bonded structure with FA through the Hoogsteen sites of MA (see Fig. 1), seems to reflect, to some extent, situation of adenine interacting with a protein in DNA. The excess electron attachment to this trimer leads to an anionic structure with an unpaired electron localized primarily on thymine and characterized by a VDE of 0.37 eV. The anionic structure is, however, only a local minimum on the potential energy surface of the anionic trimer. The values of proton affinities and deprotonation enthalpies for the relevant sites of neutral adenine and thymine suggest that intermolecular proton transfer from thymine to adenine is feasible. Indeed, two consecutive intermolecular proton transfers are thermodynamically favorable and lead to: (1) an intermediate anionic trimer built of MAH. , deprotonated FA, and MT, and (2) the global minimum structure built of MAH2

.+, deprotonated FA and deprotonated MT (see Fig. 1). In consequence of two intermolecular proton transfers the excess electron becomes localized exclusively on adenine and the VDE is as large as 2.18 eV. Thus, our computational result suggests that if adenine in DNA interacts with an amino acid of a sufficiently high acidity then an intermolecular proton transfer might occur and the unpaired electron becomes localized on adenine.

Adiabatically most stable anion originates with the complex in which the reverse Watson-Crick MAMT pair forms a cyclic hydrogen bonded structure with FA through the Hoogsteen site of MA. Although due to steric constraints this structure is not present in the non-damaged double stranded DNA there are no obstacles that could prevent its formation in the gas phase. The attachment of an electron to this structure leads to a complex built of MAH2

.+, deprotonated FA and deprotonated MT. The VDE of this anion incremented with –0.2 eV [9-17], amounts to 2.01 eV, the value that remains in excellent agreement with the maximum of

the photoelectron spectrum recorded for the MAMTFA- anionic trimer (see Fig. 2).

Figure 2. Photoelectron spectrum of the of the anionic 9-methyladenine-1-methylthymine-formic acid trimer. Spectrum recorded with 2.7 eV/photon..


71

We suggest that further understanding of DNA damage might require experimental and computational studies of DNA fragments, in which purines are engaged in hydrogen bonding with proton donating molecules through these sites that are not involved in the Watson-Crick pairing scheme.

Acknowledgements. This work was supported by the: (i) Polish State Committee for Scientific Research (KBN) Grants: BW/8000-5-0305-6 (J.R.), KBN/1T09A04930 (K.M.), and N204 127 31/2963 (M.H.), and DS/8221-4-0140-6 (MG), (ii) European Social Funds (EFS) ZPORR/2.22/II/2.6/ARP/U/2/05 (M.H.), and (iii) the National Science Foundation under Grant No. CHE-0517337 (K.B.). M.H. holds the Foundation for Polish Science (FNP) award for young scientists. The calculations were performed at the Academic Computer Center in Gdańsk (TASK) and at the Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the U.S. Department of Energy's Office of Biological and Environmental Research and located at the Pacific Northwest National Laboratory, which is operated by Battelle for the US Department of Energy. The MSCF resources were available through a Computational Grand Challenge Application grant.

References 1. Abdoul-Carime, H.; Gohlke, S.; Fischbach, E.; Scheike, J.; Illenberger, E. Chem. Phys. Lett.

2004, 387, 267-270. 2. Boudaïffa, B.; Cloutier, P.; Hunting, D.; Huels, M. A.; Sanche, L. Science 2000, 287, 1658-

1660. 3. Dabkowska, I.; Rak, J.; Gutowski, M. Eur. Phys. J. D, 2005, 35, 429-435. 4. Barrios, R.; Skurski, P.; Simons, J. J. Phys. Chem. B 2002, 106, 7991-7994. 5. Bao, X.; Wang J.; Gu, J.; Leszczynski, J. Proc. Nat. Acad. Sci., USA 2006, 103, 5658-5663. 6. Gu, J.; Wang, J.; Leszczynski, J. J. Am. Chem. Soc., 2006, 128, 9322-9323. 7. Seidel, C. A. M.; Schulz, A.; Sauer, M. H. M. J. Phys. Chem.1996, 100, 5541-5553. 8. Hoffman, M.M.; Kharpov, M.A.; Cox, J.C.; Yao, J.; Tong, J.; Ellington, A.D. Nucleic Acid

Res. 2004, 32, D174-81. 9. Gutowski, M. ; Dąbkowska, I. ; Rak, J. ; Xu, S. ; Nilles, J.M.; Radisic, D. ; Bowen Jr, K.H.

Eur. Phys. J. D, 2002, 20, 431-439. 10. Harańczyk, M.; Bachorz, R.; Rak, J.; Gutowski, M.; Radisic, D.; Stokes, S.T. ; Nilles, J.M.;

Bowen, K.H. J. Phys. Chem. B, 2003, 107, 7889-7895. 11. Harańczyk, M.; Rak, J.; Gutowski, M.; Radisic, D.; Stokes, S.T.; Nilles, J.M.; Bowen, K.H.

Isr. J. Chem. 2004, 44, 157-170. 12. Harańczyk, M.; Dąbkowska, I.; Rak, J.; Gutowski, M.; Nilles, J.M.; Stokes, S.T.; Radisic, D.;

Bowen, K.H. J. Phys. Chem. B, 2004, 108, 6919-6922. 13. Dąbkowska, I.; Rak, J.; Gutowski, M.; Nilles, J.M.; Radisic, D.; Bowen, Jr, K.H. J. Chem.

Phys. 2004, 120, 6064-6071. 14. Dąbkowska, I.; Rak, J.; Gutowski, M.; Radisic, D.; Stokes, S.T.; Nilles, J.M.; Bowen, Jr,

K.H. Phys. Chem. Chem. Phys. 2004, 6, 4351-4357. 15. Harańczyk, M.; Rak, J.; Gutowski, M.; Radisic, D.; Stokes, S.T.; Bowen, K.H. J. Phys.

Chem. B, 2005, 109, 13383-13391. 16. Radisic, D.; Bowen, K.H.; Dąbkowska, I.; Storoniak, P.; Rak, J.; Gutowski, M. J. Am. Chem.

Soc., 2005, 127, 6443-6450. 17. Mazurkiewicz, K.; Harańczyk, M.; Gutowski, M.; Rak, J.; Radisic, D.; Soren N. Eustis,

S.N.; Wang, D.; Bowen, K.H. Jr. J. Am. Chem. Soc., submitted.


72

Changing Relationship between Computation and Experiment: Metal Halide Molecular Structures

Magdolna Hargittai

Structural Chemistry Research Group of the Hungarian Academy of Sciences, Eötvös University, Pf. 32, H-1518 Budapest, Hungary

Metal halide molecules, especially those involving heavy atoms, pose difficulties for both experimental and computational studies, though for different reasons; due to their low volatility and large-amplitude vibrations on the one hand and their large size, often open-shell atoms, and, again, their floppiness, on the other. While the experimental difficulties do not become any fewer with time, the computational difficulties luckily keep diminishing.

Examples will be shown to illustrate the advantages of using experiment and computation together in solving difficult structural problems. Often, computations may help the interpretation of experimental results. Examples are metal halide systems with complex vapor composition, as the study of copper chloride illustrates [1].

Molecules in the vapor of copper chloride1

In other cases, the dimer content of the vapor of a metal halide – a dihalide, for example – is so small that reliable determination of its structure is not feasible by experiment alone. The computational study of metal dihalide dimers did not only help solving the electron diffraction structures but also resulted in uncovering some unexpected structures for the dimers [2-4].

Computations are the only possibility for determining the structure of molecules that cannot be evaporated without decomposition or cannot be brought into the vapor phase at all. Silver halides with interesting molecular structures will illustrate this [5]. From among the gold halides, the fluorides [6] and chlorides [7] could be studied by electron diffraction but the larger halides are not stable enough. The computed structures of all gold tri- and monohalides will be shown [8]. The trihalides of both gold and silver are good examples of the appearance of the Jahn-Teller as well as relativistic effects in molecular structures.


73

PES of AgF3 and AgI3 indicating very different ground-state geometries5

There are, then, cases, where the relationship between experiment and computation is reversed, and it is the experimental results that help to determine which particular computed structure corresponds to reality. The so-called quasi-linear SrCl2 illustrates this case [9]. Other examples include the aluminum trihalides [10]. Sometimes the existing computational codes are not satisfactory for metal halides as will be demonstrated with the very simple aluminum monohalides.

Acknowledgement. Our work is supported by the Hungarian Scientific Research Fund (Grant OTKA K 60365). References 1. Hargittai, M.; Schwerdtfeger, P.; Reffy, B.; Brown, R. Chem. Eur. J. 2003, 9, 327. 2. Hargittai, M. Chem. Rev. 2000, 100, 2233. 3. Hargittai, M. Struct. Chem. 2005, 127, 8133. 4. Saloni, J.; Roszak, S.; Miller, M.; Hilpert, K.; Leszczynski, J. J. Phys. Chem. A 2004, 108,

2418. 5. Muller-Rosing, H.C.; Schulz, A.; Hargittai, M. J. Am. Chem. Soc. 2005, 127, 8133. 6. Reffy, B.; Kolonits, M.; Schulz, A.; Klapotke, T.M.; Hargittai, M. J. Am. Chem. Soc. 2000,

122, 3127. 7. Hargittai, M.; Schulz, A.; Reffy, B.; Kolonits, M. J. Am. Chem. Soc. 2001, 123, 1449. 8. Schulz, A.; Hargittai, M. Chem. Eur. J. 2001, 7, 3657. 9. Varga, Z.; Lanza, G.; Minichino, C.; Hargittai, M. Chem. Eur. J. 2006 (DOI:

10.1002/chem.200600328). 10. Hargittai, M.; Reffy, B.; Kolonits, M. J. Chem. Phys. A 2006, 110, 3770.


74

Effect of Ring Annelation on Li+-Benzene Interaction: A Theoretical Study

Ayorinde Hassan, T. C. Dinadayalane and Jerzy Leszczynski*

Computational Center for Molecular Structure and Interactions, Department of Chemistry PO Box 17910, Jackson State University, Jackson, Mississippi 39217

Molecular recognition has attracted considerable attention not only in chemistry, but also in biology.1 Designing and implementing of new ligands are important for the removal of radioactive and heavy metal ions from waste water streams.2,3 Tailoring of binding sites or host molecule by different shape and arrangement for the interaction of cations has engrossed significant interest due to the importance of understanding the host-guest interactions in chemical and biological processes. Here, we have studied Li+ binding with the central six-membered ring of the tri-annelated benzenes. The monocyclic six-membered aromatic ring (benzene) and highly strained bicyclo[2.1.1]hexene are employed for annelation to the benzene ring. Benzene and other tri-annelated systems considered in this study are shown in Scheme 1. The tri-annelated compounds 4 and 5 are known experimentally.4-6

C1 C1

C2C3

C1

C2C3

C4 C5C6

C7

C1

C2C3

C4 C5C6

C7

1 2 3

4

C1 C2 C3

C4

5 Scheme 1: The host molecules for binding with Li+. The numbering is given to show the NMR chemical shift.

Effect of annelation to the benzene ring on cation-π interaction, particularly binding of Li+ has been investigated using B3LYP, MPW1B95 functionals and MP2 method in conjunction with 6-31G(d,p) basis set. The deviation of the interaction energies among the three levels is within 2 kcal/mol. The computed interaction energies clearly indicates that binding affinity of Li+ ion with benzene is enhanced by tri-annelation of benzene or highly strained bicyclo[2.1.1]hexene ring. Substantial increase of interaction energy by bicyclo[2.1.1]hexene


75

ring annelation may be attributed to the weak C-H…Li+ interaction in addition to Li+-π interaction. We have analyzed how the metal ion (Li+) binding affects the characteristic IR frequencies, 1H and 13C NMR chemical shifts of the ligands. Tris(bicyclo[2.1.1]hexeno)benzene appears to be a good receptor for cation binding.

References:

1. Ma, J. C.; Dougherty, D. A. Chem. Rev. 1997, 97, 1303. 2. Amicangelo, J. C.; Armentrout, P. B. J. Phys. Chem. A 2000, 104, 11420. 3. Zhu, D.; Herbert, B. E.; Schlautman, M. A.; Carraway, E. R. J. Environ. Qual. 2004, 33, 276. 4. Matsuura, A.; Komatsu, K. J. Am. Chem. Soc. 2001, 123, 1768. 5. Frank, N. L.; Baldridge, K. K.; Siegel, J. S. J. Am. Chem. Soc. 1995, 117, 2102. 6. Burgi, H. -B.; Baldrige, K. K.; Hardcastle, K.; Frank, N. L.; Gantzel, P.; Siegel, J. S.; Ziller, J.

Angew. Chem. Int. Ed. Engl. 1995, 34, 1454.


76

Study of the Optimised STO-nG Expansion and its Derivatives

Philip E Hoggan

LASMEA, UMR 6602 CNRS University Blaise Pascal

24 venue des Landais 63177 AUBIERE Cedex, FRANCE

For many years, it has been considered opportune to expand Slater Type Orbitals (STOs) as a sum of Gaussians. The aim of this procedure is to closely mimic the STO, although, clearly Kato's conditions (nuclear cusp and exponential decay at long range) are not satisfied. The advantage is the simple Gaussian product theorem.

In this work, the difference between an STO and its Gaussian expansion, globally optimised for exponents and coefficients is found to converge rapidly with n to a universal curve. Furthermore, the absolute error may be reduced to the nano-hartree for n=10-12 and pico-hartee for n=20. Expansions have been tested to n=30.

The zeros of the universal curve may be used to extend the expansion from n to n+2 since each curve has 2n zeros.

This method of comparing Slater integals and integrals over STO-nG is discussed in conclusion, with emphasis on the physical properties which require analytical Slater functions, because of oscillations in the derivatives of STO-nG (tested by evaluating {grad (ρ) /(ρ)} ) or by cusp and decay dependence


77

Quantum Chemical Study of the Effects of π–π Stacking of the Fullerene C20 with DNA Bases

Tiffani M. Holmes1, Dinadayalane Tandabany1, Glake A. Hill1, Jerzy Leszczynski1

1Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University; Jackson, MS 39217

The C20 caged fullerene has just very recently been identified experimentally. Various theoretical studies on the electronic and vibrational properties of C20 and slender carbon nanotubes have suggested that C20 fragments are responsible for capping tubes with diameters between 4-5 angstrom. Additional studies into the properties of nanotubes suggest the development of miniaturized devices that interact with DNA. This idea prompts interest in the current problem.

Pi-pi interactions play a significant role in science and molecular engineering. By understanding how pi-pi interactions stabilize guest-host complexes, one can visualize the C20 fullerene in stacked orientation with nucleobases. The present study investigates the stacking of the four DNA bases, adenine, thymine, guanine, and cytosine on a pentagonal face of the icosahedral C20 fullerene.

Relaxed geometries of C20, adenine, thymine, guanine and cytosine were all obtained using the second order Moller Plesset theory. The fullerene-nucleobase complexes were then visualized and optimized using the MP2 method with a 6-31G(d) basis set. The energies of the individual compounds and the complexes will be presented in addition to interaction energies and NBO analysis.


78

Electronic Structure and Bonding of {Fe(PhNO2)}6 Complexes: A Density Functional Theory Study

Olexandr Isayev†, Leonid Gorb†, Igor Zilberberg‡, Jerzy Leszczynski†

†Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, MS 39217.

‡Boreskov Institute of Catalysis, Novosibirsk 630090, Russia.

Reduction of nitro-aromatic compounds (NACs) proceeds through intermediates with a partial electron transfer into the nitro group from reducing agent. To estimate an extent of such transfer and, therefore, an activity of various model ferrous-containing reductants toward NACs degradation the unrestricted density functional theory (DFT) in the basis of paired Löwdin-Amos-Hall orbitals has been applied to complexes of nitrobenzene (NB) and model Fe(II) hydroxides including cationic [FeOH]+, then neutral Fe(OH)2 and finally anionic [Fe(OH)3]–. Electron transfer is considered as a process of unpairing electrons (without the change of total spin projection Sz) that reveals itself in a substantial spin contamination of the unrestricted solution. The unrestricted orbitals are transformed into localized paired orbitals to determine orbital channels for particular electron-transfer state and the weights of idealized charge-transfer and covalent electron structures.

This approach allowed to gain an insight into the electronic structure and bonding of the {Fe(PhNO2)}6 unit (according to Enemark and Feltham notation) using model nitrobenzene complexes. The electronic structure of this unit can be expressed in terms of π-type covalent bonding [Fe+2(d6, S=2) – PhNO2(S=0)] or charge-transfer configuration [Fe+3(d5, S=5/2) – {PhNO2}– ((π*)1, S=1/2)].


79

The Calculation of Electrostatic Potentials and Forces Using a Modified De Wette–Nijboer Method

Harsh Jain and Elijah Johnson

Environmental Sciences Institute, Florida A & M University, Tallahassee, FL 32307

A new method is presented for finding the coulomb energy and forces of a lattice of charges. In this method, the lattice sum is replaced by a sum over a relatively small number of spherical harmonic function terms. The approach is based on the De Wette-Nijboer method. The technique is applied to a number of crystals. The method requires less computation than the Ewald summation method. This should make it particularly useful to those applications which require the finding of the coulomb energy or forces a large number of times such as in the molecular dynamics and Monte Carlo methods of classical statistical mechanics.


80

A Cluster Based Approach for Conformational Sampling of Solvated Biomolecules

Samuel Keasler, Ricky B Nellas, and Bin Chen

Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803

Important biomolecules, such as proteins, are characterized by very rugged free energy landscapes. This creates sampling problems both in molecular dynamics and monte carlo simulations. In addition, these conformations are very sensitive to the solvation environment of the molecule. A great deal of work has been directed towards calculating the conformational free energetics of solvated peptides with molecular simulations.

Recent experimental work on gas phase water clusters has given new insight into solvent effects at a molecular level. A novel technique developed by us, AVUS-HR (Chen et al., JPCA 2005, Vol. 109, 1137), has enabled the study of the activated long time-scale events (such as nucleation) with atomistic simulations. We have combined this method with a thermodynamic cycle, to develop a cluster based simulation method analogous to the experiments. This technique allows both the solvent effects and the conformational preference of the solute to be quantitatively investigated. It avoids many of the sampling problems that are often observed for proteins in solution. In addition, it provides microscopic information about which solvent molecules are most important in determining conformational preference. Such information can provide unique insights into how solvent affects peptide conformation, but is difficult to obtain through bulk phase methods due to statistical averaging.

As an initial test of this new simulation approach, we applied it to the study of the effective interaction between two ions as function of their separation as well as the number of water molecules added. In addition to examining the interactions between the ions as water is added, we were able to reproduce bulk phase data for sufficiently large water clusters. Recently, we have also applied this technique to alanine dipeptide, a common model for testing simulation methods targeted at biomolecules. These results demonstrate that we can use this technique to further our inquiry into solvation effects on the conformational changes of biopolymers in solution.


81

Ab Initio Free Energy of Vacancy Formation in Photocatalytic Titanium Dioxide

J. Brandon Keith, Hao Wang, and James P. Lewis

Department of Physics, West Virginia University, P.O. Box 6315, 209 Hodges Hall, Morgantown, WV 26506

In transition metal oxides, which play an important role in heterogeneous catalysis, photoelectrolysis, and biocompatibility, defects such as bulk and surface oxygen vacancies often dominate the electronic and chemical surface properties. Prototypical among such oxides is TiO2 which has a variety of defects--oxygen and titanium vacancies, aliovalent titantium interstitials and crystallographic shear planes. As an amphoteric semiconductor, TiO2 has a complex defect phase diagram containing an n-p transition varying with oxygen partial pressure p(O2) and temperature.

TiO2 is also widely used in industry. An important application, photocatalysis, occurs when the strong oxidative potential of the positive holes oxidizes water to create hydroxyl radicals. Because TiO2 can oxidize oxygen or organic materials directly, it is added to paints, cements, windows, tiles, and so on for its sterilizing, deodorizing, and anti-fouling properties, and is also used for hydrolysis.

One drawback is that UV light is required to activate catalysis due to its wide intrinsic bandgap. Various strategies to improve photo-absorption have been devised such as anion doping or chromophore attachment for multielectron injection. Recent precursor[1] and N-dopant[2] studies indicate, however, that manipulation of bulk oxygen vacancy concentration may be one of the most effective ways to increase photocatalytic activity in the visible due to an increase in color centers capable of absorbing at these wavelengths. To understand these defects better we utilize fast ab initio methods as a thermodynamic tool to probe bulk oxygen vacancy free energies of formation in the strongly reduced n-type regime. These calculations are then used to make predictions regarding its defect kinetics using a simple mass-action model.

To calculate the Helmholtz free energy of vacancy formation Ff we use nonequilibrium thermodynamic integration[3] (TI) which performs an MD run while continuously changing the system between (1) a perfect crystal and (2) a crystal with an oxygen vacancy and a lone oxygen. This nonphysical MD run between two physical states gives the irreversible work Wirr between them. The reversible work can be obtained by either integrating adiabatically or through a suitable average of forward and reverse nonequilibrium runs, Wrev = ½[Wirr(forward) – Wirr(backward)] = ΔF. This also is the free energy difference ΔF between the two systems. Nonequilibrium TI leads to simulation times orders of magnitude smaller than equilibrium TI.

In regards to our ab initio method, we have chosen Fireball, a DFT pseudopotential (LDA/GGA) approach using confined, slightly excited “fireball”orbitals. In addition, its self-consistent functional allows precalculation of all Hamiltonian integrals and a fast interpolation during runtime which significantly reduces cpu time. The procedure for determining Wrev has been implemented in Fireball using a novel client-server algorithm that creates a Fireball client for each subsystem. These subsystems communicate with a server to average their forces at every time step to achieve the composite Hamiltonian force. This requires a simple socket in the MD loop and can easily be implemented in any electronic structure code.


82

0 100 200 300 400 500T �K�

6

7

8

9

10

11

free

energy

of

vacancy

formation

Ff

�eV

�

We use a 3d64s24p0 basis for Ti and a 2s22p4 basis for O with Troullier Martins

pseudopotentials in Kleinman-Bylander form and LDA exchange correlation. LDA is somewhat preferable to GGA when dealing with vacancies since these act as internal surfaces where GGA has known problems. To calculate the vacancy formation free energy in the monovacancy dominating regime we use a 162-atom supercell, which gives a formation energy comparable to other theoretical results.[4] Combining ΔF with a reversible scaling calculation for reference state free energy differences, we find the vacancy formation free energy as a function of temperature shown in the accompanying figure. We observe a nonlinear decrease in Ff of 4.5 eV (from 10.8 eV to 6.3 eV) which is driven largely by entropic effects.

From this data we can implement a qualitative mass-action model for TiO2 defect kinetics based solely on oxygen vacancies which gives an enthalpy of formation of 10.9 eV. This is qualitatively inline with previous conductivity measurements[5] where the standard enthalpy of formation was estimated at 6.3 eV.

[1] I.N. Martyanov, S. Uma, S. Rodrigues, and K.J. Klabunde, Chem. Commun. p. 2476 (2004). [2] M. Batzill, E.H. Morales, and U. Diebold, Phys. Rev. Lett. 96, 026103 (2006). [3] C. Chipot and D.A. Pearlman, Mol. Sim. 28, 1 (2002). [4] T. Bredow and G. Pacchioni, Chem. Phys. Lett. 355, 417 (2002). [5] J. Son and I. Yu, Korean J. Ceram. 2, 131 (1996).


83

A Theoretical Study of n-BuLi/ Li-aminoalkoxide Compounds: Aggregation vs. Reactivity

Hassan K. Khartabil a, Manuel F. Ruiz López a, Yves Fort b and Philippe Grosb

aEquipe Chimie et Biochimie Théoriques, UMR CNRS-UHP No.7565, Université Henri Poincaré-Nancy1, BP239, 54506 Vandœuvre lès Nancy, France.

b Equipe Synthèse Organométallique et Réactivité, UMR CNRS-UHP No.7565, Université Henri Poincaré-Nancy1, BP 239, 54506 Vandœuvre lès Nancy, France.

The reaction of 2-chloropyridine with alkyllithium generally results in nucleophilic addition on the azomethine bond while exclusive directed ortho lithiation is obtained using lithium dialkylamides (especially LDA and LTMP). Lithium-containing unimetallic superbases combining a chelating amino group and an electron-rich alkoxide, exhibit a different behavior. In particular, lithium (S)-N-methyl-2-pyrrolidine methoxide (LiPM) has been shown to form a mixed complex with n-BuLi that allows regioselective lithiation of pyridine rings and subsequent asymmetric addition of the lithiated pyridine to aldehydes1,2.

In this work, the mechanism of the lithiation step is discussed by means of theoretical computations at the density functional (B3LYP/6-31G*) level. Several routes for the reaction of the superbase with the substrate have been investigated. The obtained results are compared with experimental data. This comparison suggests that the 2:2 mixed complex should be the actual reactive species in low polar solvent. This complex favors metallation in contrast to n-BuLi aggregates (either dimer or tetramer) which favors alkylation. We also show that mixed 1:1 complexes favor alkylation. Interaction of lithium aggregates with the pyridinic nitrogen atom is responsible for observed regioselectivity.

1P. Gros and Y. Fort, Eur.J.Org. Chem. 2002, 3375. 2Y. Fort, P. Gros and Alain L. Rodriguez, Tetrahedron: Asymmetry 2001, 12, 2631.


84

Ab Initio Prediction of Explosives Physicochemical Properties

Yana Kholod,1,2 Leonid Gorb,1,3 Mohammad Qasim,3 Herbert Fredrickson3 and Jerzy Leszczynski1

1Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi, 39217, USA

2Dnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine 3US Army ERDC, Vicksburg, Mississippi, 39180, USA

The recent environmental studies are mainly focused on determination and prediction of the fate of chemical contaminants in the soil, ground and underground water and atmosphere as well as pharmacokinetic behavior of toxicants in living organisms.

Therefore, key physicochemical properties of problem chemicals are of high importance to be determined for utilization of those contaminants under environmental conditions. For example, octanol/water partition coefficients (Kow) have been found to be related to water solubility, soil/sediment adsorption coefficients, and bioconcentration factors for aquatic life. Because of its increasing use in the estimation of these other properties, Kow is considered a required property in studies of new or problematic chemicals. Water solubility (aqueous solubility) is used to help determine the affinity of chemicals to the aquatic receptors. The other physicochemical parameters, vapor pressure and Henry’s law constants are used for understanding of contaminants behavior in gas–liquid systems. Such physical properties as ionization potential, electron affinity and heat of formation are helpful for development of the contaminant decomposition techniques. However, experimental determination of some of those parameters is complicated and expensive with current instrumental techniques. Therefore, such data, particularly on explosives, often is not available.

In the current work we examine different computational techniques to predict certain physicochemical properties which require no additional information besides the structural chemical formula of the contaminant being studied.

These approaches (mainly based on different versions of DFT approximation) have been used for prediction of physicochemical parameters of wide-used military explosives as TNT, TNB, HMX, RDX, CL-20, etc. which are used by environmental managers to estimate risk assessment. Among them are vapor pressure, Henry's law Constants, water solubility, octanol-water partition coefficients, gas-phase ionization potentials, gas-phase electron affinity and heats of formation. Based on the calculations of nitro-compounds with known physicochemical properties we expect our predictions are in close agreement to empirically measured values.


85

The Quantum Chemical Foundations for the CL-20 Photolysis Product Identification

Yana Kholod,1,2 Sergiy Okovytyy,1,2 Leonid Gorb,1,3 Mohammad Qasim,3 and Jerzy Leszczynski1

1Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi, 39217, USA

2Dnepropetrovsk National University, Dnepropetrovsk, 49050, Ukraine 3US Army ERDC, Vicksburg, Mississippi, 39180, USA

The novel explosive compound CL-20 as well as products of its chemical transformations is high toxic contaminant to various terrestrial and aquatic receptors. Therefore, the environmental fate of these compounds is the problem of high importance. Biodegradation and alkaline hydrolysis are normally used for reduction of environmental impacts of this contaminant. Recently the other useful technique for explosive contaminants utilization – photolytic decomposition – has been proposed. The energy of UV-light is used in photolysis to generate free radicals reacting with the target compound. Photolytic reactions commonly occur in the top levels of water bodies.

Irradiation with the light of maximum absorbance wavelength in the ultraviolet-visible (UV/Vis) spectrum (λMax = 236 nm for CL-20) provide maximum efficiency of decomposition. It has been shown CL-20 is completely transformed after irradiation at their respective wavelengths of maximum absorbance: the 236 nm peak of absorbance disappears. The product of photolytic reaction has a band of high molar absorptivity at 210 nm.

In our current work an ab initio computational approach has been used for identification of the CL-20 photolysis products. The structures of possible products have been optimized at the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d,p) level of theory. The influense of the solvent has been considered using the supermolecular model. Then the UV/Vis spectra of studied systems have been modeled with the TD-DFT approach.

N N

N N

NN

NO2O2N

NO2O2N

O2N NO2

N

N

NH

NHN

N N

NHN

N

NH2

NH2HN

N

NH2HN

N

HN

N

hν

CL-20

1H-imidazole1H-imidazol-5-amine1H-imidazole-4,5-diamine

1H-imidazo[4,5-b]pyrazine1,5-dihydrodiimidazo[4,5-b:4’5’e]pyrazine

Predicted spectra have been compared with the experimentally obtained UV/Vis spectrum of the CL-20 photodegradation product. We have found the predicted spectrum of 1H-imidazole appears to be identical to the experimental spectrum of CL-20 photolysis product. It has one sharp peak at 213 nm. The UV/Vis spectrum of the standard imidazole sample confirms this prediction.


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Computing Configurational Entropy from Molecular Dynamics Simulations Using ACCENT-MM

Benjamin J. Killian and Michael K. Gilson

Center for Advanced Research in Biotechnology University of Maryland Biotechnology Institute

9600 Gudelsky Dr. Rockville, MD, 20850

Methods for computing binding affinities of host/guest and protein/ligand systems are of increasing importance in the field of drug design. While experimental and computational methods are both increasingly capable of providing accurate energy changes upon binding, binding affinities assessed using energies tend to be over-estimated due to neglect of configurational entropy losses occurring with the binding process. It would be valuable to be able to directly compute configurational entropy changes from molecular dynamics (MD) simulations, rather than employing specialized computational methods. Earlier attempts to enumerate configurational entropy from MD simulations include such methods as the Quasi-Harmonic Approximation (QHA). Previous investigations have demonstrated that the QHA, while successful for molecular systems with a single, highly-occupied energy well, tends to over-estimate the configurational entropy contributions for systems with multiply occupied energy wells.

We present a new method for the computation of classical configurational entropy from molecular dynamics trajectories: the Algorithm for Computing Configurational ENTropies for Molecular Mechanics or ACCENT-MM. The ACCENT-MM method is based upon a perturbation expansion of the configurational entropy, where the contributions of the uncorrelated entropies for all internal degrees of freedom are summed and then corrected for correlation between pairs of degrees of freedom by including pair-wise mutual information terms. In several cases, three-fold perturbations are also included as needed. The method is theoretically capable of including higher order mutual information terms up through the full internal dimensionality of the molecular system, though this is impractical from a computational view-point and is believed to be unnecessary, as preliminary studies suggest that a majority of the configurational entropy can be accounted for with low-order expansion terms. For this study, the ACCENT-MM method has been employed to evaluate the classical configurational entropy of several small molecules in the gas phase using empirical force fields. We demonstrate very favorable comparison between ACCENT-MM results and those computed from MD simulations using other methods, as well as with free energy based methods such as Mining Minima v. 2. The ACCENT-MM methods shows promise as a tool for computing configurational entropy changes directly from molecular dynamics trajectories without the need for specialized computational methods. Finally, the proposed method should allow for the identification of those degrees of freedom, such as key torsion angles, that contribute most to entropy changes on binding.


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Theoretocal Conformational Studies on DFP to Probe the Role of Its Low-Energy Conformers on Biological Activity

Wojciech. Kolodziejczyk,a D. Majumdar,b Szczepan Roszaka and Jerzy Leszczynskib

aWroclaw University of Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland; bComputational Center for Molecular Structure and Interactions, Department of Chemistry,

Jackson State University 1400 J. R. Lynch Street, Jackson, MS 39217.

Conformational studies have been carried out on di-isopropyl phophorofluaridate (DFP) at the density functional and second order Møller-Plesset perturbation levels of theory to generate potential energy surfaces in the gas phase as well as in aqueous environment. Seven low energy conformers have been found. All these conformers have been found to be connected through rotational transition states with low energy barriers. The structures of the low energy conformers together with their molecular electrostatic potential surfaces have been compared with those of the simulated non-aged acetylcholinesterase-DFP complex to locate the biologically active conformer of this molecule.


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Resonance-Enhanced Two-Photon Ionization Technique: Computer Simulation

Dmytro Kosenkov,1 Leonid Gorb,1,2 and Jerzy Leszczynski1

1Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217

2Institute of Molecular Biology and Genetics, National Academy of Sciences Kiev, Ukraine 03143

3Institute for Scintillation Materials, National Academy of Sciences of Ukraine Kharkiv 61072, Ukraine

The resonance-enhanced two-photon ionization (R2PI) spectroscopy [1] is a powerful tool for study of biological molecules in gas phase. For example, the single nucleobases and molecular clusters of several nucleobases were extensively studied with this technique [2,3]. The R2PI spectroscopy is extremely sensitive to different molecular isomers e.g. different tautomeric forms of the nucleobases. However, the concentration of those different tautomeric forms could not be measured directly. A proposed computational model of the double-resonance spectroscopy technique allows to estimate relative concentrations of isomeric forms on each stage of the R2PI experiment. The results of application of this model to R2PI experiments with guanine and cytosine molecules and its tautomeric forms are presented currently.

The R2PI experiment includes several stages to be simulated: i) Desorption of the solid sample; ii) Spectral Hole Burning (SHB) technique that includes excitation of particular isomers to reveal its IR (or UV) spectrum; iii) Two-photon ionization of the molecules and registration of ionic signal in TOF mass spectrometer. Below are the set of equations that was used to simulate these experimental stages.

The relative concentrations of N different isomers in solid phase were described by the set of N equations:

∑∑≠≠

−=

)()( ill

ili

ijj

jjii knnk

dtdn

(1)

In Eq. (1) in - population of thi isomer. ijk - rate constant for transition between thi and thj isomers. The indexes i , j and l run over N The rate constants were calculated using Transitional State Theory. The desorption stage was simulated using Eq. (2):

ii

gasi nt

dn 1−= τ (2),

where gasin - population of isomer i in gas phase, iτ - time constant for desorption of thi isomer.

The spectrum is revealed using the SHB technique [1], which can be expressed as:

∑−=v

gasivi

gasi np

dtdn

(3),

where vip - probability of excitation of thv vibrational state of thi isomer. That leads to depletion

of ground state, index v runs over all vibrational states of the thi isomer.


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The final stage before detection is two-photon ionization. The ionization was simulated using Eqs. (4-5):

)(ωigasi

exci

exci fnr

dtdn

−= (4)

exci

ioni

ioni nr

dtdn

= (5),

where excin , ion

in - populations excited and ionized isomers, excir , ion

ir - rates of excitation and ionization.

Finally, recently revealed ultrafast non-radiative deactivation process in the R2PI experiment [4] could be taken into account in our model by including decay term )(ωif in the Eq. (4). This term depends on the frequency of excitation ω and the adiabatic excitation energies of the isomer.

The cross-sections of the processes of electronic excitation and ionization were calculated in approach of finite band width with Lorentz-Gauss spectral band shape. The equations (1-5) along with additional normalization conditions constitute the computational model of the R2PI experiment.

References 1. Nir, E.; Plutzer, Ch.; Kleinermanns, K.; de Vries, M. Eur. Phys. J. D , 20, 2002, 317 2. Nir, E.; Kleinermanns, K.; de Vries, M., Nature, 408, 2000, 949-951 3. Mons, M.; Dimicoli, I.; Piuzzi, F.; Tardivel, B.; Elhanine, M. J. Phys. Chem. A 2002, 106, 5088. 4. Chen, H. ; Li, S. J. Chem. Phys. 2006 ASAP-LIST


90

The Stable 1:1 and 1:2 Complexes of Pyridoxale-5'-phosphate Methylamine Shiff Base with Water: DFT Study of Structure and

Vibrational Spectra

G.M. Kuramshinaa, S.A. Sharapovab,D.A. Sharapovb, Yu.A. Pentina, H.Takahashic

aFaculty of Chemistry, bFaculty of Physics Moscow State University (M.V.Lomonosov), Moscow 119992, Russia

cDepartment of Chemistry, School of Science and Engineering Waseda University, Tokyo 160-8555, Japan

Earlier [1] we have investigated the IR and Raman spectra of pyridoxal-5’-phosphate methylamine Schiff base. The interpretation of experimental data was proposed on a base of ab initio and DFT quantum mechanical calculations of possible isomers. The conclusion was made that it is the enol-form (I) with skewed orientation of the phosphate group (Fig.1) is the most stable and preferred configuration from 30 possible ones of pyridoxal-5’-phosphate methylamine Schiff base in the gaseous form.

Figure 1. Optimized B3LYP/6-31+G** structure of the enol form of pyridoxale-5'-phosphate methylamine Shiff base (I) (bond lengths are in Å).

The essential biological importance of pyridoxal-5’-phosphate (PLP) itself and its

derivatives (Vitamin 6 analogs) is explained by the breakthrough role of these compounds in the biological processes where they act as coenzymes catalyzing different reactions involved in the metabolism of amino acids. So their behavior in the hydrated media performs the special interest and it induced us to carry out the DFT investigations of more complex PLP derivatives including complexes of pyridoxale-5'-phosphate methylamine Shiff base with water molecules. The special attention to the hydration is explained by the importance of the surrounding water influence on the biological functions of the B6 derivatives. To simulate theoretically the hydration effects we use the modeling of the solvated compound by a complexation of the more stable isomer I with water molecules.


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Figure 2. Optimized B3LYP/6-31+G** structures for 1:1 (I) and 1:2 (II) complexes (bond lengths are in Å).

The DFT calculations were performed with the program Gaussian 03 (Revision C.02)

package. The fully optimized geometries for different configurations of enol-I – water complexes were calculated with 6-31G*, 6-31+G* and 6-31+G** basis sets and the B3LYP functional. Here we present results on 1:1 (II) and 1:2 (II) systems (Fig. 2). Simulated IR spectra of I -III structures using the B3LYP/6-31+G** frequencies, theoretical IR intensities and a Lorentzian approximation are presented in Fig. 3.


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Figure 3. Theoretical B3LYP/6-31+G** spectra of pyridoxale-5’-phosphate methylamine (a) and its 1:1 (b) and 1:2 (c) complexes with water molecules. Imbedded in c is the part of experimental IR spectrum from [1].

The software package SPECTRUM [2] was used for transformation of quantum mechanical

Cartesian force constants to the matrix in redundant internal coordinates and for normal coordinate analysis and calculating potential energy distribution of I-III.

Results of calculations show that the hydration exerts influence both on structure and vibrational spectra of investigated systems. Thus, for example it is accompanied by the remarkable contraction of N5…H18 intramolecular H-bonding (1.696, 1.655, 1.642 Å for I-III, correspondingly) and by changing of some bond lengths and bond angles, e.g. by shortening valence O13-P14 bond (1.620, 1.608, 1.596 Å for I-III, correspondingly). Optimized bond


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lengths are shown in Figs 1-3. These effects are accompanied by very significant changes in some dihedral angles in II and III upon on hydration:

angle I II III

C4-C9-13-P14 107.6 172.5 79.4 C8-C4-C9-O13 7.4 3.4 17.0 C2-C1-C4-C9 1.0 0.4 3.4

All these factors influence on the theoretical IR spectra of II-III in comparison with IR

spectrum of I (Fig.3), first of all in the high frequency region where we observe the additional bands due to the OH-stretchings. But also very important changes are observed in the mid IR region and are mainly connected with the strong band intensities redistribution. One can see that the theoretical IR spectrum of 1:2 complex is rather well corresponding to the experimental IR spectrum of solid I. Further inclusion of more water molecules in the solvating surrounding should result in more adequate description of experimental data.

Acknowledgement

This work was supported by the Russian Foundation for Basic Researches (Grants 05-03-32135 and RFBR-OB’ 05-07-98001)

References

1. G.M.Kuramshina, H.Takahashi. J. Mol. Struct., vol. 735-736, pp. 39-51, 2005. 2. A.G. Yagola, I.V. Kochikov, G.M. Kuramshina, Yu.A. Pentin. Inverse Problems of

Vibrational Spectroscopy. VSP Scientific Publishers: Zeist, 1999.


94

A Comparison of Methods for Modeling Quantitative Structure–Activity Relationships. Acetylcholinesterase Inhibitors

V.E. Kuz’min, A.G.Artemenko, E.N. Muratov

A.V.Bogatsky Phys.-Chem. Institute of the National Academy of Sciences of Ukraine, 86 Lustdorfskaya doroga, Odessa 65080, Ukraine

The purpose of this work is the comparison of Hierarchic Technology of QSAR tasks solution on the base of Simplex Representation of Molecular Structure (SiRMS) method [1-3] with the most popular present-day QSAR approaches [4-8].

In the SiRMS method any molecule can be represented as the system of different simplexes (tetratomic fragments of fixed composition, structure, chirality and symmetry) (see figure 1). At the 2D level, the connectivity of atoms in simplex atom type and bond nature were considered. Atoms in simplex can be differentiated on the base of the different characteristics, especially: 1) nuclear charge; 2) partial atom charge [9] 3) lipophilicity[10]; 4) atomic refraction; 5) donor/acceptor of hydrogen in the potential H-bond; etc. For atom characteristics, which have real values (№ 2-4 in the list) at the preliminary stage, division of values range into definite discrete groups is carried out. The number of groups (G) is a tuning parameter and can be varied (as a rule G=3-7). For atom characteristic 5 the atoms has been parted on three groups: A – (acceptor of hydrogen in H-bond), D (donor of hydrogen in H-bond), I (indifferent atom). SiRMS for alanine presented on Figure 1.

Figure 1. Simplex representation of molecule of alanine.

The use of diverse variants of differentiation of simplex vertexes (atoms) represents the

principle feature of the offered approach. We consider that realized in many QSAR methods specification of atoms by its nature (for example, C, N, O) limits the possibilities of pharmacophore fragments selection. For example, if the –NH– group has been selected as the determining activity fragment (pharmacophore) and ability of H-bond formation is the factor determining its activity, then we shall miss such donors of H-bonds as, for example, OH-group, etc. The use of atoms differentiation by donor/acceptor of H-bond allows avoiding the situation


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illustrated above. Analogical examples one can make for other atom properties (lipophilicity, partial charge, refraction, etc).

At the 3D level, the stereochemistry of molecule is taken into account. It is possible to differentiate all the simplexes as right (R), left (L), symmetrical achiral (S), plane achiral (P) ones. Stereochemical configuration of simplexes is defined by modified Kahn-Ingold-Prelog rules. The SD at this level is the number of simplexes of fixed composition, topology, chirality and symmetry (Figure 3).

For 4D QSAR models each molecular structural parameter (MSP) is calculated by summing products of descriptor value for each conformer and probability of realization of the corresponding conformer [1].

The obtained results can be represented on the molecule using color-coding according to atoms’ contribution. Realization of molecular design of compounds of given activity level via the generation of the allowed combinations of simplexes, determining investigated property, is possible on the base of SiRMS.

Thus, the proposed approach does not have a problem in optimal alignment of the set of considered molecules which takes place in CoMFA analogues. The SiRMS approach is similar to HQSAR but has none of its restrictions (only topological representation of molecular structure) and lacks (ambiguity of descriptors formation when procedure of hashing of molecular holograms is realized). Besides, on the contrary to HQSAR, in SiRMS, different physical and chemical properties of atoms (charge, lipophilicity, etc.) can be taken into account.

The ability to angiotensin converting enzyme (ACE) inhibition (pIC50) has been investigated [11]. Training set consists of 76 compounds and 38 structures were used in a test set. It is necessary to note that all of explored compounds are structurally homogeneous, that facilitates the procedure of molecules superposition in lattice methods. We have compare in the given work the resulting partial least squares (PLS) models [12-14] built with the use of descriptors generated in the followings QSAR approaches:

а) CoMFA – Comparative Molecular Fields Analysis; b) CoMSIA – Comparative Molecular Similarity Indexes Analysis; c) EVA – Eigenvalue Analysis; d) HQSAR – Hologram QSAR; e) Cerius 2 program package – method of traditional integral (whole-molecule) 2D и 2.5D1 descriptors generation; f) SiRMS.

The advantage of the developed method over others has been revealed by the comparison of such statistical descriptions of QSAR models, as correlation coefficient for training (R2) and test (R2

test) sets; correlation coefficient, calculated in the cross-validation terms (Q2); as well as the standard errors of prediction for both sets. For example for SiRMS Q2= 0.75-0.94 and for the other methods Q2 = 0.66-0.72 (see Figure 2)

1 This classification is offered by the authors of Cerius 2.


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Figure 2. Statistical characteristics (R2,Q2, R2

test) of obtained models by different QSAR methods.

Besides, HT QSAR based on SiRMS allowing determining structural fragments with

positive or negative influence on investigated property, as well as the contribution of different physical-chemical factors in the activity changes.

This work is partially financial supported by Scientific and Technology Center in Ukraine (project 3147).

References 1. Kuz’min, V.E., Artemenko, A.G., Polischuk, P.G., Muratov, E.N., Hromov, A.I., Liahovskiy,

A.V., Andronati, S.A. and Makan, S.Yu. (2005) "Hierarchic system of QSAR models (1D-4D) on the base of simplex representation of molecular structure", J. Mol. Mod., 11, 11, 457–467

2. Kuz’min, V.E., Artemenko, A.G., Lozitska, R.N., Fedtchouk, A.S., Lozitsky, V.P., Muratov, E.N. and Mescheriakov, A.K. (2005) "Investigation of anticancer activity by means of 4d qsar based on simplex representation of molecular structure", SAR and QSAR in Env. Res., 16, 219-230.

3. Muratov E.N., Artemenko A.G., Kuz'min V.E., Lozitsky V.P., Fedchuk A.S., Lozitska R.N., Boschenko Y.A., Gridina T.L. (2005) "investigation of anti-influenza activity using hierarchic QSAR technology on the base of simplex representation of molecular structure", Antiviral Research. 65, A62-A63.

4. Cramer, R.D., Patterson, D.I. and Bunce, J.D. (1988) "Comparative molecular field analysis (CoMFA). 1. Effect of shape binding to carrier proteins", J. Am. Chem. Soc. 110, 5959-5967.

5. Doweyko, A.M. (1988) "The hypothetical active site lattice. An approach to modeling active sites from data on inhibitor molecules" J. Math. Chem. 31, 1396-1406

6. Klebe G., Abraham U., Mietzner T. (1994) "Molecular similarity indeces in comparative anaysis (CoMSiA) of molecules to correlate and predict their biological activity" J. Med. Chem. 37, 4130–4146.

7. Kuz'min, V.E., Artemenko, A.G., Kovdienko, N.A., Tetko, I.V. and Livingstone, D.J. (2000) "Lattice model for QSAR studies", J. Mol. Modeling 6, 517-526.


97

8. Seel, M., Turner, D.B. and Wilett, P. (1999) "HQSAR - a highly predictive QSAR Technique based on molecular holograms", QSAR 18, 245-252.

9. Kuz'min, V.E. and Beresteckaya E.L. (1983) "Atomic charges computation program by orbital electronegativities leveling method", Zh. Struct. Khim., 24, 187-188 (in Russian).

10. Wang, R., Fu, Y. and Lai L. (1997) "A new atom–additive method for calculating partition coefficients", J. Chem. Inf. Comput. Sci., 37, 615-621.

11. Sutherland J.J., O'Brien L.A., Weaver D.F. (2004) A Comparison of Methods for Modeling Quantitative Structure-Activity Relationships, J. Med. Chem., 47,5541-5554

12. Rannar, S., Lindgren, F., Geladi, P. and Wold, S. (1994) "A PLS kernel algorithm for data sets with many variables and fewer objects. Part 1: Theory and algorithm", J. Chemometrics 8, 111-125.

13. Hasegawa K., Miyashita Y., and Funatsu K. (1997) "GA strategy for variable selection in QSAR studies: GA-based PLS analysis of calcium channel antagonists", J.Chem. Inf. Comput. Sci. 37, 306-310.

14. Lindgren, F., Geladi, P., Rännar, S. and Wold, S. (1994) "Interactive Variable Selection (IVS) for PLS. Part 1: Theory and Algorithms", Journal of Chemometrics, 8, 349-363.


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The Hierarchical QSAR Technology for Effective Virtual Screening and Molecular Design of Potential Pharmaceutical Agents

V.E. Kuz’min, A.G.Artemenko, E.N. Muratov, L.N. Ognichenko, A.I. Hromov, A.V. Liahovskij, P.G. Polischuk

A.V.Bogatsky Phys.-Chem. Institute of the National Academy of Sciences of Ukraine, 86 Lustdorfskaya doroga, Odessa 65080, Ukraine.

The Hierarchical QSAR (Quantitative Structure Activity Relationship) technology (HT) is developed for optimization of new effective pharmaceutical agents creation process[1-3]. Due to the hierarchic strategy on each stage of this technology QSAR task is not solved ab ovo, but with the use of information received from a previous stage. In fact, it is proposed to deal with the system of permanently improved solutions. The original simplex representation of molecular structure (SiRMS) has been used in the developed technology. In the frames of SiRMS any molecule can be represented as the system of different simplexes (tetratomic fragments of fixed composition, structure, chirality and symmetry). Such representation allows unifying description of spatial structure of compounds with saving of complete stereochemical information. It enables to define molecular fragments increasing or decreasing biological activity of investigated compounds.

The principle feature of the offered strategy consists in multiple-aspect hierarchy that concerned to (Fig 1-2):

• models of molecular structure description (1D → 2D → 3D → 4D); • models of atoms description in molecular simplexes (descriptor → physical-chemical →

field); • structural descriptors (local → integral); • scales of activity estimation (binomial → nominal → ordinal → continual); • mathematical methods used for establishing of structure-activity relationship (pattern

recognition → rank correlation → multivariate regression → PLS); • final aims of QSAR task solution (prediction → interpretation → structure optimization →

molecular design). The set of the different QSAR models that are supplementing each other is the result of

application of HT. These models all together, in complex, solve the problems of virtual screening, evaluation of structural factors influence on activity, modification of known molecular structures and design of new high-performance potential pharmaceutical agents [3].

The novelty of the offered technology mainly related for two following aspects: • models of representation of molecular structure, that are providing universality, variety and

flexibility of description of compounds related to different structural types; • hierarchic system that depending on the concrete aims of research allows us to construct

optimal strategy of QSAR models generation, avoiding at the same time superfluous complication that doesn't results in the adequacy increase.


99

Figure 1. Hierarchic technology for QSAR investigation

Figure 2. Hierarchic system of molecular structure representation


100

The developed strategy does not have restrictions of such well-known and widely used approaches as CoMFA (Comparative Molecular Field Analysis) [4], CoMSiA [5], HASL [6], Lattice Model [7] and others. For example, mentioned methods operate with the only one conformer that is selected accidentally. Moreover, in these approaches the acceptable decisions of QSAR tasks are possible only for the structurally homogeneous set of molecules. The base of our technology – SiRMS approach is similar to HQSAR [8] but has none of its restrictions (only topological representation of molecular structure) and lacks (ambiguity of descriptors formation when procedure of hashing of molecular holograms is realized). Moreover, on the contrary to HQSAR, in SiRMS different physical and chemical properties of atoms (charge, lipophilicity, etc.) can be taken into account obviously.

The offered hierarchical QSAR technology is more effective, than single QSAR models that are used today because on the every stage of it we can determine the molecular structure features that are important for the studied activity, and exclude the rest. HT shows unambiguously the limits of expedient QSAR models complication. It allows not to waste superfluous resources for needless calculations.

The efficiency of the HT can was shown on the example of compounds that possessing antiviral activity. If in an initial (training) set there were only 12% of highly active compounds, after application of the HT 75% of new designed compounds turned out a perspective antiviral agents.

This work is partially financial supported by Scientific and Technology Center in Ukraine (project 3147).

References 1. Kuz’min, V.E., Artemenko, A.G., Polischuk, P.G., Muratov, E.N., Hromov, A.I.,

Liahovskiy, A.V., Andronati, S.A. and Makan, S.Yu. (2005) "Hierarchic system of QSAR models (1D-4D) on the base of simplex representation of molecular structure", J. Mol. Mod., 11, 11, 457–467

2. Kuz’min, V.E., Artemenko, A.G., Lozitska, R.N., Fedtchouk, A.S., Lozitsky, V.P., Muratov, E.N. and Mescheriakov, A.K. (2005) "Investigation of anticancer activity by means of 4d qsar based on simplex representation of molecular structure", SAR and QSAR in Env. Res., 16, 219-230.

3. Muratov E.N., Artemenko A.G., Kuz'min V.E., Lozitsky V.P., Fedchuk A.S., Lozitska R.N., Boschenko Y.A., Gridina T.L. (2005) "investigation of anti-influenza activity using hierarchic QSAR technology on the base of simplex representation of molecular structure", Antiviral Research. 65, A62-A63.

4. Cramer, R.D., Patterson, D.I. and Bunce, J.D. (1988) "Comparative molecular field analysis (CoMFA). 1. Effect of shape binding to carrier proteins", J. Am. Chem. Soc. 110, 5959-5967.

5. Klebe G., Abraham U., Mietzner T. (1994) "Molecular similarity indeces in comparative anaysis (CoMSiA) of molecules to correlate and predict their biological activity" J. Med. Chem. 37, 4130–4146.

6. Doweyko, A.M. (1988) "The hypothetical active site lattice. An approach to modeling active sites from data on inhibitor molecules" J. Math. Chem. 31, 1396-1406

7. Kuz'min, V.E., Artemenko, A.G., Kovdienko, N.A., Tetko, I.V. and Livingstone, D.J. (2000) "Lattice model for QSAR studies", J. Mol. Modeling 6, 517-526.

8. Seel, M., Turner, D.B. and Wilett, P. (1999) "HQSAR - a highly predictive QSAR Technique based on molecular holograms", QSAR 18, 245-252.


101

Interaction of Metal Porphyrins with Fullerene C60: A New Insight

Meng-Sheng Liao, John D. Watts, and Ming-Ju Huang

Department of Chemistry, Jackson State University, Jackson, MS 39217

The electronic structure and bonding in the non-covalent, supramolecular complexes of fullerene C60 with a series of first-row transition metal porphines MP (M = Fe, Co, Ni, Cu, Zn) have been re-examined with DFT methods. Several density functionals and two types of basis sets were employed in the calculations. Our calculated results are rather different from those obtained in a recent paper (J. Phys. Chem. A 2005, 109, 3704-3710). The ground state of C60⋅FeP is predicted to be high spin (S = 2); the low-spin (S = 0), closed-shell state is even higher in energy than the intermediate-spin (S = 1) state. With only one electron in the Co-dz2 orbital, the calculated Co−C60 distance is in fact rather short, about 0.1 Å longer than the Fe-C60 distance in high-spin C60⋅FeP. Double occupation of an M-dz2 orbital in MP prevents close association of any axial ligand, and so the Ni−C60, Cu−C60, and Zn−C60 distances are much longer than the Co−C60 one. The evaluated MP−C60 binding energy varies from 0.5 to 0.8 eV (i.e. 11.5 to 18.5 kcal/mol), depending on the identity of the metal. The effects of the C60 contact on the redox properties of MP were also examined.


102

Electronic Structure, Absorption Spectra, and Hyperpolarizabilities of Some Novel Push-Pull Zinc Porphyrins. A DFT/TDDFT Study

Meng-Sheng Liao, P. Bonifassi, J. D. Watts, M.-J. Huang, and J. Leszczynski

Department of Chemistry, Jackson State University, Jackson, MS 39217

Metal porphyrins (MPors) are among the most interesting compounds of all known natural dyes and pigments because of their great biological importance. As highly conjugated planar molecules with an extensive delocalized π-electron system, MPors also form an important class of organic non-linear optical (NLO) materials. Synthetic MPors are typically centro-symmetric and so they do not produce second-order polarizabilities. To obtain non-centrosymmetric porphyrin systems, different strategies have been developed. One of them involves ring substitution and the chemical versatility of porphyrins allows the introduction of many different substituent groups at peripheral positions. It has been suggested that asymmetrically peripherally substituted porphyrins with suitable donor and acceptor groups exhibit strong second-order NLO response. They can be considered as push-pull systems mediated by the highly conjugated porphyrin macrocycle as a bridging group.

Recently, Zhang et al. (J. Am. Chem. Soc. 2005, 127, 9710-9720) reported a series of zinc porphyrins that contain nitro-thiophenyl and nitro-oligothiophenyl electron–accepting moieties and (4-dialkylaminophenyl)ethynyl electron-donating groups. For these compounds, large and interesting first-order hyperpolarizabilities (β) were measured via hype-Rayleigh light-scattering (HRS) experiments; the β value varies substantially despite quite uniform ground-state absorptive signatures for a given porphyrin-to-thiophene linkage topology. These compounds may thus find utility for electrooptic applications at telecom-relevant wavelengths. The authors also measured the linear optical properties and demonstrated that the terminal oligothiophene substituents had large effects on the absorption spectra of the metal porphyrins.

In this work, we describe the results of density functional theory (DFT)/time-dependent DFT (TDDFT) calculations on several novel push-pull zinc porphyrins. They include zinc 5-(4-dimethylaminophenylethynyl)-15-(4′,4′,5′,5′-tetramethyl[1′,3′,2′]dioxaborolan-2′-yl)-10,20-bis(3,5-bis(3,3-dimethyl-1-butyloxy)phenyl)porphine (here denoted as ZnPor 1), zinc 5-(4-dimethylaminophenylethynyl)-15-[5-nitro-[2,2′]bithien-5′-yl)-10,20-bis(3,5-bis(3,3-dimethyl-1-butyloxy)phenyl)porphine(denoted as ZnPor 2), and zinc 5-[4′-dimethylaminophenyl-ethynyl]-15-[5-nitro-[2,2′]bithienyl-5′-ethynyl]-10,20-bis[3′,5′-bis(3′′,3′′-dimethyl-1′′-butyloxy)phenyl]porphine (denoted as ZnPor 3). ZnPor 1, the asymmetric porphyryl-boronate complex, is a valuable precursor for the fabrication of the other zinc porphyrins in which thiophene and oligothiophene units are linked to the macrocycle meso-position. The tetramethyl-dioxaborolan-2-yl moiety [−BO2C2(CH3)4] is electron-withdrawing in nature. ZnPor 2 and ZnPor 3 feature bithiophenyl unit terminated with a 5-nitro group. In ZnPor 2, the nitro-oligothiophenyl unit is linked directly to the macrocycle meso-carbon position, while ZnPor 2 uses an intervening meso-ethynyl moiety to modify porphyrin-to-thiophene conjugation.

Our calculations were performed to determine the electronic structure, absorption spectra, and hyperpolarizabilities of these zinc porphyrins. In addition, the effects of the substituents on the various properties of the molecules were investigated. The calculated results account for numerous changes in chemical and physical properties observed for these zinc porphyrin compounds.


103

N N

NNZn

OO

O O

N BO

O

N N

NNZn

OO

O O

NS S

NO2

N N

NNZn

OO

O O

NS S

NO2

(a) ZnPor 1

(b) ZnPor 2

(c) ZnPor 3


104

Extending the Hückel 4n+2 rule to Metallofullerenes: The Txample of M2@C84 (M=Sc, Y)

Dan Liu and Frank Hagelberg

Computational Center for Molecular Structure and Interactions, Department of Physics, Atmospheric Sciences and Geoscience,

Jackson State University, Jackson, MS, 39217

By investigating the species Sc2@C84 and Y2@C84, the Hückel 4n+2 rule, well established in organic chemistry, is extended to metallofullerenes. The 4n+2 rule is demonstrated to provide an explanatory or predictive tool for the stability and structure of metallofullerenes. This is exemplified by analyzing the units Sc2@C84 and Y2@C84 in spin triplet and singlet conditions. The Sc2 core turns out to be realized by two separated ions, while Y2 forms a bound subunit. These findings are in agreement with conclusions based on the 4n + 2 rule, assisted by Nucleus Independent Chemical Shift (NICS) calculations.


105

Self-Consistent Strictly Localized Bond Orbital within the Local Self-Consistent Field Method

Pierre-François Loos and Xavier Assfeld

Equipe de Chimie et Biochimie Théoriques UMR 7565 CNRS-UHP

Université Henri Poincaré – Nancy, France

When dealing with large molecular systems, one is often oblige to use hybrid methods combining Quantum Mechanics (QM) and Molecular Mechanics (MM) [1-2]. The macromolecule is divided in two parts. The part undergoing the more substantial modifications of the electronic structure, i.e. undergoing a chemical reaction, is treated with QM and the remaining of the atoms, hereafter collectively called the surroundings, is described by means of MM force fields since its effects on the QM subsystem are mainly steric (geometrical hindrance) and electrostatic (polarization of the electronic wave function).

Many methods exist and have been applied to various field of chemistry. They differ not only from the level of theory used to represent the QM fragment and/or form the utilized force field, but also from the type of interactions taken into account between the two moieties, since some methods neglect the polarization due to the electrostatic embedding. Aside these slight differences, QM/MM methods differ mainly by the way chosen to connect the two subsystems [3-8].

In this poster, we focus our interest on the Local Self-Consistent Field (LSCF) method[8-9] which represent the frontier bond, the one connecting the QM piece to the MM one, by means of a frozen Strictly Localized Bond Orbital (SLBO). Here frozen means that the expansion the SLBO over the basis functions is kept fixed during the wave function optimization. Of course, SLBOs are modified by rotation or normation due to geometrical changes. This implies that the QM part must have a significant size to minimize the effect of the SLBO on the total wave function. This is a critical issue when one is willing to perform Molecular Dynamics (MD) calculations. If the size of the QM part is reduced then the SLBOs must readjust themselves according to the density variations of the whole wave function.

We propose a modification of the LSCF method, called Optimized Local Self-Consistent Field (OLSCF), which allows the SLBO to relax by simple linear combination with their corresponding Strictly Localized Anti-Bonding Orbital (SLABO).

The details of the OLSCF theory and its implementation in our modified version of the Gaussian03 package [10] are given in the poster. Test calculations on simple systems are compared to full ab initio calculations. We show that polarization of the optimized SLBO is correctly handled (see the figure). The adaptation of the new method to the QM/MM framework is under progress.

[1] A. Warshell and M. Levitt. J. Mol. Biol. 103 (1976) 227. [2] M.J. Field, P.A. Bash, and M. Karplus. J. Comp. Chem. 11 (1990) 700. [3] S. Ranganathan, J.E. Gready, J. Phys. Chem. B 101 (1997) 5614. [4] Y. Zhang, T.-S. Lee, W. Yang, J. Chem. Phys. 110 (1999) 46. [5] I. Antes, W. Thiel, J. Phys. Chem. A 103 (1999) 9290. [6] G.A. DiLabio, M. M Hurley, P.A. Christiansen, J. Chem. Phys. 116 (2002) 9578. [7] J. Pu, J. Gao, D.G. Truhlar, J. Phys. Chem. A 108 (2004) 632. [8] X. Assfeld and J.-L Rivail. Chem. Phys. Lett., 263 (1996) 100.


106

[9] N. Ferré, X. Assfeld and J.L. Rivail, J. Comp. Chem. 23 (2002) 610. [10] M.J. Frisch et al. Gaussian 03, Revision B.05, Gaussian Inc., Wallingford, CT (2004).

Figure: Bond polarization of the trifluoroethane molecule.


107

Conventional Strain Energy in Boracycloproane, Diboracyclopropane, Boracyclobutane and Diboracyclobutane

Brandon Magers, Harley McAlexander, and David H. Magers


The conventional strain energies for boracyclopropane, diboracyclopropane, boracyclobutane, 1,2-diboracyclobutane, and 1,3-diboracyclobutane are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory (MP2), and density functional theory. The DFT functional employed is Becke’s three-parameter hybrid functional using the LYP correlation functional. Two basis sets, both of triple zeta quality on valence electrons, are employed: 6-311G (d,p) and 6-311+G(2df,2pd). Additionally, single-point fourth-order perturbation theory and coupled-clustered calculations using the larger of the two basis sets at the optimized MP2 geometries were used to investigate the effects of higher-order electron correlation. Results are compared to the conventional strain energies of cyclopropane and cyclobutane to determine what effect boron substitution has on the conventional strain energies of these prototypical homocycles. We gratefully acknowledge support from the Mississippi College Catalysts, the alumni support group of the Department of Chemistry & Biochemistry.


108

Conventional Strain Energy and Sigma Delocalization in Small Heterocycles of Carbon and Silicon

Harley McAlexander, Brandon Magers, Crystal B. Coghlan, and David H. Magers


The conventional strain energies for three- and four-membered heterocycles of carbon and silicon are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. These include silacyclopropane, disilacyclopropane, silacyclobutane, 1,2-disilacyclobutane, 1,3-disilacyclobutane, and trisilacyclobutane. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory (MP2), and density functional theory. The DFT functional employed is Becke’s three-parameter hybrid functional using the LYP correlation functional. Two basis sets, both of triple zeta quality on valence electrons, are employed: 6-311G (d,p) and 6-311+G(2df,2pd). Additionally, single-point fourth-order perturbation theory and coupled-clustered calculations using the larger of the two basis sets at the optimized MP2 geometries were used to investigate the effects of higher-order electron correlation. Cross-sections of the electron density in the plane of the ring for each of the three-membered rings were plotted to observe how the electron density is distributed in the sigma bonds of the different systems.

Results indicate that silicon substitution reduces the conventional strain energy of cyclobutane, but increases the conventional strain energy in cyclopropane by destroying the stabilizing factor of sigma delocalization. Electron-density plots show that only in cyclopropane is the electron density thoroughly delocalized in the sigma bonds of the ring. We gratefully acknowledge support from the Mississippi College Catalysts, the alumni support group of the Department of Chemistry & Biochemistry.


109

An ab Initio Molecular Dynamics Investigation of the Various Decarboxylation Mechanisms Involved in Fatty Acid Synthesis

Matthew McKenzie and Bin Chen

Department of Chemistry Louisiana State University, Baton Rouge, LA 70803

The transfer of carbon dioxide to the CoA substrate is a critical step in Fatty acid synthesis. By targeting this transfer, one can create anti-obesity drugs which will block the creation of new fat, or the bacterial route for anti-microbial agents. The mechanistic features of this enzymatic process have been extensively characterized; however, many chemical details of the carboxyl transfer process are still unresolved. There have been numerous suggested probable enzymatic mechanisms, in which all appear to be consistent with the mechanistic studies on model systems such as aliphatic carbamates and N-carboxy-2-imidazolidinone. Constrained Car-Parrinello molecular dynamics simulations were used to examine the free energy surface along the various suggested reaction pathways proposed for these model systems. These simulation studies have revealed important effects caused by the solvent and the protonation of the model carbamates on the detailed reaction mechanism. For example, the reaction barrier for the protonated N-carboxy-2-imidazolidinone was significantly lower than the anion form by more than 4 kcal/mol, which is equivalent to a three order magnitude increase on the first-order rate constant, comparable to the experimental report of a rate constant increase of 6000 times. The various models have shown important changes in the hydrogen bonding due to charge redistribution which plays a significant catalytic role in the decarboxylation mechanism. Another overlooked detail is the protonation of the carbamate nitrogen, a probable enzymatic decarboxylation pathway, will be presented.


110

The Role of Quantum Mechanics in Structure-Based Drug Design

Kenneth M. Merz, Jr.

Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435

University of Florida, Gainesville, Florida 32611-8435

Semiempirical quantum chemical (QM) methods have had tremendous impact on our understanding of chemical and biological systems. In this presentation we will focus on the application of semiempirical QM methods to solve relevant problems in structure-based drug design (SBDD). For example, we will describe a selection of recent application of these methods to the scoring of protein-ligand poses, NMR spectroscopy, X-ray spectroscopy and pairwise energy decomposition of protein-ligand complexes. Finally, we will briefly summarize our vision of the future application of quantum chemistry to SBDD.


111

ONIOM and PCM Computational Study of the Hydration of α-L-Fucopyranose

S. Moussi, O. Ouamerali

Laboratoire de Physico-Chimie Théorique et Chimie Informatique. Faculté de Chimie, USTHB, BP 32, ElAlia 16111 BabEzzouar, Algiers, Algeria

Carbohydrates play a crucial role in biological components, such as protein and membrane, in the aqueous, frozen, and dehydrated states. It is considered as effective stabilizers. In this contest, it is also clear that water have a great importance in determining the physical and chemical stability of protein in liquid and solid formulation. Because of those importances, a considerable experimental and theoretical works have been done to study structure in carbohydrate-water system.

Our investigation is to study the hydration effects of α-L-fucopyranose using different shames of ONIOM method to analyse the behaviour of the water molecules surrounding this carbohydrates and their preferential position. For this, we use tow layered ONIOM2 calculation schemes with (MP2, B3LYP, RHF, PM3, DREIDING and UFF) according to 6-31G* bases set. We compare the resulting geometrical parameters, energy stabilisations and dipolar moment to those obtained by different PCM calculation in MP2 and B3LYP level with 6-31G* bases set.

The calculations where performed with GAUSSIAN 03 software.


112

Coordination and Hydrogen Bonding in [M(H2O)n]+ (n=1,2,3,4,5,6), M=Li, Na, K Species

Jamshid Najafpour a, Gholam Hossein Shafiee b, Abdolreza Sadjadi b, Shant Shahbazianc , Ng Seik Weng d

a) Department of Textile Chemistry, Faculty of Engineering, Islamic Azad University Shahr-e-Rey Branch, Tehran, P.O. Box: 18735/334 IRAN

b) Department of Chemistry, Islamic Azad University of Kazeroon, Kazeroon, Fars, P.O. Box: 73135-168 IRAN

c) Department of Chemistry, Faculty of science, Shahid Beheshti University, Tehran, IRAN d) Department of Chemistry, University of Malaya, 50603, Kuala Lumpur, Malaysia

In spite of the large number of ab initio calculations on hydrated species of group IA cations with various sophisticated theoretical methods, there yet remain unsolved problems such as the assignment of cation’s coordination number 1. Through our investigation to answer this question in the light of QTAIM 2, surprisingly we have found that the existence of hydrogen bonds in these species are in contrary to what have been deduced before 3. In this regard, both RHF/6-31+G(d,p) and MP2(FC)/6-31+G(d,p) models chemistries were employed to gain the electron densities at equilibrium geometries. Ab initio calculations were done using GAUSSIAN98 package. The molecular graphs of three [M(H2O)6]+ clusters where M = Li, Na, K (from left to right) have been depicted below using AIM2000 software for comparison. It is apparent from them that no H-bonds exist in [Li(H2O)6]+. Also, both HF and MP2 methods have predicted the same result for these ion molecules. In attention to our previous work on [Li(H2O)n]+, n=1,2,3 4 and some BnCn species 5, the concept of coordination has been proposed in the framework of QTAIM:

Natural definition of coordination number of a certain atom in a molecule is the number of atoms, which are connected (in a stable topological network) by one or more bond paths to this atom.

1. H. M. Lee, P. Tarakeshwar, J. Park, M. R. Kołaski, Y. J. Yoon, H. Yi, W. Y. Kim, and K. S.

Kim, J. Phys. Chem. A 2004, 108, 2949 (See also the references therein). 2. R. F. W. Bader, Chem. Rev. 1991, 91, 893. 3. E. D. Glendening, and D. Feller, J. Phys. Chem. 1995, 99, 3060. 4. J. Najafpour, A. Sadjadi, Conference on Current Trends in Computational Chemistry, 2005,

114. 5. A. Sadjadi, C. Foroutan, G. H. Shafiee, Sh. Shahbazian, Can. J. Chem. (Accepted for

Publication, Feb 2006).


113

A Coupled–Cluster Study of Isomers of the SO2Cl Radical and SO2Cl– Anion

Brian Napolion and John D. Watts

Department of Chemistry, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson State University, Jackson, MS 39217, United States

There has recently been renewed interest in the high temperature chemistry of sulfur in the atmosphere. The interaction between atmospheric sulfur and halogen containing species is expected to increase due to the rising anthropogenic injection of hydrofluorocarbons (HFCs) such as HFC-125 (CF3CHF2) and HFC 134a (CF3CH2F), which are used as chlorofluorocarbon (CFC) substitutes as a result of the implementation of the Montreal Protocol and its amendments. Although both SO2Cl and its geometric isomers are likely to be formed in the atmosphere, experimental studies on these species have been limited. These studies primarily have been restricted to SO2Cl (thionyl chloride), which is the only isomer to be identified with infrared absorption spectra in an argon/krypton gas isolation matrix from the reaction of Cl2 and SO2. Other isomers of SO2Cl, which include, OSOCl, and ClSOO have only been studied theoretically with HF, DFT, and MP2 methods, and have not been definitely identified experimentally. We have extended prior theoretical work on these isomers using the CCSD(T) method, which is the first time this method has been used to study these species. Geometries, relative energies, vibrational frequencies, heats and free energies of formation, bond dissociation energies and electron affinities have been calculated for isomers of SO2Cl using the CCSD(T) method and the 6-31+G(d), 6-31+G(2d), 6-311+G(d), and aug-cc-pVDZ basis sets. Possible transition states that connect the reactants with intermediates and products of the SO2 + Cl → SO2Cl reaction were found using the Intrinsic Reaction Coordinate routine and optimized using the CCSD(T) method and the 6-31+G(d) basis set.


114

Metalation of DNA Bases

Adria Neely, Glake Hill

Jackson State University, 1400 J.R.Lynch St., Jackson, MS 39217, USA

Metalation is the process by which a metal atom is introduced into an organic molecule to form an organometallic compound, causing a hydrogen-metal exchange. In our current study, the electrical conductivity of adenine, cytosine, guanine, thymine, and uracil are investigated under both non-metalated and metalated conditions. The optimized geometry of each DNA base was determined using the density functional B3LYP method at a starting basis set of 6-31G*. After determining these geometrically optimized structures the most probable site of metalation was determined for each structure. It is at this site of metalation that we attempt to study the properties of DNA-metal complex. Metalation of each DNA base was also computed using the density functional B3LYP method with a larger basis set of 6-311++G** for greater accuracy. The results will be discussed.


115

Application of Basis Set 6-31G** to Quantum-Chemical Calculations of Conjugated Organic Molecules

Sergey E. Nefediev

Kazan State Technological University, Karl Marx str., 68, Kazan, Russia.

Electrooptic polymer electrets is one of the most promised classes of materials for the waveguide optoelectronics. Electrooptic polymeric structures are built from the polar nonlinear optic (NLO) chromophores, incorporated in polymeric matrix and oriented under permanent electric field.

Typical NLO chromophore is represented by conjugated polyatomic group, containing π-acceptor and π-donor substituents, separated by extensive π-electronic bridge.

Precise quantum-chemical calculation of nonlinear optical properties is the rather hard problem. It is known [1], such calculations required application basis sets very large dimension. Using of such basis sets for practical quantum-chemical investigations organic molecules is inexpedient for economic reasons. In our earlier work [2-3], we have constructed the medium-size basis set [4s3p2d] allowed to calculate the first hyperpolarizability of conjugated organic molecules, containing 20-30 second-row atoms with accuracy 10-15% in comparison with calculations carried out in ANO basis sets [4-5] huge size.

However elaborated basis set can not allow to realize the serial calculations extended polyenes structures with long length of conjugation. The purpose of this report is the proof of the applicability traditional Pople basis set 6-31G** for the serial calculations of polyene molecules.

As the objects of investigation were chosen the next structures:

The results of the calculations are presented in the tables and the diagram

Table I. Values of longitudinal hyperpolarizability for the series I, calculated HF/[4s3p2d/3s]//TDHF and HF/6-31G**//TDHF methods with different length of polyene bridge.

Vnm

zzz

4210−⋅β

n = 0

n = 1

n = 2

n = 3

n = 4

n = 5

n = 6

n = 7

6-31G** 0.33 0.85 1.62 2.57 3.68 4.70 5.65 6.50

[4s3p2d/3s]

0.33 0.86 1.64 2.61 3.74 4.78 5.74 6.60

NH2 COn

I H

N

N

CN

CN

H

n

II


116

Table II. Values of longitudinal hyperpolarizability for the series II, calculated HF/[4s3p2d/3s]//TDHF and HF/6-31G**//TDHF methods with different length of polyene bridge.

Vnm

zzz

4210−⋅β

n = 0

n = 1

n = 2

n = 3

n = 4

n = 5

n = 6

n = 7

6-31G**

-0.07

0.85

3.60

7.84

12.12

15.34

17.64

19.10

[4s3p2d/3s]

-0.11

0.82

3.60

7.84

12.04

15.21

17.49

18.95

n0 2 4 6 8

β zzz

(10-2

nm

4 /V)

0

5

10

15

20

25

seriesI / 6-31G**series I / [4s3p2d/3s]series II / 6-31G**series II / [4s3p2d/3s]

This investigation show that basis set 6-31G** with increasing of conjugated length

satisfactory reproduce results of hyperpolarizability, obtained in thу basis set [4s3p2d]. It must be noted that accuracy of reproduction is no more 1 % for the length of polyene bridge n≥3. This results allowed us to apply the 6-31G** for the serial calculations of polyene molecules in future.

This work is supported by Research and Education Center (REC). References 1. G. Maroulis, J. Chem. Phys. 118, 2673 (2003). 2. M.B. Zuev, S.E. Nefediev, J. Comp. Meth. Sci. Eng. 4, 481 (2004). 3. M.B. Zuev, M.Yu. Balakina, S.E. Nefediev, J. Comp. Meth. Sci. Eng. 4, 493 (2004). 4. M. Stahelin, C.R. Moylan, D.M. Burland, A.Willetts, J.E. Rice, D.P. Shelton, E.A. Donley,

J. Chem. Phys. 98, 5595 (1993). 5. J.E. Rice, R.D. Amos, S.M. Colwell, N.C. Handy, J. Sanz, J. Chem. Phys. 93, 8828 (1990).


117

Probing the Vapor – Liquid Nucleation Mechanisms of Multicomponent Mixtures Using Atomistic Simulations

Ricky B Nellas and Bin Chen

Department of Chemistry Louisiana State University, Baton Rouge, LA 70802

For over a century, nucleation for all multi-component systems was thought simplistically as a process that advances through the formation of critical clusters with well-defined composition. With our current success in probing unary and binary vapor-liquid nucleation and in our ambition to go hand in hand with experimentalists, we extended the applicability of the AVUS-HR approach to a more challenging yet practical exploration, multicomponent nucleating systems. This poster will expose intriguing nucleation mechanisms that would challenge the aforementioned notion. Using the simple TraPPE-UA (transferable potential for phase equilibria – united atom) force field and the AVUS-HR approach (a combination of aggregation-volume-bias Monte Carlo, umbrella sampling, and histogram reweighting), the homogeneous vapor-liquid nucleation of various mixtures were investigated. From the nucleation free energy profiles (NFEs), water/ethanol system shows a single-pathway or a mutual nucleation type of mechanism. On the other hand, the water/n-nonane system exhibits a two-pathway or a reluctant co-nucleation mechanism. Most remarkable is the mechanism demonstrated by the n-nonane/1-alcohol systems, wherein, a subtle evolution from a two-pathway to a normal single pathway is evident. These nucleation free energy maps were shown to be in direct agreement with the non-ideal behavior observed experimentally. Furthermore, an in-depth scrutiny on the critical nuclei provides further proof on the existence of the above mechanisms. Interestingly within the critical nuclei is a fascinating microscopic in-homogeneity (a direct contradiction to the “well-defined composition” assumption) that resulted from aggregation thru hydrogen bonding. For the water/n-nonane/1-butanol mixture, non-ideality was also observed based on the experimentally confirmed onset activities and molecular content of critical nuclei. Although, it was speculated experimentally that the critical clusters undergo phase separation, our result showed otherwise, namely, these components do come together under certain conditions and form a mixed nuclei.


118

Nonadiabatic, Time-Dependent, Direct Dynamics of Molecular Reactive Processes

Yngve Öhrn

Quantum Theory Project, University of Florida, Gainesville, FL, 32611

Theoretical treatment of reactive molecular encounters at energies ranging from thermal to several keV is a challenging proposition. One should, in principle be able to proceed without first determining adiabatic potential energy surfaces and also to account for non-adiabatic coupling terms. Electron Nuclear Dynamics (END) is such a theoretical approach that has with some success been applied to a variety of ion-molecule and other reactions. Recent applications of this explicitly time-dependent approach have dealt with the fragmentation of polyatomic molecules subjected to collisions with energetic protons and alpha particles. Comparisons with experimental cross sections for fragmentation and charge transfer have shown that the theory at its simplest level can provide useful information.

This work was supported by NSF grant 0513386.


119

Theoretical Study of the Adsorption of Dimethyl Methylphosphonate on Calcium Oxide

Y. Paukku, A. Michalkova, and J. Leszczynski

Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS

Dimethylmethylphosphonate (CH3PO(OCH3)2) is the most commonly used stimulant molecule for toxic nerve agents such as sarin in the development, testing or calibration of detectors. Dimethylmethylphosphonate is not classified as toxic, but is harmful if inhaled, swallowed or absorbed through the skin. It is a suspected carcinogen. It is well known that the adsorption process of organic compounds from the gas phase to the solid mineral surface influences the transport and degradation of organic compounds in the environment. Metal oxide nanoparticles have been considered as solid reagents that adsorb and simultaneously destroy toxic substances. The capacities of these destructive absorbents are high, and generally the toxic substance is decomposed and converted to an innocuous metal salt. These materials have a large surface/volume ratio with, presumably, enhanced surface absorption or intercalation. Metal oxides such as CaO and MgO are well-known adsorbents which are used for the destruction of phosphorus compounds.

The study is devoted to the investigation of the adsorption and decomposition of dimethylmethylphosphonate on calcium oxide. We have designed three types of models to simulate the calcium oxide surface. Non-hydroxylated Ca4O4 (model A, Figure 1), completely hydroxylated Ca4O4(OH)2H2 (two hydroxyl groups and two hydrogen atoms are added to the surface, model B) and partially hydroxylated (a hydroxyl group and a hydrogen atom are added to the surface Ca and oxygen atoms respectively, model C).

A B C

Figure 1. Models simulating the calcium oxide surface.

The adsorption of DMMP on the small representative cluster models of calcium oxide is

investigated at the B3LYP/6-31G(d) and MP2/6-31G(d) levels of theory. The geometry of DMMP is fully optimized while the geometry of the oxide fragment is kept frozen. The structure, interactions and interaction energy (corrected by the basis set superposition error) of the adsorption systems have been investigated.


120

Figure2. The optimized structure of DMMP adsorbed on a partially hydroxylated fragment of calcium oxide (front and a top views are shown).

The optimized structure of DMMP adsorbed on a small partially hydroxylated fragment of calcium oxide is presented in Figure 2. DMMP was found to be physisorbed on the CaO surface. There are only weak intermolecular interactions (hydrogen bonds and ion-dipole interactions) formed between the DMMP molecule and the non-hydroxylated, partially and completely hydroxylated CaO fragments. The analysis of the geometrical parameters and atomic charges of adsorbed and isolated DMMP shows that the adsorption changes the structure and causes the polarization of the target molecule.


121

Conformational Isomerism in N-Triphenylmethylformamide

Diwakar M. Pawar,a Dalephine Cain-Davis,a Frank R. Fronczek,b and Eric A. Noea

aDepartment of Chemistry, Jackson State University, Jackson, MS 39217, bDepartment of Chemistry, Louisiana State University, Baton Rouge, LA 70803.

The conformational equilibrium in N-triphenylmethyl formamide (1) was investigated by solution phase 1H and 13C NMR spectroscopy, X-ray crystallography, and computational methods. The 1H NMR spectrum of 1% solution of 1 in 50:50 CH2Cl2, CD2Cl2 showed two doublets, corresponding to the E and Z conformations, and the assignments were made based on the coupling constants. The populations of the E and Z isomers at ambient temperature were 62.6% and 37.4%, respectively. The X-ray diffraction study shows the colorless crystals of 1 occur in monoclinic system, space group P21/c and the acyclic secondary amide exists as E conformation in the solid state. The compound exists as a cyclic hydrogen bonded dimer in the solid state. At the HF/6-311G* level the E-isomer is lower in free-energy by 2.02 kcal/mol at 25 oC and the dipole moments for the E and Z isomers were 4.57 and 3.73 D at this level.

This work was supported by NIH-SCORE (Grant No. S06GM0084047).

H

O

CC

N

H

H

O

C

C

N

H

E Z


122

Conformations of Cyclopentadecane and Related Compounds: A Study by Computational Methods, Dynamic NMR Spectroscopy and

X-ray Crystallography

Diwakar M. Pawar,b Frank Fronczek a and Eric A. Noeb

aDepartment of Chemistry, Louisiana State University, Baton Rouge, LA 70803. bDepartment of Chemistry, Jackson State University, 1400 J. R. Lynch Street, Jackson, MS

39217 - 0510

Crystal structure of cyclopentadecanone 2, 4-di-nitrophenylhydrazone (1) was studied by X-ray crystallography, and the structure found is shown below.

The low-temperature 13C NMR spectra of a 2% solution of the parent compound,

cyclopentadecane (2) in propane showed the presence of at least ten peaks. Conformational space was searched by the MM4 force field, and calculations were performed for low energy conformations by ab initio methods. The free energies calculated at the HF/6-311G(d,p) level indicate the highly symmetrical quinquangular D5d [33333] conformation

to be the lowest in free energy at -150 oC. This conformation could show a maximum of 2 13C peaks, in a ratio of 2:1, so it cannot be the major conformation, but could be present in solution. Calculations for twelve conformations will be discussed. This work was supported by NSF-CREST (Grant No. HRD-9805465).


123

Conformational Analysis of trans-Cyclodecene Using Calculated (GIAO) Chemical Shifts

Diwakar M. Pawar and Eric A. Noe

Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, Jackson, MS 39217 - 0510.

Recently, we have shown that complex 13C NMR spectra, originating from two or more conformations, can be successfully assigned to specific conformation(s) based in part on the calculated chemical shifts.1 In this work, the isotropic magnetic shielding tensors (GIAO) relative to reference, tetramethylsilane, were obtained for six low-energy conformations of trans-cyclodecene (1) at the HF/6-311+G(d,p) level, and results were compared with previously-obtained slow exchange NMR spectra.2 A total of eight peaks were observed2 for the olefinic carbons of 1, corresponding to a total of five conformations (3 of C1 symmetry and 2 of C2 symmetry). Further calculations are in progress.

This work was supported by NSF-CREST (Grant No. HRD-9805465).

References: 1. D. M. Pawar, J. Brown II, K.-H. Chen, N. L. Allinger, and E. A. Noe, J. Org. Chem. 2006,

71, 6512. 2. D. M. Pawar and E. A. Noe, J. Am. Chem. Soc. 1996, 118, 12821.


124

Ab Initio Study of the Epoxyendic Imide Alkaline Hydrolysis in Gas Phase and Solution

T.Petrova, a,b S.Okovytyy, a,b L. Gorb, a J.Leszczynski a

aDepartment of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910,

Jackson, MS 39217-0510, USA bDepartment of Organic Chemistry, Dnepropetrovsk National University

Dnepropetrovsk 49625, Ukraine

One of the important problems of theoretical organic chemistry is investigation of regio- and chemo-selectivity of processes. The alkaline hydrolysis of epoxyendic imide (I) results in formation of carboxylactone (II).

O

N

O

O

CH3

OH

O

O

OOHOH2

OH

(I) (II)

-

In the present work a quantum-chemical investigation of the potential energy surface for the

alkaline hydrolysis of epoxyendic imide (I) has been carried out. The calculations have been performed at the B3LYP/6-31+G(d) level of theory in the gas phase and in the presence of water as solvent (polarizable continuum model).

O

N

O

OCH3

OH

O

N

O

O

CH3

OH

O

NH

O

O CH3

OO

NH

O

OCH3

O

O

N

O

O

CH3

OH

O

N

O

O CH3

OH

O

N

O

OCH3

OH

O

N

O

O CH3

OH

-

pathway1

pathway2

=

=

=

(I)

=

=

pathway1a

pathway1b


125

The research examines two possible pathways (pathway1 and pathway2). The first one assumes breaking of C-N bond of imide without proton transfer. The pathway2 involves N-protonation, followed by addition of a hydroxyl ion, and C-N bond cleavage. Two possible directions of lactonization in pathway1 (pathway1a and pathway1b) were also considered.

Our predictions reveal that in the case of both pathways the second stage of reaction is rate-determining. Calculations predict that activation barrier for the rate-determining stage of the pathway2 is higher than one for the pathway1. We can conclude that reaction of cyclization proceeds with consequent hydrolysis of the imide bond.


126

Basis Set and Electron Correlation Effects on Lithium Carbenoid Dimerization Energies

Lawrence M. Pratt1, Diêp Hương Trần Phan2, Phuong Thảo Thi Trần2, Ngân Văn Nguỹên2

1. Dept. of Chemistry, Fisk University, 1000 17th Ave. N., Nashville, TN 37209 2. University of Pedagogy, 280 An Dương Vương, District 5, Hồ Chí Minh City, Vietnam

A systematic investigation was performed to determine which levels of theory are required to obtain accurate geometries and dimeriation energies for lithium carbenoids. Dimerization free energies of six lithium carbenoids were calculated in the gas phase at the B3LYP and MP2 levels with several different basis sets, and at the CCSD(T) level with the aug-cc-pvdz basis set. This paper seeks to answer several questions with regard to basis sets and electron correlation methods. First, what level of theory is necessary to obtain good geometries for single point energy calculations at higher levels of theory? Will DFT do the job, or are more expensive MP2 optimizations required? Secondly, what level is required to obtain accurate dimerization energies? The final issue is the calculation of thermodynamic corrections to the free energy, obtained by frequency calculations. At high levels of theory those can be prohibitively expensive, particularly for large molecules. Can satisfactory thermal corrections be obtained at lower levels of theory, and added to electronic-nuclear repulsion energies calculated at higher levels?

Computational methods

All geometry optimizations and frequency calculations were performed with the Gaussian 98 or Gaussian 03 programs. The calculated thermal corrections to the free energies were unscaled. DFT calculations were performed with the B3LYP hybrid functional. Geometry optimizations and frequency calculations were performed with the MIDIX, 6-31G(d), 6-31+G(d), 6-31+G(d,p), 6-31++G(d,p), and 6-311++G(d,p) basis sets. Single point energies were calculated with the 6-311++G(df,pd), 6-311++G(2df,2pd), and 6-311++G(3df,3pd) basis sets, and the free energies were estimated using the thermal corrections calculated with the 6-311++G(d,p) basis set. MP2 single point energies, geometry optimizations and frequency calculations were performed with the same basis sets. In addition, MP2 optimizations and frequencies were calculated with the aug-cc-pvdz and aug-cc-pvtz basis sets, and CCSD(T) single point energies were calculated with the aug-cc-pvdz basis set at the MP2/aug-cc-pvdz geometry.


127

Li

X

HH

LiX

XLi

H

HH

H

XLi

X

CH2Li

H2C

H

HLi

X

LiX

XLi

H2C

CH2Planar

X Li XLi

CH2

H2C

LiLi

X XCH2

H2C XLi

X

LiCH2H2C

1 2 3

4 5 6

7 8

Results

Six lithium carbenoids were chosen for this study. Fluoro-, chloro- and bromomethyllithium were chosen as the simplest lithium carbenoids. In addition to the monomer, (1) we previously reported a planar dimeric structure (2), and since then a second dimeric structure (3) was found during a computational study of carbenoid reaction mechanisms. The remaining three were 1-halovinyllithiums. These were of interest because preliminary work on the FBW rearrangement of those compounds suggested that the potential energy surface may be relatively flat. In addition to the monomer (4), a previous DFT study found that the dimers optimized to a nearly, but not quite planar structure. Therefore, for the dimer, planar (5), chair (6), and twist-boat (7) geometries, and an unsymmetrical dimer (8) were used as starting structures for the geometry optimizations.

Basis set effects on optimized geometries

The optimized bond lengths with the 6-311++G(d,p) basis set were nearly identical to those obtained with the 6-31+(d) basis set for both the MP2 and B3LYP methods. Therefore, single point energies using more polarization and diffuse functions on 6-31+G(d) geometries should be nearly as good as the energies obtained by full geometry optimization with the larger basis sets, at a fraction of the cost in computer time. With each basis set except the MIDIX the bond lengths were within about 0.04 Å of each other, and the largest changes in bond lengths occurred upon going from a double zeta to a triple zeta basis set.

Overall, the basis set effects on 1-halovinyllithium carbenoid structures were similar to those on the halomethyllithium structures, with remarkable similarity between the 6-31+G(d) and 6-31++G(d,p) optimized geometries. Significantly different structures were obtained using the MIDIX basis set. Perhaps the most alarming fact is that the widely used B3LYP method incorrectly predicted the planar dimeric structure to be a local minimum, and its failure to find a chair conformation for CH2=CLiF.


128

Basis set and correlation effects on dimerization energies

For fluoromethyllithium, the dimerization energies calculated with the B3LYP hybrid DFT method are within a few kcal/mol of those obtained by MP2 with the same basis sets. Larger differences between B3LYP and MP2 energies were found with chloro- and bromomethyllithium. Addition of extra polarization and diffuse functions to the 6-31+G(d) basis set had a minimal effect on the calculated dimerization energies, but larger basis sets affected the dimerization energies by several kcal/mol, particularly for the chloro- and bromomethyllithium carbenoids.

The 1-halovinyllithium carbenoids were much more sensitive to the level of theory, with the B3LYP method incorrectly predicting the planar dimer to be the most stable conformation. The G3 and G3MP2 methods failed for 1-chlorovinyllithium as the initial Hartree-Fock optimization step generated an incorrect geometry for the monomer. As with the halomethyllithium carbenoids, the coupled cluster, large basis set MP2, and G3 methods (when available) all generated comparable dimerization free energies.

Basis set effects on thermal corrections to free energies

In contrast to the free energies of dimerization, the thermal correction to the dimerization free energies is relatively insensitive to the level of theory, and even small basis sets can be used to obtain good thermal corrections. Thus, expensive frequency calculations with large basis sets can be avoided by performing geometry optimizations and frequency calculations with smaller basis sets to obtain the thermal correction, which is added to the electronic energy obtained from re-optimization with a larger basis set.


129

The Role of Parallel Computation in Quantum Chemistry

Peter Pulay1 and Jon Baker1,2

1Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AAR 72701 2Parallel Quantum Solutions, LLC, 2013 Green Acres Road, Fayetteville, AR 72703

The role of parallel computation in quantum chemistry is reviewed in a historical context, and future trends are analyzed. Parallel computation in quantum chemistry has had a checkered history. Yet it is quite clear that parallelism will play not only an important but a decisive role in any future development of electronic structure theory. Currently, the assessment of the utility of parallel computing varies wildly in the quantum chemistry community. Some groups endorse only trivial parallelism (a number of projects run in parallel, “parallelism by graduate students”), others consider only massive (>100 processors) parallelism worth while. The truth at the present time, may be somewhere in between, at mid-size parallelism (4-64 processors). However, as the price per FLOP and memory access keeps falling, the importance of algorithms that can use effectively a large number of processors is going to increase.

The parallel algorithms used in the PQS (Parallel Quantum Solutions) software will be described, in particular the Fourier Transform Coulomb (FTC) density functional code, and the new parallel CCSD/QCISDMP4(SDQ) program inn the PQS suite. FTC calculates the most expensive part in Density Functional Theory (DFT), the Coulomb en ergy of the valence shell, in an intermediate plane-wave basis, and is potentially two orders of magnitude faster than regular DFT, at full accuracy. However, to realize this speed-up, all parts of the code, in particular the calculation of the exchange-correlation (XC) potential, the contribution of the core/compact charge distributions, and matrix diagonalization (orbital update) must be speeded up proportionately, a non-trivial task.

Our parallel CCSD/QCISD program, developed by T. Janowski, will be described. By itself, CCSD is not a highly accurate method. However, if triple substitution effects are included, even perturbationally (CCSD(T)), it becomes very accurate unless there is strong nondynamical correlation. CCSD is difficult to parallelize, as it has to access large data sets. The perturbational triple contributions, on the other hand, parallelize well. Using a transparent distributed disk storage middleware, Array Files1, we were able to parallelize CCSD/QCISD efficiently, Calculations using over 1500 basis functions and no symmetry will be presented.

Will the quantum chemical method of the future be determined by the efficiency of parallelization? Quantum Monte Carlo (QMC) is currently an exotic method but it may become a major player simply because it can be efficiently parallelized on a large number of processors.

1 A. Ford, T. Janowski and P. Pulay, Array Files for Computational Chemistry: MP2 energies, J. Comp. Chem., in press.


130

Progressive Derivation of Most Likely Transformations of CL-20 and Investigation of Most Likely Bond-Breaking Sites

1Mo Qasim, 1Brett Moore, 1L. Gorb and 2J. Leszczynski

1US Army ERDC, Vicksburg, Mississippi, 39180, USA 2Computational Center for Molecular Structure and Interactions,

Jackson State University, Jackson, Mississippi, 39217, USA

This study involves the possible combinations of CL-20 carbon-carbon (C-C) bond-breaking. It has been shown theoretically and experimentally that different competing modes of reaction take place under varying conditions, depending upon methods of transformation (e.g., alkali hydrolysis, reductive, and free radical induced reactions). CL-20 has three C-C bonds, two at the base of a cyclohexane ring and one, the “attic” C-C, perpendicular to the “base” two C-Cs. Breaking the “base” C-C bonds and systematic removal of nitro groups generated different CL-20 derivatives from those resulting from breaking the “attic” C-C bond, whose alkaline hydroxide transformation produced an aromatic pyrazine derivative.

A purpose of this study was to find any trends in the breaking of the “base” C-C bonds, removal of nitro groups and to compare them with transformations derived from the breaking of the “attic” C-C. A comparison of energies involved in systematic bond-breaking might reveal the most likely transformation pathways. Also, a comparison of formation, steric, HOMOI/LUMO energy values can show the most unlikely possible derivatives

The method was to compare the breaking of these “base” C-C bond derivatives, beginning with breaking one base C-C bond and sequentially removing the nitro groups, then progressing through the breaking of both base C-C bonds and sequentially removing all nitro groups. Heats of formation as well as steric and HOMO/LUMO energies were compared; bond lengths and charges were calculated. Since these transformations are derived from the same CL-20 essential structure, MOPAC gives sufficiently accurate preliminary values which, however, can later be refined using DFT methods after eliminating unlikely derivatives.

Definite energetic trends were found. With one base C-C broken: ■ Homo energies for base C-C are always slightly higher energetically than those for the

attic C-C. However, the attic LUMO C-C energies are always slightly lower than those for the base C-Cs.

■ Heat of formation increases upon removal of nitro groups. ■ With the breaking of one base C-C, HOMO energy increases upon removal of nitro

groups, whereas LUMO energy decreases. ■ Free radical reactions, experimentally, showed simpler products—most likely not going

through the attic CC to form the aromatic pyrazine. With two base C-C broken: ■ Breaking the two base C-Cs requires a very high heat of formation (496 kcal/mol), much

higher than when one CC is broken. However, the heat of formation decreases upon removal of nitro groups with the exception that when one nitro group remains, the formation energy becomes very high again..

■ In all cases, an aromatic molecule remains after removal of all six nitro groups. ■ HOMO/LUMO are both slightly higher than with one CC. The following table summarizes some of our results.


131

ATTIC LUMO HOMO GAP Steric HF Cl-20 -2.23 -12.16 9.93 40.16 277.95 Cl-20 with one nitro group removed -3.19 -12.14 8.95 33.67 333.40 Cl-20 with two nitro groups removed -3.55 -11.92 8.37 68.46 402.61 Cl-20 with attic C-C broken and 2 nitro groups removed

-1.63 -11.62 9.99 99.12 229.65

Cl-20 with attic C-C broken and 3 nitro groups removed

-1.92 -11.82 9.90 9.93 238.96


-1.97 -11.03 9.06 19.97 225.41


-1.48 -10.37 8.89 19.48 188.04

Cl-20 with attic C-C broken and all nitro groups removed

-0.65 -9.87 9.22 22.61 151.74

Pyrazine -3.28 -10.78 7.50 27.69 229.43

ONE BASE LUMO HOMO GAP Steric HF Cl-20 -2.23 -12.16 9.93 40.16 277.95 Cl-20 with one base C-C broken -2.31 -12.06 9.75 62.34 275.54 Cl-20 with 1 base C-C broken and 1 nitro group removed

-2.25 -11.89 9.64 21.15 251.42

Cl-20 with 1 base C-C broken and 2 nitro groups removed

-2.35 -11.80 9.45 86.32 273.49


-2.63 -11.39 8.76 34.29 289.94


-2.63 -11.28 8.65 50.83 295.16


-1.82 -9.61 7.79 102.67 222.30


-3.33 -10.73 7.40 130.44 283.22

Cl-20 with 2 base C-C broken and 6 -1.96 -10.44 8.48 57.60 182.28


132

Cl-20 with attic C-C bond broken AM1 MNDO PM3

Heat of Formation 280.27089 229.65301 108.28103 Homo -12.14 -12.43 -11.41 N = 82

Lumo -2.21 -1.96 -1.38 N = 83

Cl-20 with one base C-C broken AM1 MNDO PM3

Heat of Formation 277.86939 260.98049 125.20087 Homo -12.03 -12.31 -11.24 N = 82

Lumo -2.42 -2.25 -1.61 N = 83

Cl-20 with one nitro group removed AM1 MNDO PM3

Heat of Formation 333.26126 273.41153 163.53663 Homo -12.13 -12.27 -11.44 N = 72 Lumo -3.2 -3.03 -2.46 N = 73

Cl-20 with both base C-C broken AM1 MNDO PM3

Heat of Formation 496.56925 467.75493 318.23249 Homo -10.92 -11.3 -10.04 N = 78 Lumo -3.06 -3.09 -2.42 N = 79

N

N

N

N

N

N+

O

O-

N+O

O-

N+O

-ON+

O-O

N+

O-O

N+O

O-

N

N

N

NN

N

N+O

O-N+

O O-

N+

O

O-N+

O

-O

N+

O

-O

N+

O

-O

N

N

N

NN

N

N+

O

O-

N+

O

-O

N+

O

O-

N+

O

-O

N+

O

O-

N+

O

-O

N

N

N

NN

N

N+O

O-

N+

O

-O

N+

O

O-

N+

O

O-

N+

O

-O N


133

Proton and Metal Ion Affinities of α,ω-Diamines and Heterocyclic Amines

J. Srinivasa Rao and G. Narahari Sastry*

Molecular Modeling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology, Tarnaka, Hyderabad 500 007, AP, India

Knowledge of accurate proton and metal ion binding interactions in polyfunctional macromolecules is an important step in understanding the biophysical processes. Good correlations exist between the metal ion and proton binding affinity to the bases, albeit the proton affinities are much higher. In biological system, especially in proteins, several basic motifs exist, separated by varying distances. Polyamines found to be present in the cells of microorganisms and animal organisms, contribute to the stabilization of the structure and activity of tRNA and DNA. Protonation of α,ω-diamines has been extensively studied using mass spectrometric methods and computational techniques. Intramolecular hydrogen bonding and the consequent chelating ring size were found to be the key factors controlling the stability of the protonated complexes. In contrast, studies of the alkali metal ion affinities on the diamines are scarce, except on the simplest case of ethylene diamine.

In this study metal ion and proton affinities of 7 α,ω-diamines whose chain length is ranging from 2 to 8 carban atoms are estimated using the equations 1 and 2, respectively. B3LYP/6-31G* method is used for the geometry optimisations and obtaining the thermochemical data. All the structures considered are characterised as minima on the potential energy surface. This is followed by single point calculations at MP2/6-311++G** level. Counterpoise method was used to calculate the basiset super position error (BSSE).

Metal ion affinity (ΔH298) = ΔEele + ΔEthermal + TΔS - BSSE Equn1 Proton affinity (ΔH298) = ΔEele + ΔEthermal + 5/2 RT Equn2 The relative binding affinity orderings of the computed results are in excellent agreement

with the experimental observations for both proton and Li+ ion affinities, except the change of proton affinity order between 4 and 5. Theoretically obtained proton and lithium ion affinity orders can be given as 1H+ < 2H+ < 7H+ < 6H+ ≤ 4H+ < 5H+ < 3H+ and 1Li+ < 3Li+ ≤ 2Li+ < 4Li+ < 6Li+ < 5Li+ ≈ 7Li+. Fig. 1 depicts the optimised geometries of the Li+ and protonated complexes.

While the lithium bridging is virtually symmetrical in all cases, the proton bridge is highly unsymmetrical. The contrasts in the trends of the relative stability orderings are due to an interplay of intricate conformational energetics during the formation of metal ion chelate ring. Thus, the combined experimental and computational study on the binding affinities of Li+ and H+ ion to α,ω-diamines highlight the disparities between the complexation energetics and structures. It is worth mentioning that the kinetic method amplifies even small differences between similar compounds in the measurement of important thermodynamic parameters. Thus, while both proton and metal ion α,ω-diamine complexes prefer cyclic conformations, the nature of bridging and the energy differences between the mono and bidentate complexes are quite different.


134

116.9

113.3

109.3

109.3

109.3

113.3

1.976

1.976

1.500

1.500

1.533

1.533

109.4

106.5

126.5

111.6116.1

117.9

112.8

1.989

1.981

1.4991.530

1.542

1.542

1.503

115.8112.1

115.9113.3

110.5 110.4

149.7

109.7

2.006

2.011

1.5001.532

1.538

1.544

1.531

1.503

156.4

106.0

111.6

115.4

115.0

118.1116.2

112.6

116.4

106.62.002

1.997

1.4961.531

1.541

1.540

1.538

1.541 1.5361.502

121.4

112.6

115.3

116.4

112.7

115.9115.1

111.6109.1

134.8

115.32.021

2.031

1.4971.533

1.537

1.539

1.537

1.535

1.541 1.538

1.504

115.7

115.1

178.9

109.0

115.1 115.7111.9

111.9109.1

111.9

2.011

2.011

1.4981.532

1.540

1.538

1.540

1.532 1.498

101.3

110.3

101.3

92.6110.3

2.0021.495

1.527

1.4952.002

1Li+ 2Li+ 3Li+ 4Li+ 5Li+ 6Li+ 7Li+

123.6

101.6107.7

106.186.1

1.877

1.0611.514

1.542

1.471

150.3

113.1

104.3

99.8110.41.651

1.097

1.520

1.531

1.537

1.494

109.4

165.6

107.8111.0

117.1

117.1112.3 106.4

1.545

1.133

1.5101.531

1.544

1.533

1.493

169.5

113.3112.1

114.5

116.8

116.9112.0

105.1

1.129

1.576

1.4931.533

1.541

1.552

1.5291.515

173.5

111.6

111.4

117.7

117.4

118.7

115.0

112.0

118.0

1.610

1.119

1.5131.528

1.541

1.542

1.544

1.5401.499

173.8112.3

109.9116.1

114.9

113.7

115.0 115.3112.4

121.9

114.2

1.674

1.108

1.5141.5291.541

1.545

1.549

1.545

1.537

1.532

1.502

170.5113.6

113.1115.2

114.2

116.1116.1

113.2123.9

1.108

1.664

1.503

1.538

1.541

1.535

1.540

1.541

1.528

1.517

114.3

1H+ 2H+ 3H+ 4H+ 5H+ 7H+6H+

Lithium Nitrogen Carbon Hydrogen

Fig.1. B3LYP/6-311++G** optimized geometries of cyclic H+ and Li+ ion complexes of diamines. Bond lengths in Å and bond angles in degrees.

While the computed nembers explain the observed trends, we would lide to get the right answers for right reasons. Therefor a brnchmark study to assess the reliability of the computational methods adapted appear to be an important study. A set of 24 fivemembered heterocyclic amines were taken as a test set to benchmark the computational methods.The theoretical study also unambiguously establishes the regioselectivity of protonation in all the 24 heterocyclic amines considered. G3B3 calculations have shown excellent agreement with experimental results. For the series of compounds studied here, the performance of B3LYP/6-31++G** level of theory is excellent in modeling proton affinities and is comparable to the performance of G3B3 level. While the traditional correlated levels require large basis sets to correctly reproduce the results, a basis set of double-ζ with polarization and diffuse functions on the heavy atoms and hydrogens appears to be sufficient to model the systems.


135

Ab initio quantum chemical calculations, G3B3, MP2 and hybrid density functional method

B3LYP, were employed to compute the proton affinities of twenty-four heterocyclic amines. A range of basis sets are employed starting from double-ζ polarization quality to triple-ζ quality basis set with augmented diffuse and polarization function. Experimental values were used to calibrate the performance of various theoretical models. The regioselectivity for the protonation has been unambiguously established by performing B3LYP/6-31G* calculations on the possible putative sites of attack. For the given series of compounds the performance of B3LYP/6-31++G** and G3B3 levels of theory have been in excellent agreement with the experimental results with the deviations are of the order comparable with the experimental error.

References: 1. M. K. Kumar, J. S. Rao, S. Prabhakar, M. Vairamani, and G. N. Sastry., Chem. Comm, 2005,

1420-1422. 2. J. S. Rao and G. N. Sastry., Int. J. Quantum Chem., 2006, 106, 1217-1224.


136

Multiple Linear Regression Analysis and Optimal Descriptors: Predicting the Cholesteryl Ester Transfer Protein Inhibition

Activity

Bakhtiyor F. Rasulev Andrey A. Toropov, Ashton Hamme and Jerzy Leszczynski

Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, P. O. Box 17910, Jackson, MS 39217, USA

Quantitative Structure – Activity Relationships (QSAR) analysis of Cholesteryl Ester Transfer Protein (CETP) inhibitor activity of forty organic compounds has been carried out. These forty randomly have been split into training and test sets. Best three-variable model of the activity obtained by multiple linear regression analysis has the following statistical characteristics: n=20, r2=0.9020, s=0.322, F=80 (training set) and n=20, r2=6462, s=0.622, F=15 (test set). Statistical characteristics of one-variable model based on optimal descriptors are the following: n=20, r2=0.5647, s=0.678, F=23 (training set) and n=20, r2=0.8182, s=0.549, F=81 (test set).


137

Predicting the Flavonoids Inhibition Activity towards Na,K-ATP-ase: A Computational Study Using Molecular Modeling and QSAR

GA-MLRA Analysis

B.F. Rasuleva,b, Z.A. Khushbaktovab and J. Leszczynskia

aComputational Center for Molecular Structure and Interactions, Jackson State University, 1325 J. R. Lynch Street, P.O. Box 17910, Jackson, Mississippi 39217-0510 USA

bInstitute of the Chemistry of Plant substances, 77 Kh. Abdullaeva St , Tashkent, 700170, Uzbekistan

A quantitative structure-activity relationship analysis has been applied to a data set of 25 flavonoid compounds obtained from different plant sources. Quantum-chemical molecular modeling calculations were used to find the optimum 3D geometry of the studied molecules. A number of molecular descriptors was obtained from the density functional theory (DFT) at the B3LYP/6-31G(d, p) level of calculation. Use of the genetic algorithm in the QSAR analysis allows the structural and physico-chemical parameters of the flavonoids responsible for inhibition of Na,K-ATP-ase to be determined. The resulting models showed a reliable dependence of inhibition activity of the flavonoids from topological and physico-chemical parameters.


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SH/π Interactions: Quantum Mechanical Potential Energy Surfaces of the H2S-Benzene Complex and Protein Databank Mining

Experiments

Ashley L. Ringer, Anastasia Asenenko, and C. David Sherrill

Georgia Institute of Technology, School of Chemistry and Biochemistry, Atlanta, GA

Noncovalent S/π interactions are prevalent in biochemistry and play a role in protein folding and protein stabilization. In this work, we present 2D potential surfaces for several models of the H2S-benzene complex. These surfaces vary the angle between the sulfur and the normal extending through the center of the benzene ring and the distance between the sulfur atom and the center of the benzene ring. Second-order perturbation theory (MP2) is used in conjunction with the aug-cc-pVDZ and aug-cc-pVTZ basis sets to determine the counterpoise-corrected interaction energy for the complex configurations. These surfaces are compared to the results of a data mining experiment which counts the number of short contacts between sulfurs in cystine residues and aromatic rings in various orientations in protein structures from the Brookhaven Protein Databank (PDB).


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Docking and Molecular Simulations of a Series of Estradiol Derivative Selective Estrogen Modulators

Jamar Robinson1*, John S. Cooperwood2, Musiliyu Musa1, Reginald Parker3, Jesse Edwards1

1Department of Chemistry, 2College of Pharmacy and Pharmaceutical Sciences, Florida A& M University, Tallahassee, FL, USA

3Ubiquitous Technologies Inc., Research and Technolgy Center, Tallahassee, FL, USA

Breast cancer is one of the leading causes of death in women between the ages of 35 and 55 years of age. Current treatments focus on the estrogen responsive population. This work will also focus on a unique class of selective estrogen positive receptive modulators. Three classes of selective estrogen receptor modulators (SERM’s) will be discussed in this work. These compounds were synthesized and tested for bioactivity by Dr. John Cooperwood’s group. We used the Sybyl6.9 suite of programs to perform FlexX and Cscore series of docking calculations to determine the binding energies of these ligands in the estrogen active site. Using the docking results and molecular dynamics simulations, we are able to provide evidence of intermolecular interactions between the estrogen active site and ligands of 2 classes of the compounds being studied. In particular, we used the structure of the ligand, 4-Hydroxytamoxifen a currently used pharmaceutical, bound in the active site of the PDB crystal structure 3ERT, as the reference molecule. Using the results of the docking calculations we were able to determine that scoring functions containing free energy expressions with hydrogen bonding terms provided the lowest free energy of binding on a consistent basis and exhibited the highest correlation with the experimentally determined bioactivities. In the case of the estradiol and 17-ethynyl estradiol derivatives the correlation (R2) between activity and the ChemScore (part of Cscore series) scoring functions were 0.86 and 0.89, respectively. There was only one exception, the morpholinyl derivatives received high docking scores but had the lowest bioactivities. These results suggest hydrogen bonding played an essential role in the activity of these compounds just as in the case of the crystal structure of 4-Hydroxytamoxifen. We will also, present the molecular dynamic simulations of these molecules in order to examine the motion of these systems in an aqueous environment. Also, Monte Carlo simulations results used to determine the shape and volumes of these compounds will be presented.


140

Theoretical Study of Adsorption of Selected Nucleic Acids on Dickite

T. L. Robinson, A. Michalkova, L. Gorb, and J. Leszczynski

Computational Center of Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 JR Lynch Street, Jackson, MS 39217

The universal basis of all life on Earth is DNA (deoxyribonucleic acid) and RNA (ribonucleic acid). DNA simply represents the hereditary material in humans and almost all organisms. Most DNA can be found in the cell nucleus but a small amount of DNA can also be located in the mitochondria. Deoxyribonucleic acid contains information that is stored as a code of four chemical bases: adenine (A), guanine (G), cytosine (C), and thymine (T). The order of these bases determines the information available for building and maintaining an organism. The bases pair up with each other in an ordered sequence. Adenine pairs with thymine and cytosine and guanine to form base pairs. The most important property of DNA is that it can replicate or make copies itself. Unlike DNA, RNA is the only known macromolecule that can both encode genetic information and also act as a biocatalyst. It is a polymeric constituent of all living cells and many viruses, consisting of a long, usually single-stranded chain of alternating phosphate and ribose units with the bases adenine, guanine, cytosine, and uracil (replaces thymine) bonded to the ribose. The structure and base sequence of RNA are determinants of protein synthesis and the transmission of genetic information.

Phyllosilicates contain an important group of clay minerals characterized by their abilitly to absorb large percentages of water between its silicate sheets. As a result of this, clay minerals have many important uses including manufacturing, drilling, construction and paper production, and crop production due to it being an integral component of soils. Clay minerals are divided into four major groups. Our group of interest is the kaolinite group which contains dickite. The general formula of this group is Al2Ai2O5(OH)4. This group is described as polymorphs, meaning that they have the same chemistry but different structures.

Since the mid-1960s, Dr. Cairns-Smith, an organic chemist and molecular biologist at the University of Glasgow, has developed a clay theory in the origin of life. It emphasizes the role of clay minerals in the support of organic matter in the evolution of life on Earth. This provided a roadmap for Watson, Crick, and Orgel who suggested a RNA world where the RNA catalysts may have been important in the early stages of life’s origin. This suggestion of RNA as a prebiotic cursor is a solution to the prevailing theories that the first macromolecule possessed a replication scheme. The molecular replication of RNA is capable of proposing an available, evolutionary pathway to further the development of life. To understand the possible synthetic routes that may have led to that first macromolecule, and thus to life as we know, we must first understand prebiotic chemistry. In lieu of this, our hypothesis is to construct possible scenarios en route to an RNA world by conceptualizing how the molecular building blocks could have interacted with clays under the simulated conditions of early Earth. Those building blocks include the heterocyclic RNA bases, purines, and pyrimidines. The conditions considered include the role of water and cations.

Particularly, we have performed the study of the adsorption of thymine and uracil on tetrahedral and octahedral non-hydrated and hydrated surface of dickite (1:1 dioctahedral clay mineral of the kaolinite group) with the presence of the Na+ cation. The density functional theory (DFT) using the B3LYP functional and 6-31G (d) basis set were applied for the calculations. We


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have studied the structure, interactions, charge distribution, and the interaction energies corrected by the basis set superposition error of these complexes.

The results reveal that thymine and uracil are placed in similar way on the non-hydrated tetrahedral and octahedral surface of dickite (a perpendicular orientation towards the tetrahedral surface and planar towards the octahedral surface, for example see Figure 1. that illustrates the optimized structure of thymine adsorbed on non-hydrated octahedral surface of dickite obtained at the B3LYP/6-31G (d) level of theory). These bases posses almost the same interactions with the surface (mostly hydrogen bonds formed between the N-H groups and oxygen atoms of thymine and uracil and the oxygen atoms and hydroxyl groups of the mineral surface). Small differences were found only in the strength of these intermolecular interactions. The adsorption leads to the geometrical changes and modifications in the charge distribution in all complexes. Hydration of the tetrahedral surface has a significant effect on the orientation of the target molecule (the molecule is placed planar towards the surface). In the case of the octahedral surface the hydration affects only slightly the bases’ position. Studied bases interact much more strongly with the octahedral than with the tetrahedral surface of dickite. The selected nucleic acids are much better stabilized in the complexes with the Na+ cation on both surfaces in comparison with the complexes without the cationic influence (except the D(o)-THNa, D(o)-URNa, and D(o)w-THNa systems the addition of the cation lowers the interaction energy). The most stable were found to be the D(o)w-THNa and D(o)w-URNa systems with the interaction energies -35 and -56 kcal/mol.

Figure 1. The optimized structure of thymine and sodium cation adsorbed on non-hydrated octahedral surface of dickite obtained at the B3LYP/6-31G (d) level of theory.


142

Theoretical Studies of Symmetric Five-Membered Heterocycle Derivatives of Carbasole and

Fluorene – Precursors of Conducting Polymers

Szczepan Roszak,a,b

Jacek Doskocz,a,c

Marek Doskocz,c

Jadwiga Soloducho,c and Jerzy Leszczynski

a*

aComputational Center for Molecular Structure and Interactions Department of Chemistry - Jackson State University, 1325 J.R.Lynch St.Jackson, MS 39217-0510;

bInstitute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wroclaw, Poland;

cDepartment of Chemistry, Faculty of Medicinal Chemistry and Microbiology, Wroclaw University of Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland,

Polymers containing carbazole and fluorene fragments in the main chain have attracted much attention because of their unique properties which allow for various photonic applications. To control the electronic and optical properties of such polymers one may introduce electron-rich heterocycles at the terminal polymerization sites to prepare multi-ring electropolymerizable monomers. The studied heterocycles possessing the ability for electrochemical polymerization are thiophene, ethylenedioxynothiophene, furane, methylopyrrole, and pyrrole.

The differences between HOMO-LUMO gaps, vertical ionization potentials, and distribution of total atomic spin densities of radical cations of the studied molecules could indicate the expected electropolymerization properties. The electronic states of derivatives of carbazoles and fluorenes were elucidated by molecular orbital calculations using the density functional theory. The reactivity for coupling reaction of thiophenes derivatives are inferred from calculated unpaired electron spin densities of the respective radical cations, and ionization potentials which correspond to energies for generating radical cations during the oxidative processes.

a)

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Figure 1. a) Carbasole and Fluorene derivatives b) Isovalent surfaces (0.004) of spin electron density (in blue) in thiophene carbasole. Atomic electron spin densities are given in electrons.


143

Molecular Dynamic Studies of Several HIV-1 Protease Modified Peptide Inhibitors: Shape and Size Specificity

Christina Russell1, Debra Bryan1, John West1, Ben Dunn2, Reginald Parker3, Jesse Edwards1

1Chemistry Department Florida A&M University, Tallahassee, Florida, 2Department of Biology and Biochemistry, University of Florida, Gainesville, Florida, 3Ubiquitous Technologies Inc., Research and Technology Center, Tallahassee, Florida

Protease inhibition to date is the most successful course in the treatment of HIV. In an attempt to achieve greater results in the inhibition of the HIV virus, Dunn et al synthesized a series of small polypeptides, a few amino groups long as potential protease inhibitors. The structure of these new peptides were designed to better adapt to mutations within the HIV-1 protease, providing increased inhibition. The newly synthesized peptides were modified at the central peptide bond by replacing the central carbonyl group with either hydrogen atoms, hydroxyl groups or a combination of the two. This would allow for increased flexibility of these compounds. Molecular dynamics (NVT ensemble) were used to study the flexibility of the peptides in reduced and native forms. Dynamic studies were conducted at two different dielectric constants, simulating in vacuum and in an aqueous environment (dielectric 78). In each of the cases the compound showed increased flexibility at a dielectric of 78. Also, Monte Carlo simulations were used to calculate volumes and radius of gyration of the minimized structures to determine the shapes of the HIV-1 synthesized protease inhibitors. There was apparent correlation between the calculated shape or volume and activity. Correlation between flexibility of the compound, side chain rotations, and the bioactivity will also be discussed.


144

Role of Intermolecular Interaction on Nonlinear Optical Properties and Two Photon Absorption Cross-Section of Molecular Aggregates

Zuhail Sainudeen and Paresh Chandra Ray

Department of Chemistry, Jackson State University, Jackson, MS, USA, 39217

We present quantum-chemical analysis on molecular aggregates to provide an insight into the intermolecular interactions and the relationship between structural and collective nonlinear optical properties. The first hyperpolarizabilities and two-photon absorption properties are evaluated for monomer and aggregates of a series of push-pull porphyrins, whose synthesis and formation of H and J type aggregates in solvents are reported recently in literature. The molecular geometries are obtained via B3LYP/6-31G** optimization including SCRF/PCM approach, while the dynamic NLO properties are calculated using ZINDO/CV method including solvent effects. It has been observed that the NLO properties change tremendously as monomer undergoes aggregation and the magnitudes are highly dependent on the nature of aggregates. The importance of our results with respect to the design of photonic and photo dynamic therapy materials will be discussed.


145

An ONIOM Study of Catalytic Site of the Phosphodiesterases

E. Alan Salter and Andrzej Wierzbicki

Department of Chemistry, University of South Alabama, Mobile, AL 36688, USA

The cyclic nucleotide phosphodiesterases (PDEs) are targets of high-throughput screening in order to determine selective inhibitors for a variety of therapeutic purposes. The PDEs catalyze the stereospecific hydrolysis of the second messengers adenosine and guanosine 3’, 5’- cyclic monophosphate (cAMP, cGMP) to produce 5’-AMP and 5’-GMP, respectively. The catalytic pocket where the hydrolysis takes place is a highly conserved region among the PDE super family. To investigate the hydrolysis mechanism, we have studied a model cyclic nucleotide in a truncated model of the catalytic site of PDE using ONIOM hybrid (B3LYP/6-31g(d):PM3) calculations.


146

The Two Aspects of the Protein Folding Problem

Harold A. Scheraga

Baker Laboratory of Chemistry Cornell University, Ithaca, NY 14853-1301

There are two aspects of the theoretical approach to the protein folding problem. The first is to compute the thermodynamically stable native structure, and the second is to compute the folding pathways from the unfolded to the folded native form. The evolution of physics-based computational methodology from an all-atom representation of the polypeptide chain to a united-residue representation of the chain will be discussed. Blind tests in successive CASP exercises demonstrate increasing prediction success, in computing protein structure, from one CASP test to another. As for folding pathways, two different methods are used: (1) a stochastic difference equation procedure, and (2) Lagrangian dynamics with the united-residue force field. The results of all the computations, and the methods leading to them, will be discussed.


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A Theoretical Investigation of Ionization Potentials and Spectral Origins of Guanine Tautomers

M.K. Shukla and Jerzy Leszczynski

Computational Centre for Molecular Structure and Interactions Department of Chemistry, Jackson State University, Jackson, Ms 39217

Guanine is an important building block of nucleic acids. It possesses the maximum number of tautomers in different environments. Further, it also has the lowest ionization potential and maximum negative vertical electron affinity among all nucleic acid bases. Therefore, it is the most susceptible site for oxidation in DNA. The reliable information about the tautomerism of nucleic acid bases has paramount importance due to the possibility of their involvement in mutation. The relative distribution of guanine tautomers is found to be significantly influenced by the environment. In a recent jet-cooled spectroscopic investigation Nir et al. [1] have shown the existence of three tautomers of guanine, namely, the enol-N9H (32870 cm-1), keto-N7H (33274 cm-1) and keto-N9H (33914 cm-1). In a similar study Mons et al. [2] have identified the four tautomers (keto-N9H, keto-N7H, enol-N9H and enol-N7H) of guanine. The main difference between these two investigations was that the enol-N9H tautomer assigned by earlier authors was reassigned as the enol-N7H tautomer and the enol-N9H tautomer was assigned with the spectral origin at 34755 cm-1 by the latter authors.

A recent study by Choi and Miller [3], based on the IR-spectroscopy of guanine trapped in helium droplets and the MP2 level of theoretical calculation using the 6-311++G(d,p) and aug-cc-pVDZ basis sets, shows the presence of only keto-N9H, keto-N7H and cis- and trans-forms of enol-N9H tautomer. Based on the results of Choi and Miller, Mons et al. [4] have proposed the reassignment of their experimental findings and accordingly the enol-N9H-trans, enol-N7H and two rotamers of the keto-N7H-imino tautomers of guanine are present in the supersonic jet-beam. However, it is surprising, since imino tautomers are much less stable than the canonical form of guanine. On the other hand, LeBreton and coworkers [5] studied photoelectron spectra of guanine and some methyl derivatives in the gas phase by heating the samples. Based on the similarity of photoelectron spectra of guanine and 7-methylguanine, it was concluded that the keto-N7H tautomer of guanine is the most stable form in the gas phase.

Thus, the current knowledge regarding the tautomers of guanine in the gas phase is still somewhat uncertain and therefore, detailed information about the relative stability, ionization potentials and the spectral origin of the first ππ* excited state of all possible tautomers including rotamers of guanine is needed. Therefore, we performed a detailed theoretical investigation of the computation of first vertical ionization potential and the spectral origin of lowest singlet ππ* excited state of all tautomers of guanine with an objective that our theoretical results would be very valuable for experimentalists in analyzing the complex resonance enhanced two photon ionization (R2PI) experimental data.


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K-N9H K-N9H-N3H K-N9H-Imino K-N9H-Imino-Cis

E-N9H E-N9H-Trans E-N9H-IMN1 E-N9H-IMN1-Cis

E-N9H-IMN3 E-N9H-IMN3-Cis E-N9T-IMN1 E-N9T-IMN1-Cis

E-N9T-IMN3 E-N9T-IMN3-Cis Figure 1. Structures of the N9H tautomers of guanine. The corresponding N7H forms can be obtained by replacing hydrogen attached to the N9 site to the N7 site of guanine. K represents the keto and E represents the enol.

Ground state geometries were optimized at the B3LYP level and single point energies were computed at the MP2 level using the 6-311++G(d,p) basis set at both levels. Geometries of all tautomers in the electronic lowest singlet excited states were optimized at the CI-Singles (CIS) level using the 6-311G(d,p) basis set. Since the CIS level is the HF analog for the excited state, therefore, ground state geometries were also optimized at the HF/6-311G(d,p) level. In order to obtain transition energies at the same level of the theoretical accuracy, the vertical singlet electronic transition energies were computed at the time-dependent density functional theory (TDDFT) level employing the B3LYP functional and the 6-311G(d,p) basis set using the HF ground state optimized geometries. The spectral origins (0-0 transitions) corresponding to the lowest singlet ππ* excited states of guanine tautomers were computed as the energy difference between the ground state energy obtained at the B3LYP/6-311G(d,p)//HF/6-311G(d,p) level and the corresponding singlet ππ* excited state energy obtained at the TD-B3LYP/6-311G(d,p)//CIS/6-311G(d,p) level. The vibrational frequency analysis was performed to ascertain the ground and excited state potential energies surfaces, all geometries were found to be minima at the corresponding potential energy surfaces. Relative total energies at the


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B3LYP/6-311++G(d,p) level were corrected for the scaled (scaling factor 0.9877) zero point energy (ZPE).

The keto-N9H, keto-N7H and two rotamers of the enol-N9H tautomer have similar stability in the gas phase with electronic energy within 0-1.0 kcal/mol range; the keto-N7H tautomer being the most stable. The first vertical ionization potentials of these tautomers are about 8.0 eV, except the keto-N7H tautomer which has the 8.16 eV. Among all possible guanine tautomers, we have found that generally higher energy tautomers (the relative energy more than 20 kcal/mol) have lower ionization potentials [6]. The computed spectral origin values corresponding to the lowest singlet ππ* excited state of guanine tautomers are in the qualitative agreement with the reinterpreted R2PI data. We hope that computed ionization potentials and spectral origins of guanine tautomers would be very useful for experimentalists in identifying the stable tautomers of guanine in the R2PI experiments.

Acknowledgement We are thankful to Prof. Michel Mons, Laboratoire Francis Perrin - URA CNRS 2453 -

Service des Photons, Atomes et Molecules, CEA Saclay, Bat 522, 91191 Gif-sur-Yvette, Cedex, France for reading the final version of our manuscript and for his critical suggestions. Authors are also thankful to financial supports from NSF-CREST grant No. HRD-0318519, ONR grant No. N00034-03-1-0116 and NSF-EPSCoR grant No. 02-01-0067-08/MSU. Authors are also thankful to the Mississippi Center for Supercomputing Research (MCSR) for the generous computational facility.

References 1. E. Nir, Ch. Janzen, P. Imhof, K. Kleinermanns, M.S.de Vries, J. Chem. Phys. 2001 (4604)

115. 2. M. Mons, I. Dimicoli, F. Piuzzi, B. Tardivel, M. Elhanine, J. Phys. Chem. A 2002 (5088)

106. 3. M.Y. Choi, R.E. Miller, J. Am. Chem. Soc. 128 (2006) 7320. 4. M. Mons, F. Piuzzi, I. Dimicoli, L. Gorb, J. Leszczynki, J. Phys. Chem. A (Accepted). 5. J. Lin, C. Yu, S. Peng, I. Akiyama, K. Li, L.K. Lee, P.R. LeBreton, J. Phys. Chem. 84 (1980)

1006. 6. M.K. Shukla, J. Leszczynski, Chem. Phys. Lett. 2006 (in press).


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Ionization Potential and Electron Affinity of Some Carbon Nanostructures: A Density Functional Theory Investigation

M.K. Shukla and Jerzy Leszczynski


Electronic structure and properties of some carbon nanostructures were studied at the density functional theory level. Molecular geometries were optimized using the B3LYP functional and the 6-31G(d) basis set. The studies system included carbon nano capsule, carbon nano bowl (one side closed tube), carbon nano disk and fullerene. Geometry of the silicon analog of C60 was also optimized at the same level of the theory. It was revealed that with the change in the shape and size of the cluster, it is possible to design novel nanomaterials. The computed HOMO-LUMO energy difference of disk and capsule shaped carbon nanoclusters was found to be similar to that of the corresponding gas of Si60. The bowl shaped carbon nanostructure has been found to have the band gap similar to that of germanium crystal. The electron affinity was found to be significantly increased while the ionization potential was found to be decreased in going from the C60 to the disk and capsule and open bowl shaped nano carbon clusters. Thus, due to the high electron affinity and lower ionization potential, the capsule and bowl shaped carbon nanostructures can act as an electron sink and therefore may protect certain cellular systems against ionizing radiation and free electron by ionizing itself or by accepting the electron.

Figure 1. Structure of different carbon nanoclusters: (a) Carbon fullerene (C60), (b) carbon nano disk (C96), (c) carbon nano capsule (C144) and (d) carbon nano bowl (C120H12).

Acknowledgement

Authors are thankful to financial supports from NSF-CREST grant No. HRD-0318519, ONR grant No. N00014-03-1-0498 and NSF-EPSCoR grant No. 02-01-0067-08/MSU. Authors are also thankful to the Mississippi Center for Supercomputing Research (MCSR) for the generous computational facility.


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Hydrogen-Bonded Interactions between Guanine and Amino Acid Side-Chain in Aqueous Solution: A DFT Study

Indu Shukla, Jing Wang, Jerzy Leszczynski


In the present study, the interactions between amino acid side chains and the nucleic base Guanine (G) in aqueous solution are explored. By applying the polarizable continuum model (PCM) approach, all 13 interaction models are fully optimized at B3LYP/6-311G(d,p) theoretical level. The hydrogen bonding interactions are focused on the interactions between guanine and serine/threonine, arginine, lysine, asparagines-/glutamine, aspartic acid/glutamic acid, respectively.

The calculated interaction energies reveal that the charged amino acid side chains (Lys, Asp/Glu, and Arg) are the most favorable site of interaction.

G_Asp/Glu_1 G_ Asp/Glu_2 G_ Asp/Glu_3

G_Asn/Gln_1 G_ Asn/Gln_2 G_ Asn/Gln_3

G_Ser/Thr_1 G_ Ser/Thr_2 G_Lys

G_Arg_1 G_ Arg_2 G_ Arg_3 G_ Arg_4


152

A Theoretical Study on the Interactions of Li+ with Defect-Free and Stone-Wales Defect Armchair (6,6) Single-Walled Carbon Nanotube

Tomekia Simeon, T. C. Dinadayalane and Jerzy Leszczynski*

Computational Center for Molecular Structure and Interactions, Department of Chemistry, PO Box 17910, Jackson State University, Jackson, Mississippi 39217

The hybrid density functional theory (B3LYP) method with 6-31G(d) basis set has been employed to study the interactions of Li+ with a (6,6) armchair single-walled carbon nanotube (SWNT) of perfect structure and the tube with a Stone-Wales defect (Scheme 1). Single-walled carbon nanotubes called “buckytubes” can be thought of a single graphene sheet that is wrapped into a seamless cylinder. Recent experimental and theoretical studies indicate that carbon nanotubes (CNTs) are not always perfect as they seem since the defects such as vacancies, dopants and Stone-Wales defects can exist.1-4 The Stone-Wales defect is one of the most important defects in nanotube and it can be created by 90˚ rotation of a C-C bond in the hexagonal network of the carbon nanotube.5 SWNTs are promising materials as molecular containers with applications in rechargeable lithium-batteries due to their structure and unique properties. Nanotubes containing Li+ can improve the capacity of lithium batteries by using both exterior and interior walls of the tubes. The superior battery performance of SWNTs depends on the ability of lithium ions to enter and leave the nanotube interior at a reasonable rate. In this study, we have explored the interaction of Li+ with the exterior as well as interior walls of a defect-free and Stone-Wales defect SWNT. The binding of Li+ with inner wall of SWNT is slightly more favored than the outer wall. The presence of Stone-Wales defect drastically affects the binding affinity of Li+ with the SWNT.


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ABC

(a) defect-free (6,6) armchair SWNT

(b) (6,6) armchair SWNT with a single Stone-Wales defect (SW)

Scheme 1 References:

1.Dinadayalane, T. C.; Leszczynski, J. “Toward nanomaterials: Structural, Energetic and Reactivity Aspects of Single-walled Carbon Nanotubes.” In Nanomaterials: Design and Simulation, (Eds.) Balbuena, P. B.; Seminario, J. M. 2006, pp 167-199.

2.Hashimoto, A.; Suenaga, K.; Gloter, A.; Urita, K.; Iijima, S. Nature 2004, 430, 870. 3.Lu, A.; Pan, B.C. Phys. Rev. Lett. 2004, 92, 105504. 4.Rossato, J.; Baierle, R.J.; Fazzio, A.; Mota, R. Nano Lett. 2005, 5, 197. 5.Stone, A. J.; Wales, D.J. Chem. Phys. Lett. 1986, 128, 501.


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DFT Studies on Structurally Diverse Farnesyltransferase Inhibitors: Multivariate Analysis of Correlation between Physicochemical

Properties and Antimalarial Activity

Prasanna Sivaprakasam,a Aihua Xie,a Robert J. Doerksena,b

aDepartment of Medicinal Chemistry and bResearch Institute of Pharmaceutical Sciences,

School of Pharmacy, University of Mississippi, University, MS, 38677-1848, USA;

As part of our continuing interest1,2 to explore the nature of interactions between antimalarial compounds and the farnesyltransferase enzyme (FT), we studied some recently reported tetrahydroquinolines3 together with some of the most commonly used antimalarial drugs like chloroquine, pyrimethamine and mefloquine. In our previous work,1,2 we found that steric, electrostatic and hydrophobic properties are crucial but that hydrogen bonding properties are relatively less important in governing the FT inhibitory activity in case of a large set of 2,5-diaminobenzophenone derivatives. Based on this, we chose to study accurate electronic and steric properties for the present set of compounds3 using DFT with Becke’s three-parameter exchange potential and the Lee–Yang–Parr correlation functional (B3LYP). The dipole moment, highest occupied molecular orbital energy (EHOMO), lowest unoccupied molecular orbital energy (ELUMO), HOMO–LUMO energy gap (ΔEgap) and volume were calculated on DFT optimized structures using the 6-31G* basis set (cf. Figure 1). The hydrophobic property, logP; steric property, the calculated molecular refractivity (CMR); and a representative descriptor for polar hydrogen bonding interactions, the topological polar surface area (TPSA),5 were also included as molecular descriptors. A thorough multivariate analysis using partial least square (PLS) showed molecular volume to be the most important variable, followed by logP and the dipole moment of the ligands. The results are consistent with our previous published work2 and knowledge about the nature of the active site of Plasmodium falciparum FT. The positive correlation of the dipole moment with activity shows that electrostatic interactions are crucial for these compounds to interact with the active site of FT. Volume and logP are negatively correlated suggesting that less hydrophobic and less bulky compounds could fit well into the binding pockets of FT active site. Unlike the magnitude of the dipole moment, its direction is not correlated to the FT inhibitory activity in case of the tetrahydroquinoline compounds considered.

Figure 1. DFT optimized structures of a potent and a less active tetrahydroquinoline FT inhibitor as well as chloroquine showing the direction of the dipole moment.


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References: 1. Xie, A.; Sivaprakasam, P.; Doerksen, R. J. CoMFA studies of antimalarial compounds based

on 2,5-diaminobenzophenone scaffold. 14th Conference on Current Trends in Computational Chemistry, Jackson, MS, Nov. 2005.

2. Xie, A.; Sivaprakasam, P.; Doerksen, R. J. 3D-QSAR analysis of antimalarial farnesyltransferase inhibitors based on a 2, 5-diaminobenzophenone scaffold, Bioorganic & Medicinal Chemistry, 2006, 14, xxx, in press.

3. Nallan, L.; Bauer, K. D.; Bendale, P.; Rivas, K.; Yokoyama, K.; Horney, C.P.; Pendyala, P. R.; Floyd, D.; Lombardo, L. J.; Williams, D. K.; Hamilton, A.; Sebti, S.; Windsor, W. T.; Weber, P. C.; Buckner, F. S.; Chakrabarti, D.; Gelb, M. H.; Van Voorhis, W. C. Protein farnesyltransferase inhibitors exhibit potent antimalarial activity. J. Med Chem. 2005, 48, 3704-3713.

4. Ertl, P.; Rohde, B.; Selzer, P. Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. J. Med. Chem. 2000, 43, 3714-3717.


156

Predicting Catalytic Activity of the Molecular Environment from the Knowledge of Reactant and Transition State Structures Only

Andrzej Sokalskia, Borys Szewczyka, Edyta Dyguda-Kazimierowicza, Jerzy Leszczynskib

aWrocław University of Technology, Wyb. Wyspiańskiego 27, 50-370 Wrocław, Poland bJackson State University, CCMSI, 1400 Lynch St., Jackson, MS 39217, USA

The catalytic activity of various molecular environments (enzyme, zeolite, solvent, etc.) is determined by their interactions with reactants along reaction pathway. Application of DTSS(Differential Transition State Stabilization) approach [1-2] allows to determine the most important residues and energy contributions involved. Wherever electrostatic effects are dominant, these results can be generalized in the form of catalytic fields [1-2] aiding rational catalyst design. Corresponding examples related to enzyme systems [ 2,3-4] nucleic acids [5] will be presented and possible dynamic effects discussed. In addition, the covalent nature of transition state – active site interactions will be examined here in analogous way as it has been performed recently for hydrogen bonded systems [6].

References 1. W.A. Sokalski, J.Mol.Catalysis,30, 395 (1985). 2. B. Szefczyk, A.J. Mulholland, K.E. Ranaghan, W.A. Sokalski, J.Am.Chem.Soc., 126, 16148

(2004) 3. P. Szarek, E. Dyguda-Kazimierowicz, W.A. Sokalski, to be published. 4. B. Szefczyk, A.J. Mulholland W.A. Sokalski, to be published. 5. L. Gorb, Y. Podolyan, P. Dziekonski, W.A. Sokalski, J. Leszczynski, J.Am.Chem.Soc.,

126, 10119 (2004) 6. S. Grabowski, W.A. Sokalski, E. Dyguda-Kazimierowicz, J. Leszczyński, J.Phys.Chem.B,

110, 6444 (2006).


157

A DFT Study on The Mono-Reduction of 2,4-Dinitrotoluene (DNT) by Titanium(3+) Ions in the Presence of Iron(2+) Ions

Vitaly Solkan and Jerzy Leszczynski

N. D. Zelinski Institute of Organic Chemistry, RAS, 119991 Moscow, Leninskii pr.47, Russia Computational Center for Molecular Structure and Interactions, Department of Chemistry,

Jackson State University, P.O. Box 17910, 1325 Lynch Str., Jackson, MS 39217, USA

Electron transfer (ET) reactions constitute an important class of processes in various fields of chemistry, biology and physics. Along with a wide variety of experimental studies, there have also been major theoretical developments of ET reactions mainly based on the classical theory of Marcus followed by many subsequent generalizations. In recent years, it has been observed (1) that the reduction of TNT by Ti(3+) in acidic media produce 4-amine-2,6-dinitrotoluene, whereas in the presence of ions Fe(2+), the major product becomes 2-amine-4,6-dinitrotoluene. Our objective here is to investigate theoretically the reduction of DNT by Ti(3+) in the presence of Fe(2+) ions, by considering the factors that control the regioselectivity of DNT reduction. Geometry optimizations were carried out at the DFT level using the standard SDD and 6-31G* basis sets. The calculations were performed with the use of Becke's hybrid method with the Lee, Yang and Parr (B3LYP) gradient-corrected correlation functional. Characteristics of different minima were verified by analyzing the Hessian matrices of the energy second derivatives. Both the DNT+(Ti3+)(H2O)6 and DNT+Fe(2+)(H2O)5 potential surfaces have been examined by B3LYP/SDD and B3LYP/6-31G* methods. We found the global minimum energy structure to be a DNT-para-Fe(2+)(H2O)5 (Fig. 1) and also found an DNT-ortho-Fe(2+)(H2O)5 complex. Attempts to B3LYP/6-31G* optimize the DNT-para-Ti(3+)(H2O)6 and DNT-ortho-Ti(3+)(H2O)6 (Fig. 2)complex led to DNT(H)-para-Ti(4+)(HO-) H2O)5 or DNT(H)-ortho-Ti(4+)(HO-)(H2O)5 complex (Fig. 3), respectively. Our DFT study has revealed that the electronic structure of the DNT-Ti(4+)(HO-)(H2O)5 complex could be described as the result of intra-molecular electron transfer of the first electron from the Ti(3+)(H2O)6 complex to DNT molecule followed by coupled proton transfer from a water molecule from Ti(3+)(H2O)6 solvation shell to form an intermediate containing the -NO(OH) group. When the proton is transferred to the ortho or para nitrogroups the complex Ti(4+)(HO-)(H2O)5 forms and the first step of DNT reduction reaction is completed. Thus one proton from water molecule from Ti(3+)(H2O)6 solvation shell attaches without activation to para-nitrogroup or ortho-nitrogroup, respectively. In addition, both the DNT+para-Fe(2+)(H2O)5-ortho-(Ti3+)(H2O)6 and DNT+ortho-Fe(2+)(H2O)5-para-(Ti3+)(H2O)6 potential surfaces have been examined by B3LYP/SDD and B3LYP/6-31G* method. We found the global minimum energy structure to be a DNT+para-Fe(2+)(H2O)5-ortho-(Ti3+)(H2O)6 (Fig. 4) and also found a DNT+ortho-Fe(2+)(H2O)5-para-(Ti3+)(H2O)6 complex. We have shown that the observed difference in the regioselectivity of DNT reduction by Ti(3+) in acidic media in the presence of ions Fe(2+) is caused by the fact that the DNT-para-Fe(2+)(H2O)5 complex is more stable than the DNT-ortho-Fe(2+)(H2O)5 complex. As a result, the para nitrogroup of DNT is blockated by Fe(2+) and the major product becomes 2-amine-4-nitrotoluene. 1. V. N. Leibzon, L.V. Michalchenko, M. Yu. Leonova, and V. P. Gultyai Russ. Chem. Bull.

2005. V. 54, p. 1172.


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Figure 1. The optimized geometry of complex DNT.para-Fe(2+)(H2O)5

Figure 2. The initial geometry of complex {DNT ortho-Ti(III)(H2O)6}


159

Figure 3. The optimized geometry of complex {DNT ortho-Ti(III)(H2O)6}

Figure 4. The optimized geometry of Complex {DNT Fe(II)(H2O)5Ti(III)(H2O)6}


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The Singlet Oxygen Activation by Unique Transition-Metal Ion Structures

in Fe(2+)/ZSM-5 , Co(2+)/ZSM-5 , and Zn(2+)/ZSM-5 Zeolites: Formation of the Adduct between Activated Oxygen and Ethene

Vitaly Solkan and Jerzy Leszczynski

N. D. Zelinski Institute of Organic Chemistry, RAS, 119991 Moscow, Leninskii pr. 47, Russian Federation

Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, P.O. Box 17910, 1325 Lynch Str., Jackson, MS 39217, USA.

The participation of singlet oxygen in the oxidation of hydrocarbons on heterogeneous catalysts was discussed previously [1]. However, these results are inadequately reproducible, and until the present time there is no direct evidence of the participation of thermally generated 1ΔgO2 in oxidation reactions, although the possibility of the direct thermal excitation of oxygen to a singlet state was considered by Turro [2]. Previously [3], a sensitive chemiluminescence technique for the determination of extremely low concentrations of singlet oxygen in a gas phase was developed. This technique allowed us to perform continuous measurements of equilibrium 1ΔgO2 concentrations in air at relatively low temperatures and to examine non-equilibrium thermal desorption of 1ΔgO2 from zeolites. Recently, the first direct evidence of the non-equilibrium thermal production of 1ΔgO2 on zeollite samples (ZSM-5 exchanged with alkaline and alkalin-earth cations) was obtained by chemiluminescence technique [4]. We present herein a density functional study of the interaction of molecular oxygen with Fe(2+) (3d6), Co(2+) (3d7), and Zn(2+) (3d10), exchanged zeolite ZSM-5. The cation-exchange sites in ZSM-5 are represented by a variety of model clusters, including 6T-ring (7T cluster) and 10T-ring (T denoted tetrahedral Al and Si atoms). We use Becke’s hybrid three parameter nonlocal exchange functional (B3) combined with the dynamical correlation functional of Lee, Yang and Parr (LYP) at the level B3LYP/6-31G(d, p). Iron-and cobalt containing clusters were calculated with four or three unpaired electrons, respectively. For zinc clusters spin-restricted calculation were performed. Natural bond orbital (NBO) population analysis were carried out on the optimized structures to determine the occupancies (number of electrons assigned to orbitals in each atom) and charges of atoms in the adsorption complexes. The DFT calculations were done by using the Gaussian 03 program. The applied methodology allows us accurately determine structural properties and binding energies, especially when the bonding with oxygen is involved. The oxygen adsorption on the Zn(2+) site is notable weaker than on Fe(2+) and Co(2+) site , hence 1ΔgO2 is activated to a lesser extent on the former site. This correlates with the finding (Fig. 1) that the O-O/Fe and O-O/Co bond lengths is much longer than O-O/Zn bond length. In order to elucidate the reactivity of singlet dioxygen on Fe(2+), Co(2+), and Zn(2+) site in ZSM-5 we will focus on calculations using 7T cluster at DFT/B3LYP/6-31G(d,p) level. Analytical frequencies were calculated at the same level of theory, and the nature of the stationary points was determined in each case according to the number of the negative eigenvalues of the Hessian matrix. The activated oxygen molecule on Fe(2+) (3d6) ZSM-5, Co(2+) (3d7) ZSM-5, and Zn(2+) (3d10) ZSM-5, as a one-electron acceptor, binds strongly to the ethene molecule, resulting in formation of adduct (Fig. 2). Due to the electron withdrawing effect, electron transfer from the ethene molecule occurs and inducing subsequent stronger binding of the molecular oxygen to ethene. The changes in the geometrical parameters, charge distribution and dipole moment along


161

the reaction coordinate are discussed. Some relationships between the amount of transferred electron density and the changes in geometrical parameters and energies are given. Theoretical results obtained employing DFT method provide a mechanism of ethene oxidation based on electronic effects responsible for selective reactivity of singlet oxygen adsorbed on Fe(2+)/Co(2+)/Zn(2+)-site in ZSM-5 zeolite.

1. M. Che and A. J. Tench., Adv. Catal., 1983, 32, 1. 2. N. Turro, Tetrahedron, 1985, 41, 2089. 3. A. N. Romanov, Yu.N. Rufov, Zh. Fiz. Khim., 1998, 72, 2094. 4. A. N. Romanov, Y. N. Rufov, and V.N. Korchack, Mendeleev Commun. 2000, 117.

a)

b) c)

Figure 1. The exited state geometries of 1�gO2 molecule adsorbed on Fe(2+)-10T, (a), (R(OO)=1.316 A), Co(2+)-10T, (b), (R(OO)=1.326 A), and Zn(2+)-10T, (c), (R(OO)=1.292 A), clusters from main channel of ZSM-5 zeolite.


162

a) b)

c)

Figure 2. Optimized structures of adduct between ethene and activated oxygen molecule on Fe(2+)-7T, (a), Co(2+)-7T, (b), and Zn(2+)-7T, (c) clusters from the main channel of ZSM-5.


163

DFT Study of Nitrous Oxide Decomposition Catalysed by Ga+ Ion

Vitaly Solkan

N. D. Zelinsky Institute of Organic Chemistry, RAS, 119991 Moscow, Leninskii pr.47, Russian Federation

We present herein a density functional study DFT/B3LYP of the interaction of nitrous oxide with Ga(+)/ZSM-5. The cation-exchange sites in ZSM-5 are represented by a variety of model clusters, including 10T-ring (T denoted tetrahedral Al and Si atoms), where there are single framework Al atom in ring containing ten T atoms. The largest cluster, [AlSi9O16H20](-) Ga(+), is a complete 10-membered-ring picked out from the main channel of ZSM-5 zeolite and the terminal dangling bonds are satisfied by H atoms. For practical purpose, we employed a larger basis set only for the active site region, namely, the 6-31+G(d) basis set for NNO molecule and Ga atom; the 3-21G(d) basis set for O, Si, Al, atoms; and the 3-21G basis set for hydrogen atoms. A comparison of calculated vibrational frequencies and intensities in the region of N-O and N-N stretching vibrations for free NNO molecule and NNO adsorbed on Ga(+)-10T-ring indicate the very weak perturbation of adsorbed nitrous oxide. In accordance with DFT calculations, nitrous oxide should adsorb on Ga through its O end, but if N2O approaches a bare gallium site from its O end, the site can be oxidized readily. In order to elucidate the decomposition of nitrous oxide on Ga(+) site in ZSM-5 we will focus on calculations using 3T cluster at DFT/B3LYP/6-31+G(d) level. Analytical frequencies were calculated at the same level of theory, and the nature of the stationary points was determined in each case according to the number of the negative eigenvalues of the Hessian matrix. Moreover, the correct transition states have been confirmed by intrinsic reaction coordinate (IRC) calculations. An activation barrier at DFT/B3LYP/6-31+G(d) level, E≠ = +22.2 kcal/mol, exist for reaction 3T-Ga(I) +O=N=N = 3T-Ga(III)=O +N=N at T=298 K. The imaginary frequency associated with the transition state mode is 613i cm-1 along the r(O-N) reaction coordinate that connects reactants to products. The major difference between the transition state TS1 and the adsorbed state is the bending of the N-N-O bond angle from 180° in the adsorbed state to 139.8° in the transition state (Fig. 1). Besides a significant elongation of the O-N bond (1.47 A), with a commensurate decrease in the N-N bond distance (1.13 A), was observed. In the product state, the surface oxygen is located 1.68 Å apart from the Ga atom. Taking into account that the enthalpy of reaction is ΔHR = -31,0 kcal/mol, it follows that the reverse reaction is very slow. As a result, bare gallium sites are unlikely to exist under reaction conditions in the presence of N2O. Considering the known tendency of density functionals to underestimate barriers, it is worthwhile noting that at MP4(SDTQ)/6-31+G*//B3LYP/6-31+G* level the activation barrier is higher (+28.7 kcal/mol ). It is also important to note that the activation barrier for the elementary step of the first N2O decomposition on 3T-(Ga)+ (E≠ = 22.2 kcal/mol) is 2.7 kcal/mol lower than the activation barrier of the second N2O decomposition on 3T-(Ga=O)+ (E≠ = 24.9 kcal/mol) at DFT/B3LYP/6-31+G(d) level. The imaginary frequency associated with the second transition state mode is 585i cm-1 along the r(O-N) reaction coordinate that connects reactants to products (3T-(GaO2) (Fig. 2). The major difference between the transition state and the adsorbed state is the bending of the N-N-O bond angle from 180° in the adsorbed state to 143.9° in the transition state TS2 (Fig. 2). The normal coordinate vectors (arrows) of the vibrational modes, corresponding to the imaginary frequencies of TS1 and TS2 at 613i and 585i, respectively, show that, in both cases, the dominant motions involve the rupture of O-N bond. The calculated energy of the oxygen desorption from 3T-(GaO2) cluster (Fig. 3) ΔH (298 K)=+46.5 kcal/mol and ΔG(298 K)=35.9 kcal/mol is


164

than the barriers of oxidation reactions. In accordance with DFT calculations a significant elongation of the O-O bond (1.631 A) is observed in 3T-(GaO2) cluster. Financial support of this research by RFBR (project 05-03-33103) is gratefully acknowledged.

Figure 1. The optimized geometry of TS1at DFT/6-31+G* level

Figure 2. The optimized geometry of TS2 at DFT/6-31+G* level


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Figure 3. The optimized geometry of dioxygen complex 3T-(GaO2)


166

DFT Study of Ethane Decomposition over Zn-ZSM-5

Vitaly Solkan


Very recent experiments using a DRIFT method demonstrated that an ethane molecule adsorbed by zinc cations in ZnZSM-5, reveals unusual spectra of adsorbed C2H6 species. In addition to the weakly perturbed narrow bands in the region of C-H stretching vibrations, these spectra exhibit a very intense broad IR band with a frequency that is more than 200 cm-1 lower than those of the C-H stretching vibrations of gaseous or physically adsorbed ethane [1]. We present herein a density functional study of the interaction of ethane with Zn(2+)/ZSM-5. The cation-exchange sites in ZSM-5 are represented by a variety of model clusters, including 10T-ring (T denoted tetrahedral Al and Si atoms), where there are two framework Al atoms in rings containing ten T atoms. The largest cluster, [Al2Si8O16H20](2-) Zn(2+), is a complete 10-membered-ring picked out from the main channel of ZSM-5 zeolite and the terminal dangling bonds are satisfied by H atoms. Quantum chemical calculations of the transition-state structures and minimum energy structures on the PES were performed, using DFT/B3LYP functional. For practical purpose, we employed a larger basis set only for the active site region, namely, the 6-31G(d,p) basis set for ethane molecule and Zn atom; the 3-21G(d) basis set for O, Si, Al, atoms; and the 3-21G basis set for hydrogen atoms. A comparison of calculated vibrational frequencies and intensities (Int) in the region of C-H stretching vibrations for free ethane molecule (2923 (0), 2924 (57), 2976 (0), 2976 (0), 2999 (70), 2999 (70)) and ethane adsorbed on Zn(2+)-10T-ring (Fig. 1) (2715 (176), 2734 (512), 2767 (63), 2966 (34), 2990 (12), 3030 (10)) indicate the very strong perturbation of adsorbed ethane. Moreover, a comparison of calculated Raman intensities (Int) for free ethane molecule (2923 (216), 2924 (0), 2976 (132), 2976 (132), 2999 (0), 2999 (0)) and ethane adsorbed on Zn(2+)-10T-ring (2715 (60), 2734 (604), 2767 (441), 2966 (205), 2990 (65), 3030 (48)) indicate a very strong polarizability of the corresponding vibrational mode of adsorbed ethane. In accordance with DFT calculations, ethane should adsorb on Zn through its CH3 end. It is concluded that one of these strongly polarized vibrations are closely connected with the subsequent heterolytic dissociation of ethane at moderately elevated temperatures, resulting in the formation of acidic hydroxyl groups and zinc ethyl fragments. Activation of ethane over this site with dissociation of a C-H bond yields the ethyl-Zn(I) attached to 10T-zeolite cluster. At B3LYP/6-31G(d,p) level was calculated the TS for the decomposition of ethane on Zn(2+)-10T cluster. The changes in the geometrical parameters, charge distribution and dipole moment along the reaction coordinate are discussed. Financial support of this research by RFBR (project 05-03-33103) is gratefully acknowledged.

1. V. B. Kazansky and E. A. Pidko, Phys. Chem. B, 109 (6), 2103 -2108, 2005


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Figure 1. The optimized geometry of complex 10T-(Zn-CH3CH3) at DFT/B3LYP level


168

DFT Study on the Carbon Monoxide Interaction with Small Metal Cluster Co4, Rh4, Pt4, Co3Pt, Rh3Pt Supported on Co(II)/Rh(II)-

ZSM-5 and Cluster Pt4 Supported on Co(I)/Ni(I)-ZSM-5

Vitaly Solkan


Transition metals, with their multitude of oxidation states, are among the most important industrial catalysts, and understanding the mechanisms of catalytic processes on an atomic scale is a topic of considerable current interest. Small metal clusters, with their varied structures and varying degrees of coordinative saturation of the individual atoms, are therefore very useful models for the catalytic process [1-3]. In numerous catalysts at least one of the zeolite-supported elements is completely reduced to the zerovalent state. As a result, small clusters or even isolated atoms of the transition metal are formed. We present herein a density functional study of the interaction of cation-exchanged form of ZSM-5 with different embedded clusters which contain four metal atoms (M4) namely: Co4, Rh4, Pt4, and mixed cluster Co3Pt, and Rh3Pt. The cation-exchanged sites in Co(II)/Rh(II)-ZSM-5 and Co(I)/Ni(I)-ZSM-5 are represented by a variety of model clusters, including 6T-ring (7T cluster), and 10T-ring (T denoted tetrahedral Al and Si atoms), where there are one or two framework Al atoms in rings containing six or ten T atoms. The largest 10T-cluster is picked out from the main channel of the ZSM-5 zeolite. All the calculations were performed using nonlocal hybrid density functional theory (B3LYP functional). The Gaussian-03 program package was used in this study. For practical purpose, we employed a larger basis set CEP-31G only for the metal cluster, the 3-21G(d) basis set for Si, Al atoms, and the 3-21G basis set for oxygen and hydrogen atoms. We report in detail the calculated results for 7T-Co(II)/Rh(II) M4 and 7T-Co(I)/Ni(I) M4 clusters. The geometry optimization of the studied 7T-Co(II)/Rh(II) M4 and 7T-Co(I)/Ni(I) M4 clusters has been performed only for active site including M4-moiety. The NBO charges on the M4 cluster were calculated for the structures obtained by optimization calculations. To further probe the nature of the catalytic site, we analyzed the energetics and the nature of electronic states in various clusters and carried out a Mulliken population analysis of the total charge. To investigate M4 –CO interaction, consider how an approaching CO is adsorbed by the clusters. In every case, we found that the CO molecule prefers to bind with the C end towards the molecule (Fig.1-Fig. 4). The adsorption energies (Eads) of CO on the different model cluster are calculated as the energy difference between the sum of the total energies of the cluster 7T-Co(II)-M4 and that of the free CO molecule and the total energy of the adsorbate system. Stretching frequencies of the C–O bond were calculated for Pt4, and mixed cluster Co3Pt, and Rh3Pt. The calculated harmonic stretch for CO shows a considerable shift (100-200 cm-1) compared to the gas phase and corresponds to the enhanced CO bond length. We also report how the adsorption energy, the geometrical parameters, and C–O stretching frequency of chemisorbed CO may depend on the charge of the platinum cluster. This accounts for the observation that the charged [4] and some supported [1] clusters are better catalysts than the corresponding neutral clusters. The high spin Pt4 cluster with multiplicities 2MS+1=9 anchored on 7T-Co(II) cluster is unique among all the clusters studied, reacting more efficiently than the corresponding low spin Pt4 cluster. The unique catalytic and chemisorptive properties of these clusters have been attributed to the small cluster size, as well as to possible interactions of these clusters with the zeolite support.


169

The intriguing question we have been attempting to address in our research is the following: does exist transition metal cluster M4-cation adduct in high-silica zeolite ZSM-5. Our modeling calculations at DFT/B3LYP level show clearly that transition metal cluster M4-cation adduct supported on Co(II)/Rh(II)-ZSM-5 and Co(I)/Ni(I)-ZSM-5 zeolite are stable and bearing the high negative charge. 1. U. Heiz and W.D. Schneider, J. Phys. D Appl. Phys. 33 (2000), p. R85. 2. V.E. Bondybey and M.K. Beyer, J. Phys. Chem. A 105 (2001), p. 951. 3. D.K. Bohme and H. Schwarz, Angew. Chem. Int. Ed. 44 (2005), p. 2336. 4. D.M. Cox, R.O. Brickman, K. Creegan, et al., Z. Phys. D 19(1991) 353.

a) b)

Figure 1. The optimized geometry of complex 7T-Co(II)-Pt4-CO for spin states with multiplicities (a) 2MS+1=4 ; b) 2MS+1=12 at DFT/B3LYP level

Figure 2. The optimized geometry of complex 7T-Rh(II)-Rh3Pt-CO


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Figure 3. The optimized geometry of complex 7T-Co(I)-Pt4-CO

Figure 4. The optimized geometry of complex 7T-Ni(I)-Pt4-CO


171

Singlet Oxygen Activation by Unique Metal Ion Structures in Zn(2+)/ZSM-5 Zeolites:

Formation of a Complex between Singlet Oxygen and Metyl-Zn-Z

Vitaly Solkan

N. D. Zelinski Institute of Organic Chemistry, RAS, 119991 Moscow Leninskii pr. 47, Russian Federation

The first excited state of molecular oxygen, namely, 1ΔgO2 , has been intensively investigated for nearly 45 years. Traditionally, it is referred to as singlet oxygen to distinguish it from the triplet ground state of dioxygen, which lies 22.5 kcal/mol lower in energy. The participation of singlet oxygen in the oxidation of hydrocarbons on heterogeneous catalysts was discussed previously [1]. However, these results are inadequately reproducible, and until the present time there is no direct evidence of the participation of thermally generated 1ΔgO2 in oxidation reactions. Recently, the first direct evidence of the non-equilibrium thermal production of 1ΔgO2 on zeollite samples (ZSM-5 exchanged with alkaline and alkalin-earth cations) was obtained by chemiluminescence technique [2]. We present herein a density functional study of the interaction of molecular oxygen and methane with Zn(2+) (3d10), exchanged zeolite ZSM-5. The cation-exchange sites in ZSM-5 are represented by a variety of model clusters, including 6T-ring (7T cluster) and 10T-ring (T denoted tetrahedral Al and Si atoms). In case of 7T-cluster the six-membered ring composed of two five-membered rings from the walls of the straight channels of the ZSM-5 zeolite was chosen as a possible site for Zn(2+) localization. This model was selected since it has been discussed to explain unusual catalytic and chemical properties of bivalent iron exchanged into highsilica zeolites. The quantum chemical calculations were carried out within the gradient-corrected density functional theory (DFT) using the GAUSSIAN-03 program. We use Becke’s hybrid three parameter nonlocal exchange functional (B3) combined with the dynamical correlation functional of Lee, Yang and Parr (LYP) at the level B3LYP/6-31G(d,p). Natural bond orbital (NBO) population analysis was carried out on the optimized structures to determine the occupancies (number of electrons assigned to orbitals in each atom) and charges of atoms in the adsorption complexes. The applied methodology allows us accurately determine structural properties and binding energies, especially when the bonding with oxygen is involved. The methane adsorption on the 7T-Zn(2+) site is notable weaker than on 10T-Zn(2+) site, hence methane is activated to a lesser extent on the former site. On the other hand, the dissociative methane adsorption was observed directly by appearance of DRIFT bands from the hydroxyls and metyl-zinc in case of highsilica ZSM-5 zeolite. In order to elucidate the reactivity of singlet dioxygen and methyl-zinc in ZSM-5 we will focus on calculations using 7T cluster at DFT/B3LYP/6-31G(d,p) level. Analytical frequencies were calculated at the same level of theory, and the nature of the stationary points was determined in each case according to the number of the negative eigenvalues of the Hessian matrix. The results of calculations indicate that the singlet oxygen molecule, as a one-electron acceptor, binds strongly to the 7T-Zn-CH3 cluster, resulting in formation of the complex (Fig. 1). Once the complex is formed, it can be converted into an oxidized species (peroxo) (Fig. 2). The changes in the geometrical parameters, charge distribution and dipole moment along the reaction coordinate are discussed. Some relationships between the amount of transferred electron density and the changes in geometrical parameters and energies are given. We expect that this reaction will contribute towards the oxidation of CH4 into CH3OH. Theoretical results obtained employing DFT method provide a


172

mechanism of methane oxidation in a Zn-doped zeolite catalyst based on electronic effects responsible for selective reactivity of singlet oxygen. Financial support of this research by RFBR (project 05-03-33103) is gratefully acknowledged.

1. M. Che and A. J. Tench., Adv. Catal., 1983, 32, 1. 2. N. Romanov, Y. N. Rufov, and V.N. Korchack, Mendeleev Commun. 2000, 117.

Figure 1. Optimized structures of the complex between singlet oxygen molecule and 7T-Zn-CH3

cluster.

Figure 2. Optimized structures of the peroxo product 7T-Zn-O-O-CH3


173

Modeling Excess Electrons Bound to Water Clusters

Thomas Sommerfelda, Kenneth D. Jordanb, and Albert DeFuscob

(a) Department of Chemistry and Physics, Southeastern Louisiana University SLU 10787, Hammond, LA 70402

(b) Department of Chemistry, University of Pittsburgh 209 Parkman Ave., Pittsburgh, PA 15260

Cluster anions can be divided into (A) clusters of neutrals and anions and (B) clusters of neutrals and electrons, where the extra electron is not attached to a specific monomer, but is bound in a collective manner. In this paper we consider water cluster anions as prominent examples of the latter class.

Even so it seems counterintuitive, owing to the distributed character of the excess electron, electron correlation is of greater importance in class (B) clusters, and from an electronic structure viewpoint these represent the far greater challenge. For example, in typical (H2O)6

- clusters roughly 40% of the total electron binding energy stems from electron correlation. For some clusters the correlation contribution is 100%, implying a breakdown of the one-particle picture for the anion. The correlation contribution varies strongly with the electron binding motif, and we discuss electron correlation in dipole-bound, cavity, and network permeating states (examples for these three binding motifs are shown in the three figures).

Since ab initio electronic structure methods are very costly, models for water cluster anions are needed to explore potential energy surfaces or to include finite temperature effects. Models for water cluster anions combine in general a water-water model force field with a one-electron Hamiltonian describing the interaction of the excess electron with the water cluster. The overall


174

quality of the model depends on the quality of both of its ingredients, i.e., on the quality of the water-water force field and on the quality of the one-electron Hamiltonian. Here we present a one-electron many-body model Hamiltonian where electron-water dispersion is included via quantum Drude oscillators on each monomer

HD r ,R1 ,R2 ,... He r Hosc R1 ,R2 ,... V r ,R1 ,R2 ,... .

We compare the many body Drude Hamiltonian to local one-electron potentials, and

investigate the influence of different water-water force fields used in conjunction with the Drude Hamiltonian. In particular, we find that local one-electron potentials lead to significant over-binding of the excess electron in situations where electrostatic effects are not dominating. Regarding the choice of water model, it turns out that high quality treatments of intermolecular polarization and intermolecular repulsion are needed to reproduce the energetic ordering of (H2O)6

- clusters. The reasons why other, more economical water models fail are discussed.

We then use the Drude model to perform finite-temperature parallel-tempering Monte Carlo simulations on (H2O)6

-. The huge impact of the water-water force field is clearly visible as drastically different photoelectron spectra are predicted from simulations using different force fields. Regarding the interpretation of experiments on cluster beams, our results suggest that at least for (H2O)6

- the experimentally observed cluster is not the minimal energy structure, and that there are in fact many isomers lower in energy than the experimentally observed species. Implications of the high isomer density found in the simulations for future theoretical and experimental work is discussed.


175

Enthalpies of Formation of TNT Derivatives by Homodesmotic Reactions

Amika Sood, Patricia Honea, and David H. Magers


TNT (2,4,6-trinitrotoluene) is a well known and widely used explosive. In the current study, we focus on the computation of the standard enthalpy of formation of TNT and similar aromatic compounds by homodesmotic reactions. In homodesmotic reactions the number and types of bonds and the bonding environment of each atom are conserved. We first computed standard enthalpies of formation for certain smaller aromatics whose enthalpies are known to validate our method. We obtained excellent results for these systems with the exception of 3-nitroaniline for which our computed enthalpy was almost 3 kcal/mol too high. We then used different homodesmotic reactions to compute the standard enthalpies of formation of the TNT derivatives. Results are consistent with the exception of those obtained from reactions that utilize the experimental enthalpy value for 3-nitroaniline. Better convergence is obtained with our theoretical value for this system, leading us to believe that the reference value is incorrect. We gratefully acknowledge support from the Mississippi College Catalysts, the alumni support group of the Department of Chemistry & Biochemistry.


176

Effect of Axial Ligation on Metalloporphyrin and Phthalocyanine Geometry and Spectra

Nicole Strauss, Erica Baldwin, and William A. Parkinson

Southeastern Louisiana University, Room 123 Pursley Hall, Hammond LA USA 70402

Computational studies are used to provide insight into the metalation of porphyrins and phthalocyanines. Structures optimized via perturbative and density functional methods are compared and contrasted with respect to geometry parameters including ring stain and ring diameter. Models for ring-to-metal bonding and metal-to-ring backbonding are discussed. Natural orbital studies are employed to help elucidate the ionic vs. covalent nature of metalation. Axial ligation is also investigated. The energetics of cis-and trans- octahedral complexes is presented. Finally, calculations and molecular orbital theory arguments are used in an attempt to rationalize low- and high-spin electronic configurations in octahedral and tetragonally distorted metal-ring complexes.

Porphyrins and phthalocyanines have demonstrated efficacy as photosensitizers in Photodynamic Therapy (PDT). Theoretical models are employed to build quantitative structure-activity relationships for the photochemical properties of these systems, particularly with regard to their functionalization, metalation, and axial ligation. Ab-initio CI, Time-Dependent Density Functional Theory (TDDFT) and ZINDO/S Singly Excited Configuration Interaction (CIS) methods are used to predict both gas-phase and solvated singlet and triplet excitation spectra. This information is used to gain insight into the energetics of intersystem crossing and singlet oxygen production.


177

Computational Studies of Nanoscale Self-Assembly: A New Class of Supramolecular Wires

Bobby G. Sumpter

Computer Science and Mathematics Division and Center for Nanophase Materials Sciences Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA

In recent years, the fields of chemistry, physics, biology, and materials science have been combined to produce a myriad of nanomaterials with unique properties. For example, soft materials composed of colloids, surfactants, proteins, organic molecules, and block copolymers containing nanometer size structures possess properties that are strikingly different from those of corresponding unstructured materials. Soft materials as basic building blocks for developing nanostructures and devices present the advantage of chemical diversity and that under suitable conditions their constitutive molecules can self-assemble to form stable structures. Understanding and controlling the forces that drive the self-assembly processes could lead to new possibilities in the design of functional materials. In this talk, results from electronic structure calculations and experimental characterization (TEM, SEM, DSC) will be presented to show how directional non-covalent interactions lead to efficient self-assembly of functionalized 1-aza-adamantanetrione molecules into robust one-dimensional architectures. The key to achieving self-assembly stems from the saturated tricyclic core of a 1-aza-adamantanetrione molecule that possesses one nitrogen donor atom and three carbonyl acceptors at the opposite ends of a rigid all-carbon framework. We demonstrate how shape and functionality confer unprecedented molecular-level tunability in the structure and its functionality. To taht end we have examined the evolution of the electronic structure due to self-assembly (one molecule, dimer, etc.) into a 1-D wire. Our results show delocalization of the frontier molecular orbitals through the saturated tricyclic cores that span the entire system. The electronic band structure for the 1-D wire also reveals significant dispersion and can be tuned from the insulating regime to the semiconducting regime by suitable chemical functionalization of the core. The theoretical understanding of this new class of supramolecular structures sets the stage for the tailored design of novel functional materials.


178

Conventional Strain Energy and Sigma Delocalization in Small Heterocycles of Carbon and Germanium

Lyssa A. Taylor and David H. Magers


The conventional strain energies for three- and four-membered heterocycles of carbon and germanium are determined within the isodesmic, homodesmotic, and hyperhomodesmotic models. These include germacyclopropane, digermacyclopropane, germacyclobutane, 1,2-digermacyclobutane, 1,3-digermacyclobutane, and trigermacyclobutane. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies are computed for all pertinent molecular systems using SCF theory, second-order perturbation theory (MP2), and density functional theory. The DFT functional employed is Becke’s three-parameter hybrid functional using the LYP correlation functional. Two basis sets, both of triple zeta quality on valence electrons, are employed: 6-311G(d,p) and 6-311+G(2df,2pd). Additionally, single-point fourth-order perturbation theory and coupled-clustered calculations using the larger of the two basis sets at the optimized MP2 geometries were used to investigate the effects of higher-order electron correlation. Cross-sections of the electron density in the plane of the ring for each of the three-membered rings were plotted to observe how the electron density is distributed in the sigma bonds of the different systems.

Results are compared to those obtained for heterocycles of carbon and silicon to determine if germanium has the same effect on the conventional strain energy of cyclopropane and cyclobutane as silicon which reduces the conventional strain energy of cyclobutane, but increases the conventional strain energy in cyclopropane. We gratefully acknowledge support from the Mississippi College Catalysts, the alumni support group of the Department of Chemistry & Biochemistry.


179

A Self–Consistent Coupled–Cluster Solvent Reaction Field Method

Kanchana S. Thanthiriwatte and Steven R. Gwaltney*

Department of Chemistry, Center for Environmental Health Sciences, and HPC2 Center for Computational Sciences, Mississippi State University

Mississippi State, MS 39762, USA.

We report the theory for and the implementation of an implicit Onsager–type solvent reaction field method at the coupled-cluster singles and doubles (CCSD) level. In this model a solute molecule is placed in a spherical cavity, and the outer solvent is represented by dielectric continuum medium which is characterized by the dielectric constant of the solvent. The reaction field is introduced to the system by using the multipole moment expansion of the electronic structure of the solute molecule and the dielectric constant of the solvent medium.

To begin the calculation, a Hartree–Fock (HF) self–consistent reaction field calculation is performed. These orbitals are used to solve the CCSD equations in the presence of the HF solvent reaction field. After the CCSD amplitudes (T and Λ) are calculated, the CC density, including orbital response, is determined. This correlated density is then used to calculate a new solvent reaction field. In order to ensure that both the orbitals and the amplitudes feel the effect of the correlated solvent reaction field, the procedure is repeated using the CC solvent response until reaction field converges. What makes this implementation unique is that the MOs and the CC equations are all solved self-consistently.

The SC–CCSRF code has been implemented in a development version of the Q-Chem 3.0 quantum chemistry package. The conformational equilibrium and the rotational barriers of 1,2-dichloromethane are calculated in vacuum and in different solvents. The calculated results are compared with experimental values. In addition, the solvent effects on the energetics of the nitration of benzene are reported.


180

Molecular Wrapping and Mechanical Strength in Lignin-CNT-Epoxy Composites

D. Thomas1, J. Edwards1, D. Bryan1 and R. Parker2

1Department of Chemistry, Florida A& M University, Tallahassee, FL, USA 2Ubiquitous Technologies Inc., Research and Technolgy Center, Tallahassee, FL, USA

This project employed the use of AFM, SEM, and molecular modeling analysis to determine morphological consequences of sonication time on lignin particle size and the joint sonication of lignin with carbon nanotube (CNT) during prefabrication (Figure 1). Preliminary work using an NPT ensemble molecular dynamics of a model epoxy, biomolecule, CNT system shows significant wrapping of the polymers around the CNT (Figure 2). The work presented here will yield a more fundamental understanding of the interactions between lignin and CNT. Currently, lignin provides a significant increase in mechanical strength to CNT-Epoxy nanocomposites (Figure 3). This study provides structural analysis to support the role of lignin in improving the mechanical properties of CNT-Epoxy nanocomposites. NPT and NVT ensemble dynamic simulations were conducted to examine chain size effects on the wrapping of lignin with the CNT. Additionally, this study will provide a pathway to greater details regarding improvements in mechanical strength.

Figure 1. Scanning Electron Micrograph of Lignin Particle embedded in buckypaper-like matrix

Figure 2. Molecular model of an oligomer chain of lignin interacting with a portion of a CNT molecule


181

Figure 3. Impact of lignin-CNT association using Tensile Strength

strength(MPa) @ 50=deg

3,315

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* = Lignin infiltrated


182

Interaction of DNA Bases with Amino Acids by ab Initio Calculations

Patrina C. Thompson, Glake A. Hill, Jerzy Leszczynski

Jackson State University, Jackson, MS

Potential structures of guanine and aspartic acid complexes have been calculated to establish optimal hydrogen bonding patterns between nucleotide bases and particularly guanine. All complexes have been fully optimized at Density Functional Theory (B3LYP) and Moller-Pleset Perturbation Theory (MP2) levels using different but small basis sets. The structures were calculated at DFT level in 3-21G basis set and a 6-31G(d) basis set. The MP2 calculations were performed using the same basis set as the DFT method. The IR spectra was calculated and compared with experimental data. The energetically favored structure will be discussed.


183

Correlated Transition State for the Reaction of Phenol with Formaldehyde

1Julaunica Tigner, 2Erica King, and 1Melissa S. Reeves

1Department of Chemistry, Tuskegee University, Tuskegee AL, 36088 2Miles College, Birmingham, AL 36088

The reaction of phenol with formaldehyde produces a resin with many industrial uses due to its mechanical strength and heat resistance. The initial reaction between phenol and formaldehyde can be carried out under basic aqueous conditions, producing a resole. We present a correlated transition state for the para attack of formaldehyde on the phenol, which required the presence of both a solvent field and an explicit water molecule. (Funding provided by NSF/REU and NSF/IGERT grants at Tuskegee University)


184

QSAR Modeling of Toxicity for Nitrobenzene Derivatives towards Rats: Comparative Analysis by MLRA and Optimal Descriptors

A.A. Toropov, B.F. Rasulev and J. Leszczynski

Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, P. O. Box 17910, Jackson, MS 39217, USA

Quantitative structure-activity relationships have been developed for a set of 28 benzene derivatives, where 26 of them are nitroaromatic compounds. LD50 oral toxicity for rats of these compounds expressed in log units have been modeled by multiple linear regression analysis (MLRA) based on descriptors generated by DRAGON software and optimal descriptors. Twenty eight benzene derivatives have been split into training (n=14) and test (n=14) sets. In case of the MLRA two-variable model has the best predictive potential. Comparison of the quality of MLRA and optimal descriptor models show that the predictive potential of one-variable model based on optimal descriptor is better than two-variable MLRA model.


185

Multicentered Integrated QM:QM Methods for Weakly Bound Clusters: An Efficient and Accurate 2-Body:Many-Body Treatment

of Hydrogen Bonding and Van Der Waals Interactions

Gregory S. Tschumper

Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677-1848 USA

An efficient integrated QM:QM technique for the description of weakly bound clusters is presented. The computational technique described here takes advantage of the recently developed multicentered (MC) integrated QM:QM methods and reliably describes hydrogen bonding and van der Waals interactions by treating all 2-body interactions with a high-level QM method and the many-body interactions with a low-level QM method. Even for small clusters of He, Ne, HF, and water, the MC QM:QM methods are typically 1–3 orders of magnitude faster than the high-level method while introducing an error of less than 1% in the interaction energy.


186

Heterocomplexes of DyBr3 with Alkali Halides: A Computational Study of Their Structures and Relative Stabilities

Zoltán Varga and Magdolna Hargittai

Structural Chemistry Research Group of the Hungarian Academy of Sciences, Eötvös University Pf. 32, H-1518 Budapest, Hungary

Interest in the salt mixtures of lanthanide halides with alkali halides is due to their effect on the performance of metal halide lamps. The mixture of dysprosium halides and some alkali halides is especially favored because of their excellent color rendition and high luminous efficiency.1 These complexes are the objects of our present study.

Supposing a connection between the two metal halide units through halogen bridges, there are four basic structures that can be envisioned for them, depending on the number of these bridges.2 From those, the monodentate structure – with one halogen bridge – is only stable for the fluorides and even for those, it is energetically about 100 kJ/mol higher in energy than the stable structures. The tetradentate structures are all third-order saddle points. The two remaining structures, the bi- and tridentate ones are both stable.

Figure 1. The bidentate and tridentate structures of the AlkDyBr4 complexes

All previous computations of these types of complexes utilized an effective core potential for the lanthanide atom, in which the 4f electrons were part of the core. Although these f electrons, indeed, do not participate in building up the molecular orbitals, they do have influence on the resulting structures. Therefore, we used a different type of pseudopotential, in which the 4f electrons are part of the valence shell. We used comparable basis sets for the other atoms of the molecules to get a balanced basis set.

Having the 4f electrons in the valence shell means an open electron-shell system, for which different occupations of the f orbitals are possible. For the AlkDyX4 system with 9 f electrons this results in 21 possible occupations of f orbitals. Many of these structures are close to each other energetically, thus, at the high-temperature working condition of a metal halide lamp, several of these structures might be present in noticeable amounts. Figure 2 shows the energy distribution of different electronic states for the bidentate KDyBr4 system.


187

Figure 2. Energy distribution of molecules in different electronic states of KDyBr4

For LiDyBr4 the bidentate structure appears to be more stable than the tridentate one but only by about 2 kJ/mol. For all the other complexes, the tridentate structure is more stable, with increasing energy difference between them toward the larger alkali metals. This situation, however, refers only to the computations at zero Kelvin. With increasing temperature the bidentate isomer gains stability. How soon and to what extent this happens, depends on both the alkali atom and the level of the computation. However, it seems certain that, at the working condition of a metal halide lamp, the bidentate isomer is more stable than the tridentate one.

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Figure 3. Relative abundance of the two isomers of KDyBr4 at different temperatures Acknowledgement. Our research is supported by the Hungarian Scientific Research Fund (Grant OTKA K 60365). References 1. Hildenbrand, D.L.; Lau, K.H.; Baglio, J.W.; Struck, C.W. J. Phys. Chem. A 2005, 109, 1481;

Hilpert, K.; Miller, M. J. Electrochem. Soc. 1994, 141, 2769. 2. Varga, Z.; Hargittai, M. Struct. Chem. 2006, 17, 225.


188

Theoretical Study on the Radical-Radical Reaction of CH3S with ClO

Wenliang Wanga, Yan Liu a,b, Weina Wang a

aKey Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Materials Science, Shaanxi Normal University, Xi’an 710062, People′s Republic of China

b Chemistry department, Weinan Teachers College, Weinan 71400, People′s Republic of China

The Methoxy radical (CH3O) is an important intermediate in atmospheric and combustion chemistry. Practical importance of CH3O in astronomic, atmospheric, and combustion have been studied wildly [1,2]. The reaction of CH3O with ClO radical has already been the subject of experimental and theoretical investigation [3,4]. Theoretically, Wang et al.[4] suggested a mechanism for the reaction CH3O+ClO via three channels and the formation of HOCl+CH2O to be the major reaction: CH3O+ClO→ HOCl+CH2O ΔE≠=2.37 kJ·mol-1 ΔH=-308.76 kJ·mol-1 (1)

→ CH2O2+HCl ΔE≠=132.85 kJ·mol-1 ΔH=-120.51 kJ·mol-1 (2) → CH3ClO+O2(1Δ) ΔE≠=361.01 kJ·mol-1 ΔH=-103.97kJ·mol-1 (3)

Thus the channel (1) is the major reaction pathway. In addition, the direct addition of both species leads to adducts CH3OClO and CH3OOCl which could also be energetically stable.

The methylthio radical (CH3S), sulfur analogue of CH3O, is an important intermediate in atmospheric oxidation of organic sulfur compounds, such as dimethyl sulfide (CH3SCH3), methanethiol (CH3SH), and dimethyl disulfide (CH3SSCH3)[5-7]. In this work, the mechanism of the double radicals reaction CH3S with ClO in gas phase has been investigated theoretically by means of the Gaussian 03 series program [8].

The optimized geometries of reactans, intermediates, transition states and products at B3LYP/6-311+G(3df,3pd) level of theory are displayed in Figure 1, and potential energy surface (PES) of the CH3S+ClO reaction at QCISD(T)/6-311+G(d,p) level of theory is depicted in Figure 2. Table 1 compiles the numerical data corresponding to reaction enthalpy, and activation energy of all reaction pathway. Several important results can be drawn from the calculations: (1) The reaction proceeds through addition the S atom of CH3S attacks the O or Cl atoms of ClO to form the intermediates IM1(CH3SClO) or IM2(CH3SOCl). The IM1 and IM2 undergoes different channels forming five products P1(HOCl+CH2S), P2[(ClO)CH2(SH)], P3[CH3S(O)Cl], P4(HCl+CH2SO) and P5(SO+CH3Cl). (2) All the channels are exothermic reactions, and P1 and P3 are the main products from the viewpoint of kinetics and thermodynamics, while P2, P4, P5 are the minor products. (3) NBO methods shows that the S atom of CH3S is prefer to attacks the O atom than Cl atom of ClO, and the interaction of O−S bond is strong in P3 while C−O bond is weak in P2.


189

The calculated results presented here are expected to be useful for gaining insight into the mechanism of the title reaction that could be related to the combustion processes of sulfur-containing and chlorine-containing compounds and to assist in further laboratory identification of the products.

Figure 1 Optimized geometries for the reactants, intermediates and products at the B3LYP/6-

311+G(3df,3pd) level of theory(bond lengths in nm )


190

Table 1 Activation energy (ΔE≠ ) of the rate-determining step and reaction enthalpies (ΔH)of various reaction pathways

Reaction pathway ΔE≠/(kJ⋅mol-

1) ΔH/(kJ⋅mol-1)

(1) CH3S+ClO→HOCl+CH2S (P1) -13.29 -155.85 (2) CH3S+ClO→(ClO)CH2(SH) (P2� 298.85 -227.66 (3) CH3S+ClO→CH3S(O)Cl (P3) 45.09 -369.97 (4) CH3S+ClO→CH2SO+HCl (P4) 164.55 -316.48 (5) CH3S+ClO→ CH3Cl+SO (P5) 289.53 -170.96

Figure 2 Potential energy profile of the title reaction at the QCISD(T)/6-311+G(d,p)//B3LYP/6-

311+G(3df,3pd) level References

[1] X. M. Pan, H. Sun, Z. M. Su, R. S. Wang, et al., Chem. Phys. Lett. 409(2005), 98 [2] M. Schnell, M. Muhlhauser, S. D. Peyerimhoff, J. Phys. Chem. A, 108(2004), 1298 [3] V. Daele, G. Laverdet, G. Poulet, Int. J Chem. Kinet. 28(1996), 589 [4] M. Zhao, P. J. Liu, R. S. Wang, et al., Acta Chim. Sinica 63(2005) 1013 [5] L. Barnes, J. Hjorth, N. Mihalopoulos, etal.,Chem. Rev., 106(2006), 940 [6] S. Y. Chiang, Y. P. Lee, et al., J. Chem. Phys., 95(1991), 66 [7] S. Hatakeyama, H. Akimoto, et al., J. Phys. Chem., 87(1983), 2387 [8] M. J. Frisch, G. W. Trucks, J. A. Pople, et al.,Gaussian 03, Pittsburgh, PA, 2003

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TS7


191

Theoretical Study and Rate Constant Calculation on the Hydrogen Abstraction Reaction of C2H3 with CH3F

Wenliang Wanga, Lixia Feng a,b, Weina Wang a

aKey Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Materials Science, Shaanxi Normal University, Xi’an 710062, People′s Republic of China

bChemistry department, Taiyuan Teaching College, Taiyuan 030012, People′s Republic of China

Hydrofluorocarbons(HFCs)have been considered as new and potential refrigerant and flame suppressants due to the characters of effective, nontoxic and have low global environmental impact, and the commercial productions of HFCs have come into widespread use in a variety of industrial applications as the interim replacements for the ozone-destroying chlorofluorocarbons(CFCs)and halon fire suppression agents[1,2]. With the popularization of the application and the increasing of accumulation in the atmosphere, the research on the combustion property of HFCs has gradually attracted much attention. As the simplest HFCs model, the micro-reaction dynamics data of CH3F is very helpful to better understand the reaction mechanism in flame and combustion chemistry and to estimate the atmosphere lifetime. On the other hand, vinyl radicals(C2H3)are recognized as key intermediates in hydrocarbon combustion processes, with the elementary reaction of C2H3 influencing both the decay rate and products of some chain reactions in the overall combustion processes. However, the task to study the reactive intermediate C2H3 is still challenging because it is difficult to generate cleanly in experiment. Up to now, some experimental and theoretical investigations have been performed on the C2H3 reaction with different atoms, radicals and molecules. However, as far as we know, no direct kinetic measurement on the hydrogen abstraction reaction of C2H3 with CH3F is reported in the literature, only Burgess et al. [13] present the simple Arrhenius form of the title reaction k=1.5×1011exp(-5184/T), which is obtained by analogy to the activation energy and the pre-exponential factor of the analogous hydrogen abstraction reaction of CH3 with CH3F in a narrow temperature range 466-604 K. Such estimation is very rough, and it can not reveal exactly the dynamic feature of the title reaction. Hence, we carry out the direct dynamics study on the reaction of C2H3 with CH3F in present paper.

The geometries and harmonic vibrational frequencies of all stationary points are calculated by using the B3LYP/6-311+G(d,p). At the QCISD(T)/6-311++G(d,p)//B3LYP/ 6-311G(d,p) level, the reaction energy of the title reaction is -38.2 kJ/mol, and the corresponding potential barriers ΔE≠ of the reaction R1, R2 and R3 are 43.2, 43.9 and 44.1 kJ/mol, respectively, which are in excellent agreement with the literal proposed value 43.1 kJ/mol. In present study, the rate constants of the three hydrogen abstraction reaction channels exhibit positive temperature dependence in the calculated temperature region, and the variational effects are negligible over the entire process, while the tunneling effects are considerable in the lower temperatures.

The level of variational transition-state theory (VTST) employed in the present paper is canonical variational transition theory (CVT), and the level of tunneling calculation used is the small-curvature tunneling method(SCT). The rate constants are calculated in the temperature range of 200-3000 K(Figure 1). All of the electronic structure calculations are carried out with the Gaussian 03 series program [4] and the dynamics calculations are carried out using Polyrate 8.2 program [5].


192

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m3 ⋅

mol

ecul

e-1 ⋅ s

-1)

1000 T-1 /K-1

k TST

k CVT

k CVT/SCT

Ref. [13]

Figure 1. The TST, CVT and CVT/SCT rate constant k (cm3⋅molecule-1⋅s-1) Versus the reciprocal of the temperature in 200~3 000 K (The star is the dynamic data in Ref. [3])

References [1] J. D. Farman, B. G.. Gardiner, J. D. Shanklin, Nature, 315(1985), 207 [2] S. Solomon, Nature, 347(1990), 6291 [3] D. R. Jr. Burgess, M. R. Zachariah, et al., Prog. Energy Combust. Sci., 21(1996), 453 [4] M. J. Frisch, G. W. Trucks, J. A. Pople, et al.,Gaussian03, Pittsburgh, PA, 2003 [5] Y. Y. Chuang, J. C. Corchado, P. L. Fast, et al., Polyrate-version 8.2 [CP], Minneapolis

Minnesota: University of Minnesota, 1999


193

Catalytic Phosphonylation Mechanisms of Sarin and Acetylcholinesterase: A Density Functional Study

Jing Wang,† Jiande Gu, *†‡ and Jerzy Leszczynski*†

†Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, MS 39217 U. S. A.

‡Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences,

Shanghai 201203 P. R. China

Potential energy surfaces for the phosphonylation of sarin and the catalytic triad (Glu-His-Ser) of acetylcholinesterase have been theoretically studied at the B3LYP/6-311G(d,p) level of theory. The obtained results show that the phosphonylation process involves a critical two-step addition-elimination mechanism. The first step (addition process) is the rate-determining step, which needs to overcome 13.4 kcal/mol activation energy barrier. The following steps can be occurred easily. The polarizable continuum model (PCM) self-consistent reaction field of Tomasi and co-workers with a dielectric constant є = 78.39 (water) was applied for all gas-phase-optimized structures to evaluate the solvation effects on the reaction. It is concluded that the solvate effect has subtle influences on the studied enzymatic reaction.

Reaction pathway of phosphonylation of catalytic triad of AChE with sarin (INT illustrates

the intermediates and TS describes the transition states. Gas phase in black and PCM model results in orange, energy barriers in kcal/mol).


194

Ground and Electronically Excited States of Methyl Hydroperoxide. Comparison with Hydrogen Peroxide

John D. Watts1 and Joseph S. Francisco2

1Computational Center for Molecular Structure and Interactions, Department of Chemistry, P. O. Box 17910, Jackson State University,

Jackson, MS 39217, U.S.A. 2Department of Chemistry and Department of Earth and Atmospheric Sciences,

Purdue University, West Lafayette, IN 47907-1393

Hydrogen peroxide (H2O2) and methyl hydroperoxide (CH3OOH) are two important trace species in the atmosphere that may be generated by radical association reactions. These two peroxides may be removed from the atmosphere by rainout, reaction with radicals (e.g. OH), and photodissociation. In order to assess the importance of photodissociation, it is important to characterize the electronically excited states of these molecules. While there have been several prior theoretical studies of the excited states of H2O2, there are quite large differences between the excitation energies, thus indicating the need for a new state-of-the-art study. There appears not to have been a prior theoretical study of excited states of CH3OOH. The primary focus of this research is on the excited states of these two peroxides. Aspects of the ground electronic states are also studied. Equilibrium geometries of the ground states of H2O2 and CH3OOH have been obtained using quadratic configuration interaction methods with correlation-consistent basis sets. These results are compared with experiments and prior calculations. The dipole moments of the ground states of these two molecules have been calculated. The results illustrate the sensitivity of this quantity to molecular geometry. Several excited states of H2O2 and CH3OOH were calculated using the equation-of-motion coupled-cluster singles and doubles method (EOM-CCSD). Vertical excitation energies of H2O2 are compared with prior work. There is good agreement with data from a CASPT2 study, which is arguably the best prior work. As well as vertical excitation energies, excited state energies along the O-O, O-H, and C-O dissociation pathways were calculated. The results are expected to be of assistance in resolving discrepancies in the experimental interpretation of the UV absorption spectrum and photodissociation of CH3OOH.


195

Quantum Chemical Calculations on Aliphatic Nitrate-Based Explosives. Prediction of New Conformers

David J. Watts, Ming-Ju Huang, and John D. Watts

Computational Center for Molecular Structure and Interactions Department of Chemistry, Jackson State University

P. O. Box 17910, Jackson, MS 39217

One of the benefits of quantum chemical methods is that they may be applied to chemicals that are difficult or dangerous to study experimentally or are unknown just as easily as to safe, well-known chemicals. One general class of chemicals that is difficult and dangerous to study experimentally is explosives. In this research we have applied several ab initio quantum chemical techniques to three aliphatic nitrate-based explosives, namely methyl nitrate (CH3ONO2), ethylene glycol dinitrate (O2NOCH2CH2ONO2; also known as nitroglycol), and nitroglycerin (O2NOCH(CH2ONO2)2). The Gaussian series of programs were used. Geometries have been optimized using Hartree-Fock self-consistent field theory, second-order Moller-Plessett perturbation theory (MP2), and density functional theory using the B3LYP functional. The 6-31G(d), 6-31+G(d), 6-311G(d,p), and 6-311++G(d,p) basis sets were used. In order to locate the lowest energy conformers, several different starting points were used in the geometry optimizations. The characters of the stationary points located in the geometry optimizations were determined by the calculation of harmonic vibrational frequencies. When prior results were available in the literature, our results were compared with them. For methyl nitrate, our results are in agreement with previously published data. For ethylene glycol dinitrate (EGDN), our results extend prior work and reveal a conformer that was not previously considered. Prior work on EGDN reported a conformer that we have determined to be of C2h symmetry. In addition, we have located a different conformer of Ci symmetry that is competitive in energy with the C2h conformer. In fact, according to some of the methods we have applied, the Ci conformer is the lowest-energy conformer. We have begun to locate the transition state that links the Ci and C2h conformers. For nitroglycerin, we have obtained lower energies than were obtained in prior work using the same methods and basis sets, suggesting we have located lower energy conformers than were found in prior work.


196

Energetics of Oxaspirocycle Prototypes: 1,7-Dioxaspiro[5.5]undecane

and 1,7,9-Trioxadispiro[5.1.5.3]hexadecane

Abby Jones Weldon and Gregory S. Tschumper

Department of Chemistry and Biochemistry University of Mississippi, University, Mississippi 38677-1848 USA

The relative gas-phase energetics of several low-lying isomers of 1,7-Dioxaspiro[5.5]undecane and 1,7,9-Trioxadispiro[5.1.5.3]hexadecane have been calculated with second-order Moller-Plesset perturbation theory and basis sets as large as aug-cc-pVQZ. Relative energies in THF, DCM, acetone, and DMSO have been estimated with corrections from polarized continuum model calculations at the B3LYP/6-311+G(d) level. In the most stable conformation of 1,7-Dioxaspiro[5.5] undecane, both rings adopt chair configurations, and both oxygens are axially disposed (2A).


197

It is more than 2 kcal/mol more stable than all other conformers. In agreement with previous work, the "twist-boat" trans isomer (3A) is the most stable isomer of 1,7,9-Trioxadispiro[5.1.5.3] hexadecane. However, in contrast to this earlier study, an "all-chair" configuration (3B) is found to be the most stable cis isomer of 1,7,9-Trioxadispiro[5.1.5.3]hexadecane (ΔE ≈ 0.5 kcal/mol in acetone and DMSO).


198

Gauge-Independent Atomic Orbital computations at the B3LYP/6-311+G(d) level indicate this is the only cis isomer with 13C NMR chemical shifts that are qualitatively consistent with the experimental spectra.


199

Theoretical Study of 1- Methylcytosine and Its Tatomer with Tetrahedral Edge Clay Minerals Fragments

A. Wilson, A. Michalkova, and J. Leszczynski

Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J.R. Lynch Street , Jackson , MS 39217

Clay minerals are hydrous aluminium phyllosilicates, sometimes with variable amounts of iron, magnesium, alkali metals, alkaline earths and other cations. Clays have structures similar to the micas and therefore form flat hexagonal sheets. Clay minerals are common weathering products and low temperature hydrothermal alteration products. Clay minerals are very common in fine grained sedimentary rocks such as shale, mudstone and siltstone and in fine grained metamorphic slate and phyllite. Cytosine is one of the 5 main nucleic bases used in storing and transporting genetic information within a cell in the nucleic acids DNA and RNA. It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto group at position 2). The nucleoside of cytosine is cytidine. In Watson-Crick base pairing, it forms three hydrogen bonds with guanine. Methylcytosine differs from cytosine by the presence of a methyl group at the postion of the pyrmidine ring. Methylcytosine is formed after replication by addiction of a methyl group to a cyosine already present in DNA strand. The presence of methylcytosine in human DNA has genetic and epigenetic effects on cellular development, differentiation, and neoplastic transformation. This work is devoted to the study of the interactions of methylcytosine and its imino-oxo tautomer with the tetrahedral edge mineral fragments. It can lead to a better understanding of DNA interactions with clay minerals.

The calculations were performed at the density functional theory level with the B3LYP functional applying the 6-31G(d) basis set. The studied systems were fully optimized. The tetrahedral edge mineral fragments were simulated using a single tetrahedra with the Si or Al central cation. Several different orientations of the target molecule were tested in order to find the most stable orientation. The fragment was terminated by the oxygen atom and by the hydroxyl group. We have studied the geometrical parameters and ESP charges, the interaction energies and topological characteristics of the studied systems.

The systems are mostly stabilized by the formation of the hydrogen bonds between the oxygen atoms or hydroxyl groups of the mineral fragment and the N-H, C-H groups or oxygen atoms of the target molecule. No chemical bond is created between the bases and the mineral fragment. The optimized structure of methylcytosine interacting with the [SiO(OH)3]- fragment is presented on Figure 1. The interactions of methylcytosine and its tautomer with the mineral fragment lead to changes in their structure and atomic charges in comparison with the isolated target molecules. The largest changes were found for the system containing the mineral fragment terminated by the oxygen atom containing the aluminum central cation. Methylcytosine and its tautomer interact differently with the mineral fragments despite they contain the same central cations and the same termination. The bases were found to be better stabilized on the fragment with the Al3+ central cation than in the systems containing the Si4+ cation.


200

Figure1. The optimized structure of 1-methylcytosine interacting with the [SiO(OH)3]- fragment.


201

Ethylene Production in the Collision Induced Dissociation of Metal Dication – Acetonen Complexes

Jianhua Wu1, Frank Hagelberg1 and Alexandre A. Shvartsburg2

1Computational Center for Molecular Structure and Interactions, Department of Physics, Atmospheric Sciences and Geoscience,

Jackson State University, Jackson, MS, 39217 2Pacific Northwest National Laboratories

Richland, WA 99352

Numerous recent research activities, both experimental1 and theoretical2 in nature, testify to the high attention paid currently to multiligated cations in the gas phase. This interest can be attributed to a variety of motifs. Thus, the study of these systems allows to assess the solvation behavior of cations as a function of the ligand number, and thus to understand the basic processes involved in the formation of solvation shells. Further, questions pertaining to fundamental organometallic chemistry, related to metal ion coordination and preferred disintegration pathways, can be addressed in great detail by analyzing finite metal-ligand composites which bridge the gulf between a pure ion and an ion embedded in a condensed medium. Moreover, these complexes are accessible to computational simulation from first principles, making possible a close interplay between experimental observation and theoretical interpretation in elucidating their structures and reaction mechanisms.

In the present contribution, we report and interpret Collision Induced Dissociation (CID) mass spectra for metal dication–acetone complexes of the form M2+Ln with n ≤ 6 and M = Ca, Mn, Co, Ni, Cu. The emphasis of this work is placed on an adequate understanding of the strongly differing dissociation patterns displayed by the various multiligated metal dications. The fragmentation behavior of Ca2+Ln is found to be dominated by the elimination of neutral species, where the loss of ethylene turns out to be a major disintegration pathway. For M2+Ln with M = Ni, Cu, a strong prevalence of dissociation induced by electron transfer is observed below the critical ligand number where acetone loss ceases to the predominant mode of decay. The most complex scenario is displayed by species with M = Mn, Co. Here ethylene elimination is found to compete with three major charge reduction channels, namely, [CH3CO]+ cleavage as well as electron and inter-ligand proton transfer with subsequent dissociation. The main fragmentation phenomena identified in this work can be related to the differences between the second ionization potentials of the M2+Ln metal centers. 1. J. Anichina, X. Zhao, D.K. Bohme, J. Phys. Chem. A, (2006); A.A. Shvartsburg, J.Am.Chem.Soc. 124, 12343 (2002); A.A. Shvartsburg, J.G. Wilkes, J.O. Lay; K.W.M. Siu, Chem.Phys.Lett. 350, 216 (2001); A.A. Shvartsburg, K.W.M. Siu, J. Am. Chem. Soc. 123, 10071 (2001). 2. A.M. El-Nahas, C. Xiao, F. Hagelberg, Int. J. Mass Spec. 237, 47 (2004); C. Xiao, F. Hagelberg, A.M. El-Nahas, J.Phys.Chem.A 108, 5322 (2004); C. Xiao, K. Walker, F. Hagelberg, A.M. El-Nahas, A.M., Int. J. Mass Spec. 233, 87(2004).


202

3D Quantitative Structure–Farnesyltransferase Inhibition Analysis for Some Diaminobenzophenones

Aihua Xie,a Shawna R. Clark,a,b Robert J. Doerksena,c

aDepartment of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, MS, 38677-1848, USA

bTougaloo College, Jackson, MS, 39174 cResearch Insititute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi

Malaria, caused by protozoa of the genus Plasmodium, is one of the most troubling and lethal infectious diseases in the world, leading to 300 million cases and 1.5 to 2.7 million deaths per year. Half of the world’s people, many of them poor, are at great risk of acquiring malaria. Strains resistant to existing medicines have developed. Thus there is great need for novel and inexpensive antimalarial compounds.1,2

One of the most-promising antimalarial targets is inhibition of protein farnesyltransferase (FT).3,4 The heterodimeric zinc-containing FT has been pegged as an anticancer target since it was discovered that it farnesylates Ras, which is overexpressed in certain kinds of cancer tumors.5-8 More recently, however, evidence has shown that there must be another yet to be discovered mechanism of cancer inhibition since FT inhibitors also kill tumors which do not overexpress Ras, so currently the mechanism of action is unknown.5-8 Meanwhile several FT inhibitors have proceeded into clinical trials for cancer chemotherapy.5,7 In the last few years, several groups have found that application of FT inhibitors to cells infected with P. falciparum led to a decrease in farnesylated proteins and to the associated lysis of the parasites.3,4 The FT inhibitors were selectively toxic against the parasite as compared to against mammalian cells.

As part of our continuing effort to find novel lead compounds for antimalarial drugs, in this work we performed a three-dimensional quantitative structure-activity relationship (QSAR) investigation, using the CoMFA9 and CoMSIA10 methods, of a series of diaminobenzophenone farnesyltransferase inhibitors, in order to gain understanding of the interaction between this series of compounds and FT. From the work of Schlitzer et al., who reported inhibitory activity data against yeast FT, we selected 90 compounds11-15 based on a 2,5-diaminobenzopenzophenone scaffold, including 31 N-(4-tolyacetylamino-3-benzoylphenyl)-3-arylfurylacrylic acid amides, 5 N-(4-tolyacetylamino-3-benzoylphenyl)-4-arylfurylacrylic acid amides, 24 N-(4-acylamino-3-benzoylphenyl)-3-[5-(4-nitropheyl)-2-furyl]acrylic acid amides, 14 N-(4-acylamino-3-benzoylphenyl)-4-nitrocinnamic acid amides, 8 N-(4-aminoacylamino-benzoylphenyl)-3-[5-(4-nitrophenyl)-2-furyl] acrylic acid amides, and 8 5-arylacryloylaminobenzophenones (cf. Figure 1).

We found that steric, electrostatic and hydrophobic properties of substituent groups play key roles in the bioactivity of the series of compounds, while hydrogen bonding interactions show no obvious impact. Analysis showed that some compounds such as 4-arylfuryl derivatives demonstrated a completely different structure-activity relationship, and docking studies showed that those compounds adopt a different binding mode. Thus we did not include those 5 compounds in our final QSAR models. Additionally, 5 outliers were removed for our best model. Structural analyses of the outliers may yield some interesting insight into key aspects of the ligand–receptor interactions. Our best model, based on a 65-compound training set and 16-compound test set, was a CoMSIA model containing electrostatic, steric, and hydrophobic fields, with R2 = 0.733, Q2 = 0.504, and R2

pred = 0.54. Care was taken to ensure a uniform distribution of structurally different compounds from each cluster of compounds during the test set selection.


203

The 3D analysis contour maps are consistent with our earlier 3D-QSAR work, which we published recently,16 studying a similar series of compounds but with models fit to activity data for in vitro inhibition of parasite (Plasmodium falciparum) growth.

R1

NHO

O

NHR2

O

Figure 1. Common structure of the 2,5-diaminobenzophenones. References 1. Bell, D. R.; Jorgensen, P.; Christophel, E. M.; Palmer, K. L. Nature 2005, 437, E3. 2. Snow, R. W.; Guerra, C. A.; Noor, A. M.; Myint, H. Y.; Hay, S. I. Nature 2005, 434, 214. 3. Eastman, R. T.; Buckner, F. S.; Yokoyama, K.; Gelb, M. H.; Van Voorhis, W. C. Journal of

Lipid Research 2006, 47, 233. 4. Gelb, M. H.; Van Voorhis, W. C.; Buckner, F. S.; Yokoyama, K.; Eastman, R.; Carpenter, E.

P.; Panethymitaki, C.; Brown, K. A.; Smith, D. F. Molecular & Biochemical Parasitology 2003, 126, 155.

5. Appels, N. M.; Beijnen, J. H.; Schellens, J. H. Oncologist 2005, 10, 565. 6. Pan, J.; Yeung, S. C. Cancer Research 2005, 65, 9109. 7. Dinsmore, C. J.; Bell, I. M. Current Topics in Medicinal Chemistry 2003, 3, 1075. 8. Sebti, S. M.; Hamilton, A. D. Oncogene 2000, 19, 6584. 9. Cramer, III, R. D.; Patterson, D. E.; Bunce, J. D. Journal of the American Chemical Society

1988, 110, 5959. 10. Klebe, G.; Abraham, U.; Mietzner, T. Journal of Medicinal Chemistry 1994, 37, 4130. 11. Mitsch, A.; Winer, P.; Silber, K.; Haebel, P.; Sattler, I.; Klebe, G.; Schlitzer, M. Bioorganic

& Medicinal Chemistry 2004, 12, 4585. 12. Sakowski, J.; Sattler, I.; Schlitzer, M. Bioorganic & Medicinal Chemistry 2002, 10, 233. 13. Mitsch, A.; Bohm, M.; Winer, P.; Sattler, I.; Schlitzer, M. Bioorganic & Medicinal

Chemistry 2002, 10, 2657. 14. Kettler, K.; Sakowski, J.; Silber, K.; Sattler, I.; Klebe, G.; Schlitzer, M. Bioorganic &

Medicinal Chemistry 2003, 11, 1521. 15. Kettler, K.; Wiesner, J.; Silber, K.; Haebel, P.; Ortmann, R.; Sattler, I.; Dahse, H.-M.; Jomaa,

H.; Klebe, G.; Schlitzer, M. European Journal of Medicinal Chemistry 2005, 40, 93. 16. Xie, A.; Sivaprakasam, P.; Doerksen, R. J. Bioorganic & Medicinal Chemistry 2006, 14,

7311.


204

Computer Simulation Studies of Water Borne Two-Component Polyurethane Film Formation

Shihai Yang1, Ras Pandey1, Marek Urban2

1Department of Physics and Astronomy 2School of Polymers and High Performance Materials

The University of Southern Mississippi Hattiesburg, MS 39406

A computer simulation model is developed to determine processes leading to the film growth and morphological changes in polyurethane film formation. The surface roughness of the film is related with the solution properties in aqueous (A) phase containing hydrophobic (H, R-N=C=O) and hydrophilic (P, R’-OH) components in a simple three dimensional lattice of size Lx×Ly×Lz on an absorbing substrate. The model captures constituents’ characteristics such as phenomenological interactions, reaction kinetics as well as molecular weight ratios. Cross-linking reactions among appropriate constituents proceed isotropically in the evolving film. Thermodynamic equilibration via stochastic motion of each constituent can be arrested by covalent bonding and destabilized by evaporation of aqueous components. Saturated thickness (hs) of the film growth, its roughness (Ws), and distribution of constituents, are studied as a function of temperature, initial water concentration, and stoichiometry. Film roughness Ws increases with reducing the temperature, increasing the initial water concentration and NCO:OH ratio. Simulation data suggest that higher NCO:OH ratios lead to higher urea and urethane contents, however, higher initial water concentration results in higher urea but lower urethane concentration in the film. These simulation results are consistent with the experimental observation qualitatively.


205

Quantum Transport in Porphirin: Interaction with Metals

Ilya Yanov, Yana Kholod and Jerzy Leszczynski

Jackson State University, Dept. of Chemistry Jackson MS, 39217

Transmission spectra and current-voltage dependence of porphyrin molecule between gold electrodes have been calculated in the presence of interaction with metal atoms. Several metal-porphirin complexes, which are most common in biochemistry ( Fe(II), Fe(III), Mn(II), and Zn(II)-porphirines) have been used .

The scheme of electric circuit is shown in the Figure. Initial geometries were optimized at the UB3LYP/STO-3G and UB3LYP/6-31G(d) level of theory using GAUSSIAN98 program set. Christensen core pseudotentials were used for Au atoms.

The results of the calculations of transmission spectra of considered systems are presented. It is shown that because the estimated Fermi level of the system almost coincides with the LUMO level of molecules, Fe(II)-porphyrin and Fe(III)-porphyrin exhibit significant conductance at small voltage biases. Conductance of Mn(II)-porphyrin and Zn(II)-porphyrin are much lower, and decrease from Mn to Zn.

It was confirmed that performing spin-unrestricted calculations is essential to obtain the correct splitting of the original molecular orbitals levels.


206

Electron Propagator Calculations on the C60 Photoelectron Spectrum

V.G. Zakrzewski, O. Dolgounitcheva, and J.V.Ortiz

Dept. of Chemistry and Biochemistry, Auburn University, Auburn, AL 36849

Electron propagator calculations of C60 photoelectron spectrum have been performed using both diagonal quasipartical approximation know as Outer Valence Green Function (OVGF) and non-diagonal renormalized approximation known as ADC(3). 6-311G(d) basis has been used. Both OVGF and ADC(3) results are in excellent agreement with the experimental results for the ionization from the HOMO. Gaussian-03 suite of programs was used.

Experimental Photoelectron Spectrum (PES) of C60 has been reported in an article by D. L. Lichtenberger et. al. (Chem. Phys. Lett., 176 (1991), 203) and pertains to a thin film of three monolayers of C60 deposited on gold.

Experimental spectrum has only one relatively sharp peak at about 7.6 eV. This peak was assigned to ionization from the HOMO (hu symmetry).

Our theoretical results are very close to this experimental value. The OVGF produces 7.67 eV and ADC(3) value is 7.68 eV. The next experimental feature is at about 8.95eV and accounts for ionization from two MOs with hg and gg symmetry. OVGF values are 9.18 eV and 9.23 eV and ADC(3) 9.17 eV and 9.23 eV, respectively. Polestrengths for these lines are about 0.88 in OVGF and 0.84 in ADC(3). Thus, these ionizations can still be considered as one-electron processes. The next feature represents a broad band in the range of 10.82 – 11.59 eV. It is possible to assign four states originating from MOs gu, t2u, hu, and hg with the energies of 11.33, 11.88, 11.79, and 12.13 eV (OVGF). The OVGF polestrengths for the first two lines are 0.78 and 0.79. It is likely that ionization processes in this range have significant inputs from shake-up states and represent essentially many-body processes. The next experimental band is in between 12.42 and 13.82 eV. OVGF results suggest that these are ionizations originating from next MOs of hg, gu and t2u symmetry with the energies of 13.54, 13.37 and 14.13 eV, respectively. The polestrength of the first line is only 0.66 which shows that many-body effects are very strong, and this ionization cannot be treated as a one-electron process.

ADC(3) calculation also produced vertical electron affinities of C60. The first bound state arises from electron attachment to the LUMO (t1u MO) and its energy is 1.65 eV. Another vertically bound state with the energy of 0.23 eV is predicted as the result of electron attachment to the LUMO+1 MO (t1g).

Almost all unoccupied MOs of C60 are degenerate (t, g, or h representations with 3-, 4-, or 5- fold degeneracy). Therefore, C60

anion should be distorted from Ih point group symmetry. We performed geometry optimization of C60 anion using DFT B3LYP approximation. It leads to lowering of the point group symmetry to the Ci group, and the anion adopts the 2Au electronic state. ΔMP2 method with the 6-311+G(d) basis set was used to produce vertical electron detachment energy at the geometry of the anion. The value obtained is 2.93 eV.


207

A Fast and Reliable Method for Predicting pKa Values

Shuming Zhang, Jon Baker and Peter Pulay

Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701

We have developed a fast and reliable protocol for predicting the acid/base dissociation constants (pKa) of organic molecules in water. The geometries are optimized at the OLYP/3-21G(d) level using the COSMO continuum solvation model. The energy difference between the protonated/ deprotonated system, ∆H, calculated at the OLYP/6-311+G (d,p) level, yields the pKa for functional group f through a simple linear fit: pKa (f) = αf ∆H + βf. To date we have parameterized seven “functional groups” in 700 molecules. The fitting parameters help account for specific solvation effects. It is important to carry out the optimization in the presence of the solvent. The mean absolute deviation between experimental and calculated pKa values is less than 0.50 pKa units for organic acids and less than 0.55 pKa units for bases. We use the resulting fitting parameters to predict the pKa values for 30 dicarboxylic acids, 20 standard amino acids, and 47 drug-like molecules with a mean absolute deviation of less than 0.50 pKa units.


208

The Most Stable Structure of Fullerene[20] and Its Derivatives C20(C2H2)n and C20(C2H4)n (n=1−4): A Theoretical Study

Congjie Zhang1 Wenxiu Sun1 Zexing Cao2

1School of Chemistry & Materials Science, Shaanxi Normal University, Xi’an, 710062, China 2Department of Chemistry, State Key Laboratory for Physical Chemistry of Solid Surface,

Xiamen University, Xiamen, 361005, China

Structures and stabilities of fullerene C20 and C20− have been investigated by the density

functional theory and CCSD(T) calculations. In consideration of Jahn-Teller distortion of Ih-symmetric C20, twelve kinds of possible subgroup symmetries (D5d, C5v, D3d, C3v, D2h, D2, C2h, C2v, C2, Cs, Ci, C1) have been used in the full geometry optimization. On the basis of relative energetics, vibrational analyses, and electron affinities, fullerenes C20 and C20

− have most stable D2h and Ci structures (see Figure 1), respectively. The controversy on the relative stability of fullerene[20] arises from use of different subgroups in calculation and the basis set dependence in vibrational analysis. Predicted NICS values show that the most stable fullerene C20 and its derivatives C20(C2H2)n and C20(C2H4)n (n=1-3) exhibit remarkable aromaticity, while C20(C2H2)4 and C20(C2H4)4 have no spherical aromaticity. The C20 (D2h) cage has remarkable activity toward addition of olefin, and such feasibility of addition reaction is ascribed to strong bonding interactions among frontier molecular orbitals from C20 and olefin. Calculations indicate that both C20(C2H2)n and C20(C2H4)n have similar features in electronic spectra.

1.3971

1.4418

1.4432

1.4857

1.53531.3984

1.4404

1.4792

1.4378

1.5202 1.43491.4201

C20 C20-

Figure 1. B3LYP-optimized geometries of the most stable fullerenes C20 (D2h) and C20

−(Ci)


209

Do Methanethiol Adsorbates on The Au(III) Surface Dissociate?

Jian-Ge Zhou and Frank Hagelberg

Computational Center for Molecular Structure and Interactions Jackson State University, Jackson, MS 39217

The interaction of methanethiol molecules CH3SH with the Au(111) surface is investigated, and it is found for the first time that the S-H bond remains intact when the methanethiol molecules are adsorbed on the regular Au(111) surface. However, it breaks if defects are present in the Au(111) surface. At low coverage, the fcc region is favored for S atom adsorption, but at saturated coverage the adsorption energies at various sites are almost iso-energetic. The presented calculations show that a methanethiol layer on the regular Au(111) surface does not dimerize.

[1] J. Zhou, F. Hagelberg, Phys. Rev. Lett. 97, 045505 (2006). [2] I. Rzeznicka, J. Lee, P. Maksymovych, and J. Yates, Jr., J. Phys. Chem. B 109, 15992 (2005).


210

Comprehensive Conformational Analysis of 2'-Deoxynucleosides: Nonempirical Quantum-Mechanical Study

Roman Zhurakivsky1, Dmytro Hovorun2

1 Taras Shevchenko Kyiv National University, Faculty of Radiophysics, 2 Hlushkova av., build. 5, 03127 Kyiv, Ukraine

2 Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnoho str., 03143 Kyiv, Ukraine

In spite that conformational analysis of deoxyribonucleosides is a classical tool of molecular and structural biology, the information on conformational possibilities of some biomolecules in the gas phase remains very limited. To fill up this gap, we performed comprehensive quantum-mechanical (MP2/6-311++G(d,p)//DFT B3LYP/6-31G(d,p) level of theory) conformational analysis of isolated 2'-deoxyuridine (dUrd), 2'-deoxythymidine (dThd), 2'-deoxycytidine (dCyd), 2'-deoxyadeosine (dAdo) and 2'-deoxyguanosine (dGuo) on basis of the appropriate results of analysis completed for 1',2'-deoxyribose - the model sugar residue of 2'-deoxyribonucleosides.

The most important information is presented in Table (ΔG is Gibbs free energy difference of all possible conformers at normal conditions):

Number of conformers Conformational equilibrium, % Nucleoside

Total Syn Anti

ΔG, kcal/mol

Syn/Anti S/N dUrd 94 41 53 8,95 62,8:37,2 77,5:22,5 dThd 92 39 53 7,49 61,6:38,4 74,5:25,5 dCyd 89 38 51 8,01 82,1:17,9 78,3:21,7 dAdo 88 37 51 8,39 99,4:0,6 98,5:1,5 dGuo 96 43 53 10,02 99,7:0,3 95,6:4,4

The intramolecular hydrogen bonds (H-bonds) that stabilize all possible conformers of the

nucleosides under study are revealed by analysis of electron density topology (the so-called Atoms-in-Molecules Bader’s theory):

• pyrimidines: C1'H...O2, C2'H2...O5', C2'H2...O2, C3'H...O2, C5'H1...O2, C5'H2...O2, C6H...O4', C6H...O5', C3'H...HC6, O3'H...O5', O5'H...O3', O5'H...O2, O5'H...O4' (dUrd, dCyd), O5'H...HC6 (dUrd, dThd);

• purines: C2'H2...O5', C2'H2…N3, C3'H…N3, C5'H1…N3, C5'H1…C8, C5'H2…N3, C8H…O5', C3'H...HC8, C5'H1...HC8, C5'H2...HC8, O5'H...HC8, O3'H...O5', O5'H...O3', O5'H…N3, N2H...O5' (dGuo), C2'H1…N3 (dAdo), C5'H2…C8 (dAdo), O5'H…N9 (dAdo). (H-bonds specific for certain nucleosides are bracketed.)

Biological significance of the obtained results is discussed. Authors express their sincere acknowledgement to “GAUSSIAN” corporation (USA) for

kindly granted “GAUSSIAN03” program package.


Jackson, Miss.

List of Participants Conference on Current Trends in Computational Chemistry 2006

213

Timothy D. Ables Associate Director US Army Corps of Engineer Research and Development Center ERDC Executive Office 3909 Halls Ferry Road Vicksburg, Mississippi 39180-6199

Dmytro Afanasyev 1004 Cedar St. Center for Computational Quantum Chemistry University of Georgia Athens, GA 30602 USA Email: [email protected]

Lovell Agwaramgbo Dillard University 2601 Gentilly Blvd New Orleans, LA 70122 USA Tel: 504-595-2522 Email: [email protected]

Reeshemah Allen Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601 979-3979 Fax: 601 979-7823 Email: [email protected]

Julie Anderson Department of Chemistry and Biochemistry 107 Coulter Hall University, MS 38677 USA Tel: 662-915-3891 Fax: 662-915-7300 Email: [email protected]

Xavier Assfeld BP 239 UMR7565 equipe de chimie et biochimie theoriques Faculte des Sciences et techniques Nancy, 54506 France Tel: (33) 3 83 68 43 82 Fax: (33) 3 83 68 43 71 Email: [email protected]

Jon Baker Parallel Quantum Solutions 2013 Green Acres Rd Suite A Fayetteville, AR 72703 USA Tel: 479-521-5118 Fax: 479-521-5167 Email: [email protected]

Anuoluwa Bamgbelu Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601 979 3723 Email: [email protected]

Mikhail Basilevsky Karpov Institute of Physical Chemistry Department of Quantum Chemistry and Statistical Physics Moscow, 103064 Russia Tel: +7 95-916-6627 Fax: +7 95-975-2450 Email: [email protected]

Pierre Bonifassi Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-3981 Fax: 601-979-7823 Email: [email protected]

Russell J. Boyd Dalhousie University Department of Chemistry Halifax, Nova Scotia B3H 4J3 Canada Tel: (902) 494-8883 Fax: (902) 494-1310 Email: [email protected]

Jean-Luc Bredas Georgia Institute of Technology School of Chemistry and Biochemistry 770 State St. Atlanta, GA 30332-0400 USA Tel: 404-385-4986 Fax: 404-894-7452 [email protected]

Jaroslav Burda Ke Karlovu 3 Charles University Prague, 12116 Czech Republic Tel: +420221911246 Fax: +420221911249 Email: [email protected]

Peter Butko 118 College Dr. #5043 University of Southern Mississippi Dept. Chemistry & Biochemistry Hattiesburg, MS 39406 USA Tel: 601 266-6044 Fax: 425-696-9603 Email: [email protected]

Conference on Current Trends in Computational Chemistry 2006 List of Participants

214

Mauricio Cafiero Department of Chemistry Rhodes College 2000 North Parkway Memphis, TN 38112 USA Tel: 901-843-3955 Email: [email protected]

Louis Carlacci 1425 Porter St Network CS Inc. / USAMRIID Frederick, MD 21702 USA Tel: 301-619-6732 Email: [email protected]

Minghui Chai Dow 342, Depratment of Chemistry Central Michigan University Mt. Pleasant, MI 48859 USA Tel: 989-774-3955 Fax: 989-774-3883 Email: [email protected]

Bin Chen Louisiana State University Department of Chemistry 232 Choppin Hall Baton Rouge, LA 70803 USA Tel: (225) 5784094 Fax: (225) 5783458 Email: [email protected]

Qianyi Cheng Box 4036 Department of Chemistry & Biochemistry Mississippi College Clinton, MS 39058 USA Tel: 601-925-3852 Fax: 601-925-3933 Email: [email protected]

David Close East Tenn. St. Univ. Physics Dept. Box 70652 Johnson City, TN 37614 USA Tel: 423-439-5646 Fax: 423-439-6907 Email: [email protected]

Sheritta Cooks Chemistry 201 Department of Chemistry University of Alabama in Birmingham Birmingham, AL 35294 USA Tel: 205-934-4300 Email: [email protected]

Victoria Crockett Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-6509 Email: [email protected]

Jessica Cross Rhodes College Department of Chemistry 2000 North Parkway Memphis, TN 38112 USA Tel: 901-843-3955 Email: [email protected] John Cullinane Technical Director, Environmental Engineering and Cleanup US Army Corps of Engineer Research and Development Center ERDC Executive Office 3909 Halls Ferry Road Vicksburg, Mississippi 39180-6199

Pankaj Daga 417, Faser Hall, School of Pharmacy University of Mississippi University, MS 38677 USA Tel: 662 915 1853 Email: [email protected]

Gopala Darbha Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601 979 6559 Email: [email protected]

Deborah F. Dent Acting Director, ITL US Army Corps of Engineer Research and Development Center ERDC Executive Office 3909 Halls Ferry Road Vicksburg, Mississippi 39180-6199

Yuanqing Ding National Center for the Natural Products Research University, MS 38677 USA Tel: 662-915-1027 Fax: 662-915-798 Email: [email protected]


215

Robert Doerksen 421 Faser Hall University of Mississippi Department of Medicinal Chemistry University, MS 38677 USA Tel: 16629155880 Fax: 16629155638 Email: [email protected]

Olga Dolgounitcheva 179 Chemistry Building Auburn University Auburn, AL 36849 USA Tel: 224-844-7920 Fax: 334-844-6959 Email: [email protected]

Jacek Doskocz Department of Chemistry Faculty of Medicinal Chemistry and Microbiology Wroclaw University of Technology Wroclaw, 50-370 Poland Tel: +48 71 320 2675 Email: [email protected]

Jinsong Duan 417 Faser Hall, Dept. of Medicinal Chemistry, School of Pharmacy University of Mississippi Oxford, MS 38677 USA Tel: 662 915 1853 Email: [email protected]

Jesse Edwards 219 Jones Hall Florida A&M University Tallahassee, FL 32307 USA Tel: 950-5993-3638 Fax: 850-561-2388 Email: [email protected]

Mostafa A. El-Sayed Georgia Institute of Technology School of Chemistry and Biochemistry 770 State St. Atlanta, GA 30332-0400 USA Tel: 404-894-0292 Fax: 404-894-7452 Email: [email protected]

Adel ElSohly Department of Chemistry and Biochemistry 107 Coulter Hall University, MS 38655 USA Tel: 662-915-3891 Fax: 662-915-7300 Email: [email protected]

Floyd Fayton 525 College Street NW Howard University Chemistry Department Washington, DC 20059 USA Tel: 202-806-6882 Email: [email protected]

James Fells Department of Chemistry 213 Smith Chemistry Building Memphis, TN 38152 USA Tel: 901-678-4425 Fax: 901-678-3447 Email: [email protected]

Jason Ford-Green Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 850-443-9233 Email: [email protected]

Ryan Fortenberry Box 4036 Department of Chemistry & Biochemistry Mississippi College Clinton, MS 39058 USA Tel: 601-925-3852 Fax: 601-925-3933 Email: [email protected] Velvelyn B. Foster Vice President for Academic Affairs and Student Life Office of the Vice President for Academic Affairs and Student Life Jackson State University P.O. Box 17199 Jackson, Mississippi 39217 Tel: 601 979-2244 Fax: 601 979-8246

Fillmore Freeman Department of Chemistry University of California, Irvine Irvine, CA 92697-2025 USA Tel: 949-824-6501 Fax: 949-824-6501 Email: [email protected]

Miguel Fuentes-Cabrera P.O. Box 2008 Center for Nanophase Materials Sciences Oak Ridge National Laboratory Oak Ridge, TN 37831 USA Tel: (865) 574-2206 Email: [email protected]


216

Al'ona Furmanchuk Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-1134 Fax: 601-979-7823 Email: [email protected]

Earl Garrett Box 4036 Department of Chemistry Mississippi College Clinton, MS 39058 USA Tel: 601.925.3852 Fax: 601.925.3933 Email: [email protected]

Ainsley Gibson 525 College Street, MW Howard University Dept. of Chemistry Washington, DC 20059 USA Tel: (202) 806-6882 Fax: (202) 806-5442 Email: [email protected]

Gurvinder Gill Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 6019792122 Fax: 6019793674 Email: [email protected]

Leonid Gorb US Army ERDC (SpecPro) 3909 Halls Ferry Rd Vicksburg, MS 39180 USA Tel: 601-634-3863 Email: [email protected]

Helen Grebneva Donetsk Physical and Technical Institute, NAS of Ukraine Donetsk, 830114 Ukraine Tel: +380 62 304 8121 Email: [email protected]

Jiande Gu Shanghai Institute of Materia Medica, CAS Shanghai, Shanghai 203201 P. R. China Tel: 86-21-50806720 Email: [email protected]

Steven Gwaltney Box 9573 Mississippi State University Mississippi State, MS 39762 USA Tel: (662) 325-7602 Fax: (662) 325-1618 Email: [email protected]

Sharon Hammes-Schiffer 104 Chemistry Building Chemistry Department Pennsylvania State University University Park, PA 16802 USA Tel: 814-865-6442 Fax: 814-863-5319 Email: [email protected] Mark G. Hardy Interim Dean, College of Science, Engineering, and Technology Jackson State University Jackson, MS 39217 Tel: 601-979-3449 Email: [email protected]

Ayorinde Hassan Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601 979 6786 Email: [email protected]

Frances Hill Network Computing Services, Inc 1200 Washington Ave South Minneapolis, MN 55415 USA Tel: 612-337-3569 Fax: 612-337-3400 Email: [email protected] Glake Hill, Jr. Jackson State University Department of Chemistry 1325 Lynch St. Jackson, MS 39217 U.S.A. Phone: (601) 979-1699 Fax: (601) 979-7823 E-mail: [email protected] Shonda Allen Hill Jackson State University Department of Chemistry 1325 Lynch St. Jackson, MS 39217 U.S.A. Phone: (601) 979-3723 Fax: (601) 979-7823 E-mail: [email protected]


217

Meghan Hofto Rhodes College Department of Chemistry 2000 North Parkway Memphis, TN 38112 USA Tel: (901) 487-0901 Email: [email protected]

Philip Hoggan U Blaise Pascal 24 Avenue Landais Clermont Ferrand, 63000 France Tel: 33-4-73407197 Fax: 33-4-73407750 Email: [email protected]

Jeffrey Holland Acting Deputy Director US Army Corps of Engineer Research and Development Center ERDC Executive Office 3909 Halls Ferry Road Vicksburg, Mississippi 39180-6199

Tiffani Holmes Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 228-623-0673 Email: [email protected]

James R. Houston Director US Army Corps of Engineer Research and Development Center ERDC Executive Office 3909 Halls Ferry Road Vicksburg, Mississippi 39180-6199

Dmytro Hovorun 150, Zabolotnoho str. Kiev, 03143 Ukraine Tel: 1 601 634 3863 Email: [email protected]

Ming-Ju Huang Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: (601)-979-3492 Email: [email protected]

Danielle Hudson Tuskegee University Department of Chemistry Armstrong Hall Room 102 Tuskegee, AL 36088 USA Tel: 334-727-8878 Fax: 334-724-4492 Email: [email protected]

Olexandr Isayev Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-1134 Fax: 601-979-7823 Email: [email protected]

Harsh Jain Florida A&M University 1515 Martin Luther King, Jr. Blvd Environmental Sciences Institute Tallahassee, FL 32307-6600 United States Tel: 850 599-3672 Email: [email protected]

Srinivasa Rao Jampani Molecular Modleling lab, Oraganic-1 Indian Institute of Chemical Technology Tarnaka Hyderabad, Andhra Pradesh 500007 India Tel: 091 40 27160123 2619 Fax: 091 40 27160512 Email: [email protected]

Richard B. Jenkins Commander US Army Corps of Engineer Research and Development Center ERDC Executive Office 3909 Halls Ferry Road Vicksburg, Mississippi 39180-6199

Samuel Keasler Louisiana State University 400 Choppin Hall Baton Rouge, LA 70803 USA Tel: 225 578-4417 Fax: 225 578-4417 Email: [email protected]

James Keith PO Box 6315 210 Hodges Hall Dept. of Physics West Virginia University Morgantown, WV 26506-6315 USA Tel: (304) 293-3422-1430 Fax: (304) 293-5732 Email: [email protected]


218

Hassan Khartabil Equipe de Chimie et Biochimie Théoriques UMR UHP-CNRS n°75656 "SRSMC" Faculté des Sciences et Techniques Vandoeuvre-lès-Nancy, 54506 France Tel: 00 33 3 83 68 40 00 Fax: 00 33 3 83 68 43 71 [email protected]

Yana Kholod Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 1 (601) 979 7824 Fax: 1 (601) 979 7823 Email: [email protected]

Benjamin Killian 9600 Gudelsky Dr. Center for Advanced Research in Biotechnology University of Maryland Biotechnology Institute Rockville, MD 20850 USA Tel: 240-314-6136 Fax: 240-314-6255 Email: [email protected]

Erica King Department of Chemistry Miles College 5500 Myron Massey Blvd Fairfield, AL 35064 USA Tel: 334-727-8237 Email: [email protected]

Wojciech Kolodziejczyk Politechnika Wroclawska Instytut Chemii Fizycznej i Teoretycznej Wyb. Wyspianskiego 27 Wroclaw, Dolnoslaskie50-370 Poland Tel: +48 71 320 28 94 [email protected]

Lynn Koplitz 6363 St. Charles Ave. Chemistry Department Loyola University New Orleans, LA 70118 USA Tel: 504 865 3274 Fax: 504 865 2269 Email: [email protected]

Dmytro Kosenkov Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 6019793979 Fax: 6019792378 Email: [email protected]

Vitalina Kukueva Fire Safety Institute Onoprienko str. 8 Cherkassy, 18034 Ukraine Tel: 80472362233 Fax: (80472) 55-09-71 Email: [email protected]

Gulnara Kuramshina Department of Physical Chemistry, Faculty of Chemistry Moscow State University (M.V.Lomonosov) Moscow, 119992 Russia Tel: +7(495) 939 2950 Fax: +7(495) 932 8846 Email: [email protected]

William A Lester Jr University of California, Berkeley Department of Chemistry University of California, Berkeley Berkeley, CA 94720-1460 U.S.A. Tel: 510-643-9590 Fax: 510-642-1088 Email: [email protected]

Danuta Leszczynska Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-3482 Fax: 601-979-7823 Email: [email protected]

Jerzy Leszczynski Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-3482 Fax: 601-979-7823 Email: [email protected]

Mengsheng Liao Department of Chemistry Jackson State University 1400 J. R. Lynch Street Jackson, MS 39217 USA Tel: (601)979-3714 Fax: (601)979-3674 Email: [email protected]

Dan Liu Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601 979 3640 Email: [email protected]


219

Pierre-Francois Loos Boulevard des Aiguillettes BP 239 Theoretical Chemi. and Biochem. Group UMR 7565 - CNRS Université Henri Poincaré, Nancy I Vandoeuvre-lès-Nancy Cede, 54506 France Tel: +33 (0)3 83 68 Fax: +33 (0)3 83 68 Email: [email protected]

Brandon Magers Box 4036 Dept. of Chemistry Mississippi College Clinton, MS 39056 USA Tel: 6019259852 Fax: 6019253933 Email: [email protected]

David Magers 200 South Capitol Street Department of Chemistry & Biochemistry Mississippi College Clinton, MS 39058 USA Tel: 601-925-3851 Fax: 601-925-3933 Email: [email protected]

Robert Maier MSRC Assistant Director US Army Corps of Engineer Research and Development Center ERDC Executive Office 3909 Halls Ferry Road Vicksburg, Mississippi 39180-6199

Devashis Majumdar Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-7824 Fax: 601-979-7823 Email: [email protected]

Massimo Malagoli Parallel Quantum Solutions 2013 Green Acres Rd Suite A Fayetteville, AR 72703 USA Tel: 479-521-5118 Fax: 479-521-5167 Email: [email protected]

Ronald Mason President, Jackson State University 1400 Lynch St. Jackson, MS 39217-0280 USA Tel: 601.979.2323 Fax: 601.979.2948 E-mail: [email protected]

Harley McAlexander P.O. Box 3046 Department of Chemistry Mississippi College Clinton, MS 39058 USA Tel: 6019253852 Fax: 6019253933 Email: [email protected]

Dwight McGee 219 Jones Hall Chemistry Department Florida A&M University Tallahassee, FL 32307 USA Tel: 850-599-3638 Fax: 850-561-2388 Email: [email protected]

Matt McKenzie Louisiana State University Choppin 400 Baton Rouge, LA 70803 USA Tel: 225-229-5811 Email: [email protected]

Kenneth M. Merz Quantum Theory Project, Department of Chemistry University of Florida 2328 New Physics Bldg, PO Box 118435 Gainesville, FL 32611-8435 USA Tel: 352-392-6973 Fax: 352-392-8722 Email: [email protected]

Andrea Michalkova Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-9791041 Fax: 601-9797823 Email: [email protected]

Jane Murray University of New Orleans Department of Chemistry New Orleans, LA 70148 USA Tel: 202-351-1554 Fax: 440-331-1785 Email: [email protected]

Paul C. Muzio Executive Director for Infrastructure, Army HPC Research Center and VP-Government Programs Network Computing Services, Inc. 1200 Washington Avenue S. Minneapolis, MN 55415 USA Tel: 612-337-3420 Fax: 612-337-3400 Email: [email protected]


220

Jamshid Najafpour Khalig-e-fars Ave. Tehran, Tehran 18735-334 Iran Tel: +98-9126458634 Fax: +98-21-22296122 Email: [email protected]

Abdul K. Mohamed Dean Emeritus, College of Science, Engineering & Technology Jackson State University Jackson, MS 39217 USA Tel: 601-979-2153 Email: [email protected]

Brian Napolion 115 Pemberton Street Vicksburg, MS 39183 U.S.A. Tel: 601-955-7696 Email: [email protected]

Edmund Moses Ndip East Queen & Tyler Streets Hampton University Hampton, VA 23668 USA Tel: 757 727 5043 Fax: 757 727 5604 Email: [email protected]

Adria Neely Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-639-6069 Email: [email protected]

Sergey Nefediev Karl Marx str., 68 Kazan, 420015 Russia Tel: 7-(843)-231-41-00 Email: [email protected]

Ricky Nellas Rm 400 Choppin Hall Department of Chemistry Louisiana State University Baton Rouge, LA 70802 USA Tel: 225-235-8429 Email: [email protected]

Srinivas Odde 417 Faser Hall, Department of Medcinal Chemistry University of Mississippi Mississippi Oxford, MS 38677 USA Tel: 662-91-1853 Fax: 662-915-5638 Email: [email protected]

Yngve Ohrn University of Florida PO Box 118435 Gainesville, FL 32611-8435 USA Tel: 352-392-6979 Fax: 352-392-8722 Email: [email protected]

Felix Okojie Vice President for Research and Strategic Initiatives Jackson State University Jackson, MS 39217 USA Tel: 601-979-2931 Fax: 601-979-3664 Email: [email protected]

Sergiy Okovytyy Dneporpetrovsk National University Nauchny St., 13 Dnepropetrovsk, 49625 Ukraine Tel: +(38056)776-46-08 Email: [email protected]

Daniel Osborne University of Tennessee Health Science Center 894 Union Ave. 503 Nash Building Memphis, TN 38163 USA Tel: 205-913-6117 Email: [email protected]

Ourida Ouamerali USTHB University BP N° 32 El Alia Bab- Ezzouar Algiers, 16111 Algeria Tel: +213247311 Fax: 213247311 Email: [email protected]

William Parkinson Southeastern Louisiana University Department of Chemistry and Physics Hammond, LA 70401 USA Tel: 9855495124 Fax: 9855495126 Email: [email protected]


221

Yuliya Paukku Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: (601)979-7824 Fax: (601)979-7823 Email: [email protected]

James Perkins Director of Research, Industrial & Community Relations Jackson State University College of Science, Engineering & Technology (CSET) Jackson, MS 39217 USA Phone: 601-979- 2024 E-mail: [email protected]

Tetyana Petrova Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: (601) 979-3979 Fax: (601) 979-7823 Email: [email protected]

Lucjan Piela Warsaw University Department of Chemistry, Quantum Chemistry Laboratory 1 L. Pasteura St Warsaw, 02-093 Poland Tel: +48 22 8220211 (282) Fax: +48 22 8222309 Email: [email protected]

Yevgeniy Podolyan Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-4114 Fax: 601-979-7823 Email: [email protected]

Peter Politzer University of New Orleans Department of Chemistry New Orleans, LA 70148 USA Tel: 202-351-1555 Fax: 440-331-1785 Email: [email protected]

Morgan Ponder Samford University Department of Chemistry Birmingham, AL 35229-2236 U.S.A. Tel: 205-726-2680 Fax: 205-726-2479 Email: [email protected]

Lawrence Pratt Fisk University 1000 17th Ave N. Nashville, TN 37208 USA Tel: 515.329.8559 Email: [email protected] Rita Presley Associate Vice President for Research & Sponsored Programs Jackson State University Jackson, MS 39217 USA Phone: 601.979.2457 E-mail: [email protected] Richard A. Price Research Agronomist US Army Corps of Engineer Research and Development Center ERDC Executive Office 3909 Halls Ferry Road Vicksburg, Mississippi 39180-6199 Email: [email protected]

Peter Pulay Department of Chemistry and Biochemistry University of Arkansas Fayetteville, AR 72701 USA Tel: (479)-575-6612 Fax: (479)-575-4049 Email: [email protected]

Mohammad Mo Qasim 3909 Halls Ferry Road ERDC-EL-MS Vicksburg, MSWarren 39180 USA Tel: (601) 634 3422 Fax: (601) 634 2742 Email: [email protected]

N. Radhakrishnan Vice Chancellor for Research and Economic Development Fort IRC Bldg., 1601 East Market Street, Greensboro, NC 27411 Tel: (336) 334-7500 Fax: (336) 334-7946 E-mail: [email protected]

Janusz Rak Deapratment of Chemistry University of Gdansk Gdansk, Pomorskie80-952 Poland Tel: (+4858) 34 50 322 Fax: (+4858) 34 50 472 Email: [email protected]


222

James Rall West Virginia University Department of Physics PO Box 6315 Morgantown, WV 26506 USA Tel: (304) 685-1303 Email: [email protected]

Bakhtiyor Rasulev Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-7824 Fax: 601-979-7823 Email: [email protected]

Melissa Reeves Department of Chemistry Armstrong Hall Rm 102 Tuskegee University Tuskegee, AL 36088 USA Tel: 3347278237 Fax: 3347278907 Email: [email protected]

Ashley Ringer Georgia Institute of Technology 770 State Street Atlanta, GA 30332-0400 USA Tel: 404 385 1310 Fax: 404 894 7452 [email protected]

Jamar Robinson 219 Jones Hall Chemistry Department Florida A&M University Tallahassee, FL 32307 USA Tel: 850-599-3638 Fax: 850-561-2388 Email: [email protected]

Teri Robinson Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-3981 Fax: 601-979-7824 Email: [email protected]

Dr. Dorris Robinson-Gardner Dean, Division of Graduate Studies Jackson State University Jackson, MS 39217 Tel: 601-979-2455 Email:[email protected]

Szczepan Roszak Wroclaw University of Technology Wroclaw, 50370 Poland Tel: 48-71-3202675 Email: [email protected]

Christina Russell 219 Jones Hall Chemistry Department Florida A&M University Tallahassee, FL 32307 USA Tel: 850-599-3638 Fax: 850-561-2388 Email: [email protected]

Zuhail Sainudeen Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601 9403390 Email: [email protected]

Julia Saloni Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-1632 Fax: 601-979-7823 Email: [email protected]

Henry F. Schaefer III University of Georgia Center for Computational Chemistry 1004 Cedar St. Athens, GA 30602-2556 USA Tel: (706) 542-2067 Fax: (706) 542-0406 Email: [email protected]

Harold A. Scheraga Cornell University Baker Laboratory of Chemistry Ithaca, NY 14853-1301 USA Tel: (607) 255-4034 Fax: (607) 254-4700 Email: [email protected]

Joe Scoggin Department of Chemistry Mississippi State University Mississippi State, MS 39762 USA Tel: (662)-325-9535 Fax: (662)-325-1618 Email: [email protected]


223

Shashi Shekhar Director, Army High Performance Computing Research Center 1200 Washington Avenue S. Minneapolis, MN 55415 USA Tel: (612) 624-8307 Fax: (612) 625-0572 Email: [email protected]

Yinghong Sheng Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601.979.1219 Fax: 601.979.7823 Email: [email protected]

Indu Shukla Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-7824 Fax: 601-979-7823 Email: [email protected]

Manoj Shukla Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-1136 Fax: 601-979-7823 Email: [email protected]

Tomekia Simeon Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601.918.3425 Email: [email protected]

Prasanna Sivaprakasam 417, Faser Hall Department of medicinal chemistry School of Pharmacy University, MS 38677 USA Tel: 662-915-1853 Email: [email protected]

Bri Smith Florida State University 1817 Call Ave Tallahassee, FL 32304 USA Tel: 850-599-3600 Email: [email protected]

W. Andrzej Sokalski Wroclaw University of Technology Institute of Physical and Theoretical Chemistry Wyb. Wyspianskiego 27 Wroclaw, 50-370 Poland Tel: +48 (71) 320 2457 Fax: +48 (71) 320 3364 Email: [email protected]

Vitaly Solkan N. D. Zelinsky Institute of Organic Chemistry Moscow, 119991 Russia Tel: +7(495)1356425 Fax: +7(495)1355328 Email: [email protected]

Thomas Sommerfeld SLU 10787 Southeastern Louisiana University Department of Chemistry and Physics Hammond, LA 70402 USA Tel: 985-549-5973 Fax: 985-549-5126 Email: [email protected]

Amika Sood Mississippi College Department of Chemistry Box 4036 Clinton, MS 39058 USA Tel: 601-925-3852 Fax: 601-925-3933 Email: [email protected]

Mary Spulak 300 LaSalle Court Loyola University New Orleans, LA 70118 USA Tel: 504 865 2267 Email: [email protected]

Bobby G. Sumpter Oak Ridge National Laboratory Computer Science and Mathematics Division P. O. Box 2008, MS 6197 Oak Ridge, TN 37831 USA Tel: 865-574-4973 Fax: 865-574-0680 Email: [email protected] Shelton Swanier Director of The Office of Strategic Initiatives College of Science, Engineering and Technology Jackson State University Jackson, MS 39217 Tel: 601-979-2312 Email: [email protected]


224

Dinadayalane Tandabany Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-7824 Fax: 601-979-7823 Email: [email protected]

Lyssa Taylor Mississippi College Department of Chemistry Box 4036 Clinton, MS 39058 USA Tel: 601-925-3852 Fax: 601-925-3933 Email: [email protected]

Tamara Taylor Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-454-0052 Fax: 601-979-7823 Email: [email protected]

Paul B. Tchounwou Interim Associate Dean College of Science, Engineering and Technology Jackson State University 1325 Lynch St Jackson, MS 39217 601-979-2153 E-mail: [email protected]

Kanchana S. Thanthiriwatte Department of Chemistry Mississippi State University Box 9573 Mississippi State, MS 39762 USA Tel: (662)-325-4633 Fax: (662)-325-1618 Email: [email protected]

Dabrisha Thomas 219 Jones Hall Department of Chemistry Florida A&M University Tallahassee, FL 32307 USA Tel: 850-599-3638 Fax: 850-561-2388 Email: [email protected]

Patrina Thompson Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-606-5824 Email: [email protected]

Julaunica Tigner Department of Chemistry Armstrong Hall Rm 102 Tuskegee University Tuskegee, AL 36088 USA Tel: (334)727-8878 Email: [email protected]

Andrey Toropov Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-7824 Fax: 601-979-7823 Email: [email protected]

Gregory Tschumper Department of Chemistry and Biochemistry 105 Coulter Hall University of Mississippi University, MS 38677 USA Tel: 662-915-5331 Fax: 662-915-7300 Email: [email protected]

Jing Wang Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-1159 Fax: 601-979-7823 Email: [email protected]

John Watts Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601 979 3488 Fax: 601 979 3674 Email: [email protected]

Charles R. Welch Director, Shock and Vibration Information Analysis Center, IT Laboratory US Army Engineer Research and Development Center 3909 Halls Ferry Road Vicksburg, MS 39180 Phone: 601.634.3297 Email: [email protected]

Abby Weldon Department of Chemistry and Biochemistry 107 Coulter Hall University, MS 38677 USA Tel: 662-915-3891 Fax: 662-915-7300 Email: [email protected]


225

Max Wentlandt 300 LaSalle Court Loyola University New Orleans, LA 70118 USA Tel: 504 865 2267 Email: [email protected]

John E. West Acting Deputy Director, ITL US Army Corps of Engineer Research and Development Center ERDC Executive Office 3909 Halls Ferry Road Vicksburg, Mississippi 39180-6199

Robert W. Whalin Associate Dean, College of Science, Engineering & Technology Jackson State University Jackson, MS 39217 USA Tel: 601-979-4043 Email: [email protected]

Andrzej Wierzbicki Department of Chemistry University of South Alabama Mobile, AL 36688 USA Tel: 251-4607436 Fax: 251-4607359 Email: [email protected]

Adrian Wilson Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: 601-979-7824 Fax: 601-979-3723 Email: [email protected]

Jianhua Wu Jackson State University Department of Physics Jackson, MS 39217 USA Tel: 6019793640 Email: [email protected]

Aihua Xie Faser Hall 417 Department of Medicinal Chemistry University of Mississippi University , MS 38677 USA Tel: 662-915-1857 Email: [email protected]

Shihai Yang University of Southern Mississippi Hattiesburg, MS 39401 USA Tel: 601-297-5459 Email: [email protected]

Ilya Yanov Jackson State University Department of Chemistry 1325 J.R. Lynch Street P.O. Box 17910 Jackson, MS 39217 U.S.A. Tel: (601)979-7824 Fax: (601)979-7823 Email: [email protected]

Anthony Yau US Army Research Laboratory BLDG 394 RM 216-B ABER PROV GRD, MD 21005 USA Tel: 410 278 9565 Fax: 410 297 9521 Email: [email protected] Hongtao Yu Jackson State University Department of Chemistry 1325 Lynch St. Jackson, MS 39217 U.S.A. Tel: (601)979-2174 Fax: (601)979-3674 Email: [email protected]

Viatcheslav Zakrzewski 179 Chemistry Building Auburn University Auburn, AL 36849 USA Tel: 334-844-7920 Fax: 334-844-6959 Email: [email protected]

Shuming Zhang 101 Chemistry Bldg 348 N Arkansas Ave Fayetteville, AR 72701 USA Tel: 479-575-5080 Email: [email protected]

Jian-Ge Zhou 1400 Lynch Street Department of Physics Jackson State University Jackson, MS 39217 USA Tel: 601-979-3640 Fax: 601-979-3630 Email: [email protected]

Author Index Conference on Current Trends in Computational Chemistry 2006

227

Author Index

Anderson, J.A..................................... 19 Artemenko, A.G............................. 94,98 Asenenko, A..................................... 138 Assfeld, X. ....................................... 105 Baker, J..................................... 129,207 Baldwin, E. ...................................... 176 Bamgbelu, A. .................................... 20 Basilevsky, M.V. ................................. 21 Bishop, G.R........................................ 60 Black, S.M. ........................................ 20 Bolshakov, V.I...............................22, 24 Bonifassi, P. ................................27,102 Bowen, K.H........................................ 69 Boyd, R.J........................................... 28 Bredas, J.-L. ...................................... 29 Brown, J. ........................................ 30 Bryan, D.................................... 143,180 Burda,J.V........................................... 31 Cafiero, M.......................................... 36 Cain-Davis, D. ................................. 121 Cao, Z............................................. 208 Cha, C............................................... 57 Chen, B. ................................80,109,117 Cheng, Q. ......................................... 32 Clark, S.R. ...................................... 202 Coghlan, C.B. .................................. 108 Cooks, S.M. ....................................... 33 Cooperwood, J.S. ............................. 139 Crews, B............................................ 34 Crockett, V. ...................................... 35 Cross, J. ........................................... 36 Culberson, L. .................................... 36 Daga, P.R. ........................................ 37 Darbha, G.K. ..................................... 39 de Vries M.S. ..................................... 34 DeFusco, A. ..................................... 173 Derek, E. .......................................... 57 Dinadayalane, T. C. .............40,74,77,152 Ding, Y. ............................................ 43 Do, C. .............................................. 57 Doerksen, R.J.........................37,154,202 Dolgounitcheva, O. ......................44,206 Doskocz, J. ..................................... 142 Doskocz, M. .................................... 142 Dula, C. E. ......................................... 46 Dunn, B........................................... 143 Dyguda-Kazimierowicz, E. ................. 156 Edwards, J. ..........................139,143,180 El-Sayed, M.A. .................................. 49 ElSohly, A.M....................................... 50 Eustis, S............................................ 69 Fayton, F. Jr....................................... 51 Fayton, F.A. ....................................... 62 Fells, J.I. Sr. ..................................... 52 Feng, L............................................ 191 Ferreira, D. ........................................ 43 Ford-Green, J. ................................... 53 Fort, Y............................................... 83 Fortenberry, R.................................... 54 Fortner, A. ......................................... 39 Francisco, J.S. .................................. 194

Fredrickson , H. .................................. 84 Freeman, F. ..................................56,57 Fronczek, F.R. ............................ 121,122 Fronczek, F. ..........................30,121,122 Fuentes-Cabrera, M. ........................... 58 Furmanchuk, A. .................................. 59 Garrett, E.C. ...................................... 60 Gibson, A.A. ..................................51,62 Gilson, M.K. ....................................... 86 Gorb, L..........59,78,84,85,88,124,130,140 Grebneva, H. A................................... 63 Griffin, J. ........................................... 39 Gros, P.............................................. 83 Gu, J. ........................................67,193 Gutowski, M. ...................................... 69 Gwaltney,S.R. .................................. 179 Hagelberg,F. ........................104,201,209 Hamme, A. ..................................... 136 Hammes-Schiffer, S. ........................... 68 Hamilton, T........................................ 33 Haranczyk, M. .................................... 69 Hargittai, M..................................72,186 Harkless, J.A.W. .............................51,62 Hassan, A. ......................................... 74 Hercules, W.A. ...............................51,62 Hill, G.A. ......................34,35,77,114,182 Hofto, M. ........................................... 36 Hoggan, P.E. ...................................... 76 Holmes,T.M........................................ 77 Honea, P. ....................................... 175 Hopkins, B.W. ................................... 50 Hovorun, R.D. .................................. 210 Hoyle, C.E. ........................................ 54 Hromov, A.I. ...................................... 98 Huang, M.-J. ........................101,102,195 Hwang, J.H. ...................................... 57 Isayev,O........................................59,78 Jain, H. ............................................ 79 Johnson, E. ........................................ 79 Jordan, K.D...................................... 173 Kaczmarek, A.................................35,40 Keasler, S.......................................... 80 Keith, J.B........................................... 81 Khartabil, H.K..................................... 83 Kholod, Y. .............................. 84,84,205 Khushbaktova, Z.A. .......................... 137 Killian, B.J. ....................................... 86 King, E. ........................................... 183 Kittle, A.G.......................................... 36 Kolodziejczyk, W.............................34,87 Kosenkov, D. ..................................... 88 Kuramshina, G.M. ............................. 90 Kuz’min, V.E. .................................94,98 Leszczynski, J.................................... 22, 24,27,31,34,35,40,53,59,67,74,77,78,84, 85,87,88,102,119,124,130,136,137,140, 142,147,150,151,152,156,157,160,182, 184,193,199,205 Lewis, J.P. ......................................... 81 Li, X.-C. ............................................ 43 Liahovskij, A.V. .................................. 98

Conference on Current Trends in Computational Chemistry 2006 Author Index

228

Liao, M.-S. ................................ 101,102 Liu, D. ............................................ 104 Liu, Y. ............................................. 188 Loos, P.-F. ...................................... 105 Lopez, M.F.R. ..................................... 83 Lukaszewicz, J.................................... 40 Magers, B. ................................ 107, 108 Magers, D.H..... 32,54,60,107,108,175,178 Majumdar, D. .................................53,87 McAlexander, H. ......................... 107,108 McKenzie, M. ................................... 109 Merz, K.M. Jr.................................... 110 Miao, W. .......................................... 54 Michalkova, A. .....................119,140,199 Moore, B. ........................................ 130 Moussi, S. ....................................... 111 Muratov, E.N..................................94,98 Musa, M. ........................................ 139 Najafpour, J. ................................... 112 Napolion, B. ................................... 113 Ndip, E. M. N. .................................... 46 Neely, A. ......................................... 114 Nefediev, S.E. .................................. 115 Nellas, R.B...................................80,117 Nguyen, N.V. ................................... 126 Noe, E. A. ....................... 30,121,122,123 Ognichenko, L.N. ................................ 98 Ohrn, Y. .......................................... 118 Okovytyy, S.I......................22,24,85,124 Ortiz, J. V. ...................................44,206 Ouamerali, O.................................... 111 Pandey, R. ....................................... 204 Parker, R. ............................139,143,180 Parkinson, W.A................................. 176 Parrill, A.L. ........................................ 52 Paukku, Y. ....................................... 119 Pawar, D.M. .................... 30,121,122,123 Pentin, Yu.A. ...................................... 90 Petit, L. ............................................. 58 Petrova, T........................................ 124 Pham, D.J.A. ...................................... 56 Phan, D.H.T. ................................... 126 Phung, L............................................ 57 Phung, Q.T. ....................................... 57 Picorelli, T.......................................... 57 Polischuk, P.G. ................................... 98 Pratt, L.M. ...................................... 126 Pulay, P. ................................... 129,207 Qasim, M................................ 84,85,130 Ra, P.C............................................ 144 Radisic, D. ......................................... 69 Rak, J. ..........................................67,69 Rao,J.S. .......................................... 133 Rasulev, B. F........................136,137,184 Ray, P.C. .......................................27,39 Reeves,M.S...................................... 183 Ringer, A.L....................................... 138 Robinson, J. ..................................... 139 Robinson, T. L. ................................. 140 Rossikhin, V.V. ..............................22, 24 Roszak, S. ..................................87,142 Russell, C. ....................................... 143 Sadjadi, A........................................ 112

Sainudeen, Z. .................................. 144 Salter, E.A. ..................................... 145 Sastry,G.N....................................... 133 Scheraga, H.A. ................................. 146 Scott, D.E. ........................................ 46 Shafiee, G.H. ................................... 112 Shahbazian, S. ................................ 112 Sharapov, D.A. .................................. 90 Sharapova, S.A. ................................ 90 Sherrill, C.D. .................................... 138 Shukla, I. ........................................ 151 Shukla, M.K. ............................. 147,150 Shvartsburg, A.A. ............................. 201 Sibedwo, G.K. .................................... 46 Simeon, T. ...................................... 152 Sivaprakasam, P. ............................. 154 Skwara, B.......................................... 35 Sokalski, A. .................................... 156 Soloducho, J. ................................... 142 Sommerfeld, T. ............................... 173 Sood, A. ......................................... 175 Sponer, J........................................... 58 Sponer, J.E. ...................................... 58 Strauss, N. ..................................... 176 Sumpter, B.G. ..............................58,177 Sun, W. .......................................... 208 Szewczyk, B..................................... 156 Takahashi, H. ..................................... 90 Taylor, L.A. ..................................... 178 Thanthiriwatte,K.S. .......................... 179 Thomas, D. ................................... 180 Thompson, P.C. ..........................34,182 Tigner, J. ........................................ 183 Tigyi, G. ............................................ 52 Toropov, A.A. ............................. 136,184 Tran, P.T.T. ..................................... 126 Tschumper, G.S................. 19,50,185,196 Tsukahara, R. .................................... 52 Urban, M. ........................................ 204 van Sickle, K. .................................... 36 Varga, Z. ........................................ 186 Solkan, V.......... 157,160,163,166,168,171 Voronkov, E.O. ..............................22, 24 Wang, D. ........................................... 69 Wang, H. ........................................... 81 Wang, J.................................67,151,193 Wang, T. ........................................... 57 Wang, Weina ............................. 188,191 Wang, Wenliang ......................... 188,191 Watts, J. D.............. 101,102,113,194,195 Watts, D.J........................................ 195 Weldon, A.J. .................................... 196 Wells, J.C. ......................................... 58 Weng, N.S. ...................................... 112 West, J............................................ 143 Wierzbicki, A. ................................... 145 Wilson, A. ........................................ 199 Wu, J. ............................................ 201 Xie, A........................................ 154,202 Yang, S. .......................................... 204 Yanov, I. ......................................... 205 Zakjevskii, V.V. .................................. 44 Zakrzewski, V.G. ..........................44,206

Author Index Conference on Current Trends in Computational Chemistry 2006

229

Zhang, C. ....................................... 208 Zhang, S. ....................................... 207 Zhou, J.-G. ..................................... 209 Zhurakivsky, R. ............................... 210 Zilberberg, I....................................... 78


231

Complexation of PPI Dendrimers with Zn(II) Ions: A Comprehensive Experimental and Computational Study

Aaron Holley, Hosam Abdelhady, Michael Kruskamp, †Leela Rakesh, Minghui Chai*, ‡Jing Wang and ‡Jerzy Leszczynski*

Department of Chemistry, †Center for Polymer Fluid Dynamics & Applied Mathematics, Central Michigan University, Mt. Pleasant, MI 48859

‡Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217

PPI [poly(propyleneimine)] dendrimers are multidentate ligands which can chelate with metal ions to form complexes using the primary and tertiary amino groups in their structures. In this study we used NMR spectroscopy to probe the preferred binding sites of different generation (G1-G3) PPI dendrimers with Zn(II) ions. AFM (atomic force microscopy) was also used to detect the sizes of these dendrimer-metal complexes as well as to explore their surface morphology. The results from the NMR study clearly show that Zn(II) ions prefer to chelate with the primary and tertiary amino groups on the exterior of the dendrimer. For a 1:8 ratio of the PPI-3/Zn(II) complex, interestingly all eleven unique protons can be well resolved in the 2D COSY spectrum. Based on the resolved 1H resonances, the 13C NMR resonances can be unambiguously assigned using 2D 1H{13C} HMQC experiments. In addition, the AFM study shows that the surface of the PPI-Zn(II) complexes is “harder” than the surface of the PPI dendrimers, which also indicates that the coordination between the dendrimer and the Zn(II) ion mainly occurs on the exterior of the dendrimer. Furthermore, the results from molecular dynamics simulations and ab initio calculations on the complexes of a different generation PPI dendrimers with Zn(II) ions are consistent with the conclusions from NMR studies. Therefore this work provides an insightful view of where and how metal ions bind with the dendrimers.

Figure (a) Energy of PPI-3/Zn(II) complexes vs. the ratio of PPI-3 to the Zn(II) ions based on molecular dynamic simulation. (b) The optimized structure of the 1:2 system of PPI-1 with Zn(II) ions obtained from ab initio calculations at HF/6-31G level. (Color representation: gray, carbon; blue, nitrogen; orange, zinc. Hydrogen atoms are not displayed.)

0 2 4 6 8 10 12 14 16 18-1600

-1400

-1200

-1000

-800

-600

-400

-200

0

200

400

Min

imiz

ed to

tal e

nerg

y (k

cal/m

ol)

Ratio of PPI-3 to Zn(II)

(a (b)


232

Molecular Dynamics Simulations of the Bt Toxin Cyt1A in Solution

Xiaochuan Li1, Kerrick Nevels1, Dexuan Xie2, and Peter Butko1

1Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406, USA

2Department of Mathematical Sciences, University of Wisconsin, Milwaukee, WI 53201, USA

Cyt1A is a cytolytic toxin from Bacillus thuringiensis (Bt) var. israelensis, used as an environmentally friendly insecticide. Amongst all the Cyt toxins, only the structure of Cyt2A (homologous with Cyt1A) has been determined experimentally. The Cyt toxins interact with lipids and damage lipid membranes. The mechanism of action and the membrane-bound conformation of the Cyt toxins are currently not known with certainty (Butko, 2003). We address these issues by simulating the structure of the toxin in silico. The present results of the molecular dynamics simulations of Cyt1A in solution represent the first step of the project.

The structure of Cyt1A was predicted by homology modeling based on the X-ray structure of the toxin Cyt2A. The conformation of the toxin in explicit and implicit water environments was studied by CHARMM (MacKerrell, Jr., et al., 1998and NAMD, using the Steepest Descent (SD), Adopted Basis Newton-Raphson (ABNR), and the Conjugate Gradient (CG) methods to minimize the energy of the predicted structure.

The model was validated by fluorescence spectroscopy: fluorescence resonance energy transfer (FRET) was used to measure the average distance between the two tryptophans 158/161 and the fluorescently labeled cysteine 191. FRET is often called the molecular ruler because it is suitable to measure small distances within and between the molecules (van der Meer et al., 1994). This is due to the fact that the efficiency E of FRET is a steep function of distance:

E = R0

6/(R6 + R06), (1)

where R0 is a constant specific for each donor/acceptor pair. The basic prerequisite for FRET is spectral overlap between the emission of the donor fluorophore and the absorption of the acceptor fluorophore. We labeled the single cysteine in Cyt1A by 5-({[(2-iodoacetyl)amino]ethyl}amino)-naphthalene-1-sulphonic acid (IAEDANS), which is a good acceptor for tryptophan. The lablel-to-protein ratio was close to one and the labeled toxin was 100% active in a hemolysis assay. The experimental value of the distance between the two tryptophans and the cysteine was 2.14 nm, while the in silico distance was 2.17 nm. We are aware of the interpretational difficulty with two FRET donors instead of one. The calculated distance was between the cysteine and the center of gravity between the two tryptophans. The good accord between the experimental value and the model suggests that our assumption (that each of the two tryptophans donates the same amount of energy to the acceptor) is reasonable.

Upon validation, the computer model was employed to study the significance of two previous experimental observations: (i) amino-acid sequences of all Cyt toxins contain four blocks of highly conserved residues (Butko, 2003) and (ii) several single-point mutations drastically abrogated Cyt1A’s toxicity and binding to lipid.

To address the first issue we devised a scheme, called selective randomization, in which atoms of selected blocks of amino-acid residues were slightly (by a fraction of an angstrom) or less slightly (by a few angstroms) shifted in random directions according to the equation

rnew = rold + rand(0;1) x f, (2)


233

where r is the position vector of an atom and f is a factor that governs the magnitude of the position change: f = 1 for the small perturbation and f = 20 for the large one). The vector rand(0;1) consists of four random numbers between 0 and 1: the first three were used for the coordinate transformation, while the fourth determined the sign of the factor f: when rand4 < 0.5, the sign of f was negative, otherwise it was positive. We compared values of total energy, which included the bond-stretching, bond-bending, bond-torsion and improper energies, as well as van der Waals and Coulomb energies, between the native conformation and the randomized ones. The small perturbations (f = 1) were not informative; they only slightly raised the energy, regardless of what segments of the Cyt1A molecule were randomized (not shown). But with f = 20, the conformation that had the atoms in the conserved blocks randomized exhibited much higher energy than the one, in which only non-block atoms were randomized (see Table). This allows us to conclude that the conserved blocks play a role in proper folding and provide stability to the toxin molecule.

Conformation Number of

randomized atoms Total energy

(kcal/mol) Initial 0 -3404 Non-block 2692 -2733 Block 1154 +849

The mutant K225A, in which lysine 225 was replaced by alanine, was chosen to study the

effect of a single-point mutation. This particular mutation turns off the electrostatic interaction between Lys 225 and Thr 125 (see Figure A). The molecular

dynamics simulations revealed that its consequences are the disruption of the central β sheet and significant changes in the positions of the five flanking α helices (see Figure B, which compares the conformations of the native and mutated toxin). The fact that the conformational differences spread far away from the site of the mutation suggests that the mutant’s loss of toxicity is due to an overall change in conformation and a diminished stability rather than due to a localized alteration of the “binding site” or “active site”, which is often observed in enzymes and binding proteins.

References

1. Butko, P. Cytolytic toxin CytA and its mechanism of membrane damage: Data and

hypotheses. Applied and Environmental Microbiology, 69(5):2415–2422, 2003.


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2. Kale, L., R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten. NAMD2: Greater scalability for parallel molecular dynamics. Journal of Computational Physics, 151(7):283–312, 1999.

3. MacKerell, Jr., A.D., B. Brooks, C.L. Brooks III, B. Roux L. Nilsson, Y. Won, and M. Karplus. CHARMM: The energy function and its parameterization with an overview of the program. The Encyclopedia of Computational Chemistry, 1:271–277, 1998.

4. van der Meer, B. W., G. Coker, and S.Y. Chen. Resonance Energy Transfer: Theory and Data. VCH Publishers, 1994.

5. Ward, E. S., D.J. Ellar, and C.N. Chilcott. Single amino acid changes in the Bacillus thuringiensis var. israelensis delta-endotoxin affect the toxicity and expression of the protein. J. Mol. Biol., 202:527–535, 1988.

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