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8th Theoretical and Computational

Chemistry Workshop

Isfahan University of Technology, Isfahan, Iran

26-27 February 2019

Fundamental concepts and recent researches in theoretical and

computational chemistry

Molecular dynamics simulation workshop

Introduction to GAMESS Software

PROGRAMS

Wednesday, 27 Feb

Time

8:30-9:00 Opening ceremony

9:00-9:35 Dr. E. Keshavarzi Application of CDFT in prediction of the capacitance curve and ion selective

adsorption by nanopores

9.35-10:10 Dr. S. M. Azami Natural Deformation Analysis

10:10-10:50 Poster Presentation & Break

10:50-11:25 Dr. M. Zarif Mapping diffusivity of narrow channels into one-dimension

11:25-12:00 Dr. A. Bordbar Computational Approaches Applied to Rational Drug Design and Discovery

12:00-12:35 Dr. N. Jamshidi How To Identify Molecular Plasmonic?

12:35-14:00 Prayer & Lunch

14:00-14:35 Dr. A. Nassimi Mapping Approach for Simulating Quantum-Classical Dynamics

14:35-15:10 Dr. M. Tabrizchi Ion mobility mass spectroscopy and physical chemistry

15:10-15:45 Dr. Y. Valadbeigi Theoretical and experimental study of ion/molecule reactions

15:45-16:20 Dr. B. Bamdad Parallel computing in computational chemistry

16:20-16:55 Break time

16:55-19:55 workshop 1 Introduction to GAMESS Software

19:55-21:00 Dinner

Thursday, 28 Feb

Time

8:30-9:05 Dr. H. Sabzyan

9:05-9:40 Dr. A. Mohajeri Machine Learning Methods for the Accurate Description of Non-Covalent

Interactions

9:40-10:15 Dr. M. H. Karimi Jafari Diverse sampling from structural space of proteins

10:15-10:50 Poster Presentation &

Break

10:50-11:25 Dr. M. Alaei Ab-initio estimation of magnetic exchange parameters

11:25-12:00 Dr. S. J. Hashemifar Some insights into structure search over the Born-Oppenheimer potential energy

surface

12:00-12:35 Dr. I. Abdolhosseini Highly Anisotropic Thermal Conductivity of 2D group-VA semiconductors

12:35-13:10 Dr. M. H. Kowsari Tracing the dynamics, self-diffusion, and structure of simple guest molecules inside

the nanoporous Li-LSX zeolite by MD simulation

13:10-14:30 Prayer & Lunch

14:30-17:30 workshop 2 Molecular dynamics simulation(GROMACS Software)

15:10-15:45 Break time

19:00-20:00 Dinner

COMMITTEE

Organizing Committee:

Prof. Behzad Rezaei

Prof. Ali A. Ensafi

Dr. Kiamars Eskandari (Scientific director)

Dr. Hossein Farrokhpour (Executive director)

Dr. Mahmood Ashrafizadeh

Executive Committee:

Dr. Hamidreza Jouypazadeh (Executive manager)

Samaneh Khoshkhou

Nasim Orangi

Mostafa Yousefvand

Sara Sadat Karachi

Mahsa Abareghi

Razieh Rabiei

Soraya Abedi

Ali Asghar Mohammadi

Scientific Committee:

Dr. Seyed Mohammad Azami

Yasuj University

Dr. Kiamars Eskandari (Chair)

Isfahan University of Technology

Dr. Hossein Farrokhpour

Isfahan University of Technology

Dr. Alireza Ghasemi

Institute for Advance Studies in Basic Sciences

Dr. Zahra Jamshidi

Chemistry and Chemical Engineering Research Center of Iran

Dr. Fariba Nazari

Institute for Advance Studies in Basic Sciences

Dr. Siamak Noorizadeh

Shahid Chamran University

Dr. Shant Shahbazian

Shahid Beheshti University

Eighth Theoretical and Computational Chemistry Workshop

Isfahan University of Technology, Isfahan

Feb 27–28, 2019

Mapping diffusivity of narrow channels into one-dimension

Mahdi Zarif a*

a Department of Physical and Computational Chemistry, Shahid Beheshti University, Tehran 19839-9411, Iran

Molecular dynamics simulation is used to study the dynamics of two-dimensional hard disks, confined to long, narrow, structureless channels with hard walls. In highly confined systems, particles follow the single-file diffusion (SFD), in which, particles passing each other is forbidden (quasi-1D dynamics). We used the exact equation of diffusion in a purely 1D system as a reference to scale quasi-1D behavior into 1D diffusion [1]. We find that the self-diffusivity data of the quasi-1D system can be collapsed onto a single curve with the 1D data using an effective packing density. Our findings show that the dynamics in highly confined systems are intimately connected to thermodynamics.

Keywords: Diffusion coefficient, SFD, narrow channel, Excess entropy.

References [1] Mahdi Zarif, Richard Bowles, In Preparation



Feb 27–28, 2019

Tracing the dynamics, self-diffusion, and structure of simple guest molecules inside the

nanoporous Li-LSX zeolite by MD simulation

Mohammad H. Kowsaria,b,*

a Department of Chemistry, Institute for Advanced Studies in Basic Sciences (IASBS),

Zanjan 45137-66731, Iran b Center for Research in Climate Change and Global Warming (CRCC), Institute for Advanced

Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran

From 1990ʼs up to now, Li-LSX zeolite, with a faujasite (FAU) based framework, has been

used in chemical industry for the diffusion-selective N2/O2 separation and selective N2

adsorption in dry conditions by cyclic pressure or vacuum swing adsorption (PSA/VSA)

processes. In our recent papers,[1,2] we reported new experimentally compatible molecular

dynamics (MD) studies of the adsorption of both single component and binary mixtures of N2

and O2 guest species within Li-LSX zeolite with the aim of help to understand the air

separation process at the molecular-level. The single-particle dynamics is characterized by

studying the mean-square displacement and velocity autocorrelation function for the centers

of mass of the guest molecules. The intracrystalline self-diffusion coefficient and microscopic

structure of guest species in this zeolite are determined at different temperatures and practical

loadings. The effects of the pendulum-like internal surface motion of extra-framework Li+ in

site III (or fixing it) on the guest static and dynamic processes within the zeolite are also

investigated. N2 component diffuses significantly slower than O2 within the zeolite,

especially with a greater relative diffusivity difference for simulations with fixed Li+ in site

III at low temperatures which correspond to favorable selective adsorption conditions.

Keywords: Molecular dynamics simulation, Self-diffusion, Li-LSX zeolite, Air separation,

Loading effect, Extra-framework cations

References

[1] M. H. Kowsari, Micropor. Mesopor. Mater.,2018, 264, 181.

[2] M. H. Kowsari, J. Phys. Chem. C, 2017, 121, 1770.



Feb 27–28, 2019

Fluorine-Fluorine Non-covalent Interactions

Nasim Orangi a, Gholamreza Zargari b, Kiamars Eskandari c

Department of Chemistry, Isfahan University of Technology, Isfahan, 84156-83111, Iran.

Halogen bonds are noncovalent interactions between halogen atoms (Lewis acids) and

neutral or anionic Lewis bases [1]. In the halogen-halogen interactions (a type of halogen

bond), one of the halogens plays the role of Lewis acid and the other one acts as a Lewis base

[2]. In the present work, the interactions of F...F in some complexes have been investigated.

Since the charge, electrostatic potential and electron density distribution of the interacting

fluorine atoms of the current work are identical, their interaction cannot be regarded as a

Lewis acid-base interaction. So, the F…F interactions cannot be categorized as halogen

bonds. Although the interacting fluorines are completely identical, they connected by a bond

path and hence a bond critical point. Interacting quantum atom (IQA) analysis [3] shows that

the fluorine-fluorine interactions are repulsive in nature and destabilize the complex.

Partitioning the interatomic interactions into classical and quantum components, shows that

the attractive exchange-correlation interaction (with negative value) is not large enough to

compensate the classical repulsion. In other words, the F…F interaction is not responsible for

the formation of their complexes. Instead, the secondary interactions (i.e. the interactions

between not connected atoms) are the driving force for the complex formation.

Keywords: Fluorine-Fluorine interaction, bond path, IQA.

References

[1] M. H. Kolar, P. Hobza, Chem. Rev. 2016, 116, 5155-5187.

[2] R.A. Cormanich, R. Rittner, D. O’Hagan, M. Bühl, J. Phys. Chem. A. 2014, 118, 7901–7910.

[3] A. M. Pendás, E. Francisco, M. Blanco, J. Comput. Chem. 2005, 26, 344-351.



Feb 27–28, 2019

Directional affinity of a spherical Gold nanoparticle for the adsorption of DNA bases

Soraya Abedi and Hossein Farrokhpour*

Department of Chemistry, Isfahan University of Technology, Isfahan, Iran

In this work, the adsorption activities of different facets of a spherical gold nanoparticle for

adenine (ADE) and cytosine (CYT) in two different environments including gas phase and in

the presence of solvent (water) have been investigated, separately. It has been found that the

adsorption energy (Ead) and geometry of the DNA bases depend strongly on the kind of

nanoparticle facet. Comparison of the Eads of bases calculated in the gas phase with those

obtained in the presence of water showed that the electrostatic field of solvent decreases the

Eads of bases, especially, for the Au (110) facet. The adsorption geometry of the CYT

showed strong dependency on the kind of nanoparticle facet compared to ADE. The atoms in

molecules (AIM) analysis has been employed to determine the bond paths (BPs) and bond

critical points (BCPs) between the bases and facets. The infrared (IR) spectra of the bases

adsorbed on the selected facets were calculated and compared with each other and with the

spectra of the isolated bases. It was found that the symmetric and unsymmetric stretching of

the N-H of NH2 group, C-H stretching of the rings and C=O stretching of bases can be used

for the discrimination of the selected facets.

Keywords: Nanoparticle; Au(111); Au(100); Au(110); Adsorption; Directional Affinity; Interaction

References

[1] M. Rosa, W. Sun, Interaction of DNA Bases with Gold Substrates, Journal of Self-Assembly and Molecular

Electronics 1(1) (2013) 41-68.

[2] S. Piana, A. Bilic, The nature of the adsorption of nucleobases on the gold [111] surface, The Journal of

Physical Chemistry B 110(46) (2006) 23467-23471.

[3] L. Liu, D. Xia, The self-assembled behavior of DNA bases on the interface, International journal of

molecular sciences 15(2) (2014) 1901-1914.



Feb 27–28, 2019

TD-DFT and SAC-CI study of the desorption of neutral and ionic alkali metal from the

excited Na+(H2O)n=1..4 and Li+(H2O)n=1..4 models

Samaneh Khoshkhou and Hossein Farrokhpour*

Department of Chemistry, Isfahan University of Technology, Isfahan, Iran

In this work, the potential energy curves of the first and second dissociative electronic

states of ionic alkylated water clusters (M+(H2O)n=1..4 ; M = Li and Na) with one M-O

bond related to the stretching of M-O bond were calculated. Two theoretical methods

including the time-dependent density functional theory (TD-DFT) and direct-symmetry

adapted cluster-configuration interaction (Direct-SAC-CI) were used for calculating the

dissociative states, separately. It was shown that the number of water molecules and their

arrangements in the cluster had the significant effect on the dissociation energy so that the

increase of the size of water cluster led to the decrease of it. Also, it was observed that the

increase of water cluster size caused appearing the bonding electronic states near the

dissociative states. The first dissociative state of M+(H2O)n clusters leads to neutral M and

[(H2O)n]+ in their ground electronic states which shows an electron transfer reaction. In the

second dissociative state, the M+(H2O)n clusters are fragmented to neutral M in its first

excited electronic state (2P) and [(H2O)n]+ in its ground electronic state based on the TD-

DFT method while the assignment of fragments depends on the size of water cluster in the

Direct-SAC-CI method. In addition, the calculations were also performed in the presence of

water as solvent using the TD-DFT method to see the effect of electrostatic field of solvent

on the dissociative states. It was observed that the electrostatic field of solvent prevents the

electron transfer from the water cluster to M+ in the dissociative states and increases the

bonding character of these states.

Keywords: Dissociative states; Excited state; TD-DFT; SAC-CI; Alkylated water clusters; Photo

stimulated

References

[1] Arismendi-Arrieta, D. J.; Riera, M.; Bajaj, P.; Prosmiti, R.; Paesani, F., I-Ttm Model for Ab Initio-Based

Ion–Water Interaction Potentials. 1. Halide–Water Potential Energy Functions. The Journal of Physical

Chemistry B, 2015, 120, 1822-1832.

[2] Schulz, F.; Hartke, B., Structural Information on Alkali Cation Microhydration Clusters from Infrared

Spectra. Physical Chemistry Chemical Physics, 2003, 5, 5021-5030.

[3] Schulz, C.; Haugstätter, R.; Tittes, H.-U.; Hertel, I., Free Sodium-Water Clusters: Photoionisation Studies in

a Pulsed Molecular Beam Source. Zeitschrift für Physik D Atoms, Molecules and Clusters, 1988, 10, 279-290.

[4] Ali, S. M.; De, S.; Maity, D., Microhydration of Cs+ ion: A Density Functional Theory Study on Cs+–(H2O)n

Clusters (n= 1–10). The Journal of chemical physics, 2007, 127, 044303.

[5] Glendening, E. D.; Feller, D., Cation-Water Interactions: The M+ (H2O)n Clusters for Alkali Metals, M= Li,

Na, K, Rb, and Cs. The Journal of Physical Chemistry, 1995, 99, 3060-3067.



Feb 27–28, 2019

Theoretical studies on the potentials of some nanocages

(Al12N12, Al12P12, B12N12, Be12O12, C12Si12, Mg12O12

and C24) on the detection and adsorption of Tabun molecule: DFT

and TD-DFT study

Paria Fallahi, Hamidreza Jouypazadeh* and Hossein Farrokhpour*

Department of chemistry, Isfahan University of Technology, Isfahan, Iran, 84156-83111

In the present study, the adsorption of tabun molecule on the some important nanocages such

as Al12N12, Al12P12, B12N12, Be12O12, C12Si12, Mg12O12 and C24 was studied theoretically in

details. The calculated adsorption energies (Eads) showed that Mg12O12 has the highest value

of Ead without any chemical change in the structure of tabun while Al12N12 has one advantage

compared to Mg12O12 which is the destruction of tabun on the surface of cage. The important

atoms of tabun responsible for the interaction with nanocages were determined. It was found

that the O atoms of P=O bonds of tabun interacts with the Al, Be, B, Si and C atoms. The

quantum theory of atoms in molecule (QTAIM) was used to determine the nature of the

interaction between the tabun and selected nanocages. It was found that the interaction

change from van der Waals to nearly covalent. The potential of the nanocages for sensing the

tabun molecule were studied by calculating both the UV absorption spectra of complexes and

their density of states (DOS). The calculations showed that four nanocages including Al12P12,

Be12O12, B12N12 and C24 have potential as good sensor for tabun.

Keyword: Tabun, Adsorption, Sensing, Nanocage, DFT-D3, TD-DFT



Feb 27–28, 2019

A Comparative Investigation of the Adsorption of CH4, CH3F, CH3Cl, and CH3Br

onto the Surface of the Pristine, Al-doped, and Ga-doped Boron Nitride Nanocage

(B12N12): DFT and MP2 Study

Mohsen Doust Mohammadi, Majid Hamzehloo*

School of Chemistry, College of Science, University of Tehran, Tehran, Iran

The first application of carbon nanotube (CNT) as a sensor was an opening gate to the

nanoscience world; afterward, there was an increasing interest to synthesis of the modified

and activated surfaces of nanotubes by using functionalizing or surface defecting methods. It

goes without saying that in today's scientific world, the study of nanostructures as an absorber

in combination with gases could be a paramount consideration for researchers in this field

who seeking for the affordable nanosubstances with salient properties [1,2]. Accordingly,

theoretical studies focused on functionalization of nanocage types of nanostructure surfaces

to enhance their sensitivity into specific absorbents are in minority. There are many

molecules could be absorbed through chemical or physical mechanism onto the exterior

surface of the decorated nanostructures with large binding energy, which suggests that the

improved nanocages would be a sensitive sensor.

In the present work, a comparative investigation of the adsorption of methane (CH4),

fluoromethane (CH3F), chloromethane (CH3Cl), and bromomethane (CH3Br) onto the

exterior surface of the pristine, aluminium-doped (Al-doped), and gallium-doped (Ga-doped)

boron nitride nanocage (B12N12) was investigated. The geometry optimization calculations

were performed by using DFT method at both PBEh-3c/Def2-SVP and B3LYP/def2-SVP

levels of theories. To further investigation, single point energy calculation using CAM-

B3LYP/Def2-TZVP and MP2/cc-PVTZ were also performed. Moreover, natural bond orbital

(NBO) and quantum theory of atoms in molecules (QTAIM) analyses were approved the

electronic properties. In this regard, the Wiberg bond index (WBI), natural charge, natural

electron configuration, donor-acceptor NBO interactions, and the second-order perturbation

energies are considered. These analyses denote that the tendency of the CH4 and halomethane

molecules to adsorb onto the surfaces of the nanocages were on the order of B11(Al)N12 >

B11(Ga)N12 > B12N12 and the order of the adsorption of the gas molecules regarding the

affinity to adsorb onto the nanocages is consistently repeated as follows: CH3F > CH3Br >

CH3Cl > CH4. The results show that the strongest adsorptions of the halomethanes have been

occurred on the aluminium-doped nanocage and this nanocage may be a good candidate for

sensing the halomethane gases.

Keyword: B12N12; DFT; Halomethane; Nanocage; QTAIM.

References

[1] M. Abbasi, E. Nemati-Kande, M.D. Mohammadi, Computational and Theoretical Chemistry, 1132 (2018) 1-

11.

[2] E. Nemati-Kande, M. Abbasi, M.D. Mohammadi, Chemistry Select 3 (34), 9833-9840



Feb 27–28, 2019

Density functional theory study of the adsorption of methanol on the surface of pristine

graphdiyne

Maryam Ebadia, Adel Reisi-Vanania*

aDepartment of Physical Chemistry, Faculty of Chemistry, University of Kashan, Kashan, Iran

Abstract

Over the last decade, carbon nanostructures such as carbon nanotubes and graphene due to

their interesing electrical properties and unique structures have been extensively investigated

in many applications. These nanomaterials have been successfully used as sensing materials

[1, 2]. Graphdiyne (GDY) is a new carbon allotrope, consisting of an s‒p and s‒p2 hybridized

carbon network. GDY was successfully synthesized via cross-coupling reaction using

hexaethynylbenzene on the surface of copper [3]. Methanol is the second most plentiful

organic molecule in atmosphere after methane, and it is the simplest of the alcohols. It is

apply for instance as a replacement fuel, a solvent and as a source for manufacture of other

chemicals. In this work, the adsorption energies and orientations of single methanol molecule

on the pristine GDY was investigated by first-principles density functional (DFT)

calculations with dispersion correction. It is discovered that for adsorption of methanol on

pristine GDY, relatively parallel orientation is more favorable than other orientations. It is

found that methanol molecule is physisorbed on the pristine GDY with small adsorption

energy of -0.35 eV. We realized that methanol prefer to orient relatively parallely with O

atom close to the sheet. electronic properties of pristine GDY are insensitive to the methanol

adsorption. However, methanol adsorption can not alter the electronic properties of pristine

GDY. The charge transfer between methanol and GDY was earned from lowdin population

analysis. For methanol on GDY, the calculated partial charges on the –OH and –CH3

fragments of the molecule are about –0.074e and +0.332e, respectively. As a result, charge

(0.258e) is transferred from methanol to the GDY.

Keywords: Graphdiyne; Nano-sheet; Electronic properties; Carbon 2-D structure, Methanol

References

[1] Ueda T, Bhuiyan M, Norimatsu H, Katsuki S, Ikegami T, Mitsugi F. Development of

carbon nanotube-based gas sensors for NOx gas detection working at low temperature.

Physica E: Low-dimensional Systems and Nanostructures 2008;40:2272-7.

[2] Nguyen L, Phi T, Phan P, Vu H, Nguyen-Duc C, Fossard F. Synthesis of multi-walled

carbon nanotubes for NH3 gas detection. Physica E: Low-dimensional Systems and

Nanostructures 2007;37:54-7.

[3] Li G, Li Y, Liu H, Guo Y, Li Y, Zhu D. Architecture of graphdiyne nanoscale films.

Chemical Communications 2010;46:3256-8.



Feb 27–28, 2019

Effort on the establishment of an explicit relationship between potential function and

state dependence of energy perturbation terms in nanostructures modeled by particle

in-a-box approach

Iraj Ahadzadeha*, Amin Norouzi

b

a,bResearch Laboratory for Electrochemical Instrumentation and Energy Systems, Department of

Physical Chemistry, Faculty of Chemistry, University of Tabriz, 29 Bahman Blvd. Tabriz, IRAN

Abstract

Among well-established theoretical models used for investigation of

nanostructures, particle–in–a– box model has a central position due to its rather simplicity

of the mathematics involved and very satisfactory subsequent predictions of the behavior

of such systems. Perturbation theory is one of the well-developed approaches to

approximately solve the Schrödinger equation for real systems in which due to the special

form of the potential function involved, exact solutions is unknown [1]. Due to the

deterministic role of the potential function on systems further properties, it seems quite

necessary to seek for more possible basic relationships between exact explicit from of the

potential function of a particle–in–a–box model and its properties such as the way this

perturbing potential affects the approximate energy levels, convergence or divergence of

the perturbation part of energy at large quantum numbers and so on. The importance of

this approach lies in the fact that potential function of particle–in–a–box systems can be

arbitrarily tailored with insertion of different atoms and/or molecules. Also it is possible to

design 1D, 2D, and 3D quantum wells for specific research and/or application purposes

such as solid state opto-electronic nanodevices. We focused on the development of a

hopefully working relationship between general form of an arbitrary potential function and

perturbation energy (basically first order correction term) for 1D, 2D, and 3D particle–in–

a-box models. This approach is mainly based on time independent perturbation theory

along with expansion of the general perturbing potential on suitably chosen orthonormal

sets. All involved mathematical calculations are performed by Maple™ mathematical

software. Our preliminary mathematically non–rigorous investigations showed that for

some forms potentials, perturbation terms take a constant value independent of the

quantum state of the system, while for other forms there is an explicit state dependence for

the perturbation energy term for which a decreasing or increasing behavior vs. quantum

number of the system is observed. Effort is being made so that in the development of the

method proposed here, the exact dependence of the perturbation 1st order and possibly

higher terms in energy could be revealed on the basis of the potential at hand for a specific

system. This could further facilitate the analysis of real quantum mechanical systems and

could help to predict behavior of such systems.

Keywords: Time independent Perturbation Theory, Particle-in-a-box, Nanostructures, Potential

function, State dependence

References

[1] I. Petousis, et. al., Phys. Rev., 2016, B 93, 115151.



Feb 27–28, 2019

Investigating the effect of external electric field on Charge-Transfer SERS spectra of

Pyrazine and 4-MethylPyridine molecules

Sahar Ashtari-Jafaria, Zahra Jamshidib*

a b Chemistry & Chemical Engineering Research Center of Iran (CCERCI), Pajohesh Blvd, 17th Km

of Tehran-Karaj Highway, P. O. Box 1496813151 Tehran, Iran.

Since the discovery of surface-enhanced resonance Raman (SERS), elucidating the charge-

transfer (CT) mechanism has been a challenging and controversial process [1]. Different

theoretical models have been proposed concerning the rule of electrode potential on the

SERS-CT enhancement[2], however, achieving a well and conserved trend of experimental

observation and explaining the nature of selective enhancement of the signal is not the trivial

task and still questionable. The good performance and the accuracy of time-dependent

excited-state gradient approximation under the effect of uniform finite electric field for

simulation of the experimental spectra of pyridine on Ag electrode has been previously

presented in our group [3]. The singular pattern of experimental spectra of symmetric and non-

symmetric benzene-like derivative compounds and the well-trend of their enhancements

under variation of electrode potentials motivates us to extend our simulation to 4-

MethylPyridine and Pyrazine molecules on the silver metal cluster. For these molecules the

selective enhancement and de-enhancement of totally symmetric and non-totally symmetric

modes upon changing the field are obtained and matched well with the experiment. The

selective enhancement of each signal in zero-field is explained by following the properties of

transitions such as; shape and symmetry of excited-state charge density difference

and the direction of excited-state vector gradients. On the other hand, turning on the field

perturbs the geometry and electronic structure of the molecules and therefore, influences the

magnitude of specific excited state vector gradients and dimensionless displacements, and

moreover, the pattern of spectra. However, such an interpretation gives an insight into the

nature of selective enhancements and can be a promising investigation for proposing the

selection-rules of SERS-CT.

Keywords: SERS, CT, TD-DFT, Benzene-like derivatives

References

[1] E. C. Le Ru, S. A. Meyer, C. Artur, P. G. Etchegoin, J. Grand, P. Lang and F. Maurel, Chem. Comm., 2011,

47, 3903.

[2] F. Avila, C. Ruano, I. Lopez-Tocon, J. F. Arenas, J. Soto and J. C. Otero, Chem. Comm., 2011, 47, 4213.

[3] M. Mohammadpour, M. H. Khodabandeh, L. Visscher and Z. Jamshidi, J. Phys. Chem. Chem. Phys., 2017,

19, 7833.



Feb 27–28, 2019

Stability of Floxuridine anti-cancer drug adsorbed on N-doped C20 fullerene; a

theoretical study

Foad Buazara*

, Mohamad Hosein Sayahib , Elham Farajollah

b

a Department of Marine Chemistry, Khorramshahr University of Marine Sciences and Technology,

P.O. Box 669, Khorramshahr, Iran

b Payam Noor University of Ahwaz, Ahvaz, 61556-63314, Iran

Nano-medicine is a growing research field dealing with the creation and manipulation of

materials at a nanometer scale for the better treatment, diagnosis and imaging of diseases. As

unique nanoparticles, fullerenes have attracted much attention due to their unparalleled

physical, chemical and biological properties [1]. In this study, the effects of absorption of

floxuridine anticancer drug on nanoparticles of N-doped fullerene were investigated using

density functional theory methods by Gaussian 09 software [2-4]. The binding energie (Eb) of

interaction state of A are calculated to be -0.05141 kcal/mol. The binding energy (Eb) of A

turns out to be energetically more favorable than the other structures. At the point of

Hardness A is more favorable than other structures with -0.4389 kcal/mol hardness and At

the point of Electrophilicity, A is more favorable than other structures with 4.9572 kcal/mol

Electrophilicity.

Keywords: N-doped fullerene - Floxuridine - HOMO-LUMO Energy gap - Density Functional

Theory.

References

[1] H. Prinzbach, A. Weiler, P. Landenberger, F. Wahl, L. T. Scott, M. Gelmont, D. Olevano and B. V.

Issendorff, Nature, 2000,407, 60.

[2] M.Z. Kassaee , F. Buazar , M. Koohi , THEOCHEM, 2010,940, 19.

[3] M.Z. Kassaee, S.M. Musavi, F. Buazar, THEOCHEM, 2005,728, 15.

[4] M.T. Baei, Nanostruc,. 2012, 20, 681.



Feb 27–28, 2019

N-Heterocyclic germylenes in focus: Steric effects on nucleophilicity of novel tetrazole-

5-germavinylidenes at DFT

Somayyeh Rahmatia, Mohammad Zaman Kassaeeb*

a bDepartment of Chemistry, Faculty of Science, Tarbiat Modares University, Tehran, Iran

Discovery of N-heterocyclic germylenes (NHGes) began years before Arduengo s report on

N-hetrocyclic carbenes (NHCs) in 19911. In this work 20 novel NHGes are characterized at

B3LYP/6-311++G**level of theory. Nucleophilicity (N) is anticipated to be a crucial factor for coordination of NHGes to transition metal complexes2,3. Hence, comparison is made

between N of a series of 1,4-disubstituted tetrazol-5-germavinylidenes (“normal”, 1R), and their corresponding ten 1,3-disubstituted isomers (“mesoionic, or abnormal”, 2R), where R =

H, methyl, ethyl, i-propyl, and t-butyl. Similarly to their corresponding carbenes where a singlet is more nucleophilic than its corresponding triplet, all of our ten singlet NHGes appear

more nucleophilic than their related triplet isomers. In addition, N increases as the size of the substituent increases. The global electrophilicity (ω) trend takes on an exactly opposite

direction. It means that electrophilicity of each triplet NHGes is more than its corresponding

singlet isomer. Stabilities of 1R and 2R are presumed to be related to their singlet–triplet

energy gaps (∆ES-T, kcal mol-1

).Every triplet normal 1R appears more stable than its

corresponding singlet normal 1R and every triplet abnormal 2R isomer appears more stable

than its corresponding singlet abnormal 2R . The most stable germylene among the normal

and abnormal series is 2iso-propyl; while the least stable one is 1t-butyl.

Every triplet shows a wider band gap than its corresponding singlet, for showing a larger

ΔEHOMO- LUMO .The highest value of band gap is for triplet 1H, ΔEHOMO-LUMO = 85.67 kcal

mol-1

and the lowest is for singlet 2iso-propyl, ΔEHOMO-LUMO = 18.57 kcal mol-1

.

Keywords: DFT, Germylene, Nucleophilicity, steric effect.

References

[1] M.B. Smith, J. March, Advanced Organic Chemistry, fifth ed., Wiley-Interscience, New York, 2001

(Chapter 5).

[2] A.J. Arduengo, R.L. Harlow, M. Kline, A stable crystalline carbene, J. Am. Chem.Soc. 113, 1991, 361–363.

[3] O. Kuhl, Coordination. Chem. Rev. 248, 2004, 411.



Feb 27–28, 2019

Investigation study of Stabilization Level of Fullerene Interaction with Diclofenac and

Naproxen Drugs

Foad Buazara*, Mouhammad hussain Sayahi, Khadijeh Sayahi

b


P.O. Box 669, Khorramshahr, Iran

b Payam Noor University of Ahwaz, Ahvaz, 61556-63314, Iran

Abstract

As unique nanoparticles, fullerenes have attracted much attention due to their unparalleled


Diclofenac and Naproxen druges on nanoparticles of fullerene C20 were investigated using

density functional theory methods by Gaussian 09 software, We used DFT / B3LYP method

and 6-311+G* basis set, we first obtained the values of EHomo, ELumo and system energy for

Diclofenac, Naproxen, fullerenes, drug-fullerene complexes[2].

The binding energies (Eb) of two interaction states of C20-Diclo OO and C20-Napro O24 are

calculated to be -0.058170237 kcal/mol, 0.270382621 kcal/mol respectively, The negative

energy of Diclofenac drug indicate that this drug is willing to make complexed with

fullerene, But the Positive energy of Naproxen indicate that this drug is not willing to make

complexed with fullerene, t by increasing the temperature can be done.

The binding energy (Eb) and Electrophilicity (with 0.032439584 kcal/mol) of C20-Diclo OO

turns out to be energetically more favorable than the other structures. But at the point of

Hardness, C20-Napro O24 is more favorable than other structures with 7.744149244 kcal/mol

hardness.

Keywords: Naproxen, Fulleren, drug delivery

References

[1] H. Prinzbach, A. Weiler, P. Landenberger, F. Wahl, L. T. Scott, M. Gelmont, D. Olevano and B. V.


[2]M.Kassaee,F.Buazar,M.Koohi, Heteroatom impacts on structure, stability and aromaticity of XnC20n

fullerenes: A theoretical prediction , Thochem, 2010, 940,11.

[3] Maryam Hesabi, Masoumeh Hessabi,, The interaction between carbon nanotube and skin anti-cancer drugs:

a DFT and NBO approach ,Thochem, 2013,3:22,6.

[4] Goenka, S., Sant, V. and Sant, S, Graphene - based nanomaterials for drug delivery and tissue engineering.

Journal of Controlled Release ,2014, 173,pp. 75-88.



Feb 27–28, 2019

Computational study of absorption Naproxen drug on fullerene C20

Foad Buazara*, Mouhammad hussain Sayahi, Khadijeh Sayahi

b


P.O. Box 669, Khorramshahr, Iran b Payam Noor University of Ahwaz, Ahvaz, 61556-63314, Iran

Abstract

As unique nanoparticles, fullerenes have attracted much attention due to their unparalleled


Naproxen drug on nanoparticles of fullerene C20 were investigated using density functional

theory methods by Gaussian 09 software, We used DFT / B3LYP method and 6-311+G*

basis set, we first obtained the values of EHomo, ELumo and system energy for Diclofenac,

fullerenes, Diclofenac-fullerene complexes[2].

The binding energies (Eb) of tow interaction states of C20-Napro O24 and (C20-Napro H29).

are calculated to be 0.270382621 kcal/mol, 0.217042443 kcal/mol respectively, this positive

energy indicate that the drug is not willing to make complexed with fuleren. this bonding

only by increasing the temperature can be done.

The binding energy (Eb) of C20-Napro H29 turns out to be energetically more favorable than

the other structures. But at the point of Hardness and Electrophilicity, C20-Napro O24 is more

favorable than other structures with 7.744149244 kcal/mol hardness and 0.454829075

kcal/mol Electrophilicity. Keywords: Naproxen, Fulleren, drug delivery

References [1] H. Prinzbach, A. Weiler, P. Landenberger, F. Wahl, L. T. Scott, M. Gelmont, D. Olevano and B. V.


[2]M.Kassaee,F.Buazar,M.Koohi, Heteroatom impacts on structure, stability and aromaticity of XnC20n

fullerenes: A theoretical prediction , Thochem, 2010, 940,11.

[3] Maryam Hesabi, Masoumeh Hessabi,, The interaction between carbon nanotube and skin anti-cancer drugs:

a DFT and NBO approach ,Thochem, 2013,3:22,6.

[4] Goenka, S., Sant, V. and Sant, S, Graphene - based nanomaterials for drug delivery and tissue engineering.

Journal of Controlled Release ,2014, 173,pp. 75-88.



Feb 27–28, 2019

Energy conversion ability of natural dyes based on flavonoid: A

computational study

Samira Sabagh, Mohammad Izadyar*, Foroogh Arkan

Computational Chemistry Research Labratory, Department of Chemistry, Faculty of Science, Ferdowsi

University of Mashhad, Mashhad, Iran *[email protected]

In this research, we theoretically investigated the photovoltaic properties of the flavonoid-

based dyes in the natural dye-sensitized solar cells. Also, the ability of the conversion energy

of chlcones and butein dyes (Fig. 1) was estimated through the light harvesting efficiency

(LHE) and the incident photon to current conversion efficiency (IPCE) parameters. The

calculations were done by density functional theory, natural bond orbital analysis and time-

dependent methods [1]. These calculations were done by Gaussian 09 program [2].

Negative values of the Gibbs energies of electron injection (ΔGinj) of these natural dyes

show an efficient electron transfer from the excited dye to TiO2. The results showed that

chlcones-based solar cell has a higher IPCE originated from a greater LHE and a higher

negative character of ΔGinj in comparison with butein. Also, a less excited state oxidation

potential (EOX(dye*) of the chlcones dye improves its energy conversion ability.

Fig. 1. Optimized structures of chlcones and butein dyes.

Keywords: Natural dye, Energy conversion, Solar cell, Excited state

References

[1] R. E. Stratmann, G. E. Scuseria and M. J. Frisch, Journal of Chemical Physics, 1998, 109, 8218-8224.

[2] M. Frisch, G. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, G. Scalmani, V. Barone,

B. Mennucci and G. Petersson,Gaussian 09, revision a. 02, gaussian, Inc., Wallingford, CT 200, 2009



Feb 27–28, 2019

Photon to current efficiency of nobiletin dye as a function of maximum

wavelengths: A theoretical study

Samira Sabagh, Mohammad Izadyar*, Foroogh Arkan

Computational Chemistry Research Labratory, Department of Chemistry, Faculty of Science, Ferdowsi

University of Mashhad, Mashhad, Iran *[email protected]

In this computational work, we focused on the behavior of nobiletin dye (Fig. 1) in

different wavelengths and in the presence of TiO2 and I-/I-3 as the electrolyte. For this goal,

we used Gaussian 09 program [1] and calculated the structural and electronic properties of

nobiletin dye by density functional theory [2]. Also, the spectroscopic properties of the dye

were obtained by the time-dependent method.

On the basis of the results, nobiletin is a good candidate to be applied in the natural dye-

sensitized solar cells, due to an efficient arrangement of the frontier molecular orbitals. In this

system, the LUMO level of the dye (-2.06 eV) lies over the CB of TiO2 [3] and its HOMO

level (-6.29 eV) is under the reduction potential energy of the electrolyte, which facilitate a

proper electron/hole transfer process. Light harvesting efficiency (LHE) and incident photon

to current conversion efficiency (IPCE) of nobiletin as the functions of the maximum

wavelength were predicted at B3LYP/6-311++G(2d,2p) level of theory. The obtained results

showed that IPCE and LHE behaviors in different wavelengths are equal. This presents a

stronger effect of LHE on the IPCE parameters relative to Gibbs energies of electron

injection (ΔGinj). Moreover, the maximum values of the studied efficiencies were observed in

305.96 nm.

Fig. 1. Optimized structures of the nobiletin dye at B3LYP/6-311++G(2d,2p) level of theory .

Keywords: Natural dye, Light harvesting efficiency, Wavelength, Molecular orbital

References

[1] M. Frisch, G. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, G. Scalmani, V. Barone,

B. Mennucci and G. Petersson,Gaussian 09, revision a. 02, gaussian, Inc., Wallingford, CT 200, 2009

[2] M. Dresselhaus, G. Dresselhaus, S. B. Cronin and A. G. Souza Filho, Solid State Properties, 2018, DOI:

10.23647/ca.md20182004

[3] L.-J. He, J. Chen, F.-Q. Bai, R. Jia, J. Wang and H.-X. Zhang, Dyes Pigm, 2017, 251, 261.



Feb 27–28, 2019

Theoretical rationalization of intermolecular interactions:

A perspective from DFT energy partitioning schemes

Faezeh Taravata, Mojtaba Alipoura*

a Department of Chemistry, College of Sciences, Shiraz University, Shiraz 71946-84795, Iran

*Corresponding Author Email: [email protected]

The energy partitioning schemes are powerful tools bridging the gap between elementary

quantum chemistry and conceptually interpretation of intermolecular interactions. In this

study, the density functional theory (DFT)-based energy partitioning schemes through

conventional and modern formalisms have been utilized to find out what energetic

components govern the nature and origin of different types of intermolecular interactions.[1,2]

Diverse datasets covering wide ranges of interactions at equilibrium geometries as well as

during the potential energy curves are investigated. With more or less different roles of the

stabilization and destabilization factors, the electrostatic, exchange–correlation, and steric

effects are shown to be the dominant factors contributing to the total interaction energies.

Furthermore, the obtained profiles of the energetic components and their changing pattern

ascertain that exchange–correlation effects alongside electrostatic and noninteracting kinetic

energy components are determinant contributions following the variations trend of interaction

energies. We also find the reasonable and meaningful correlations between interaction

energies and any of their components based on one- to three-variables fittings for both

equilibrium and nonequlibrium geometries of the formed complexes in each category.

Finally, our results unveil that the traditional and novel DFT energy partitioning schemes can

be employed to figure out the essence of intermolecular interactions, where the DFT

energetic components come into play and further evidences of their quality to theoretical

rationalization of intermolecular interactions are showcased. [3]

Keywords: DFT, energy partitioning scheme, intermolecular interaction

References

[1] R. G. Parr and W. Yang, Density Functional Theory of Atoms and Molecules; Oxford: New York, 1989.

[2] S.Liu, J. Chem. Phys. 2007, 126, 244103.

[3] M.Alipour and F.Taravat, Theor. Chem. Acc., 2018, 137, 143.



Feb 27–28, 2019

Exploring the role of electrostatic and steric forces in

theoretical appreciating chemical reactivity-related phenomena

Faezeh Taravata, Mojtaba Alipoura*

a Department of Chemistry, College of Sciences, Shiraz University, Shiraz 71946-84795, Iran

*Corresponding Author Email: [email protected]

Rationalisation of computational results towards appreciating and predicting chemical

reactivity is a topic worthy of investigation in theoretical chemistry. In this regard, a robust

and generally applicable framework to comprehend the problem is still lacking. However,

based on the density functional theory (DFT) energy partition scheme where the total

electronic energy is decomposed into three independent effects as steric, electrostatic and the

fermionic quantum, the fundamental driving forces of chemical processes to understand

molecular reactivity have recently been proposed. [1, 2]

Herein, the two related descriptors, electrostatic and steric forces, are used to evaluate their

applicability for comprehending some chemical reactivity properties like the electrophilic and

nucleophilic regioselectivity, stereoselectivity and etherification reaction of phenolic

derivatives as illustrative examples.

Highlighting the distinguished characteristics of the descriptors under study, their

usefulness for analysing the chemical reactivity properties and reproducing experimental

evidences is showcased. Overall, our findings corroborate that the DFT energy partitioning

scheme and the associated reactivity descriptors can pave the way towards theoretical

rationalisation of chemical reactivity-related phenomena. [3]

Keywords: DFT, energy partitioning scheme, electronic force, chemical reactivity

References

[1] S.Liu, J. Chem. Phys., 2007, 126, 244103.

[2] C. Liu, T. Rong and S. Lu, Phys. Chem. Chem. Phys., 2017, 19, 1496.

[3] M.Alipour and F. Taravat, Mol. Phys., 2019, 117, 136.



Feb 27–28, 2019

The theoretical conceptual investigation of intramolecular hydrogen bond strength in

the O-H…O=C systems

Hadi Zare a, Mohammad Vakili a*

a Department of Chemistry, Faculty of science, Ferdowsi University of Mashhad, Mashhad, Iran

Hydrogen bond, for the first time, was suggested by Huggins in 1919 [1].

After this, large number of theoretical and experimental studies have been conducted to investigate

the properties of intramolecular and intermolecular hydrogen bonding [2-3]. In an intramolecular

hydrogen bond (IHB) system, both proton donor and proton acceptor groups, which may be of various

kinds of functional groups, are located in the same molecule. The cis-enol forms of β-diketone, β-

aminoenone, and β-enaminoimine molecules are engaged in such a hydrogen bond system and could

be stabilized by a six membered-chelated ring [4]. The aim of this study is Intramolecular hydrogen

bonding (IHB) of a series of molecules, as the simplest resonance-assisted hydrogen bond system in

symmetric O–H…O class, have been studied at the DFT-B3LYP/6-311++G(d,p) level of theory.

Good linear regressions between IHB energies based on Espinosa’s equation [5] with total electronic

density, Laplacian of total electronic density in critical points, geometrical bond lengths, bond angels

and NMR chemical shifts of bridged hydrogen were obtained.

Keywords: Atom In Molecule; DFT.

References

[1] M L. Huggins, Thesis, University of California, 1919.

[2] F. Fuster and S. J. Grabowski, J. Phys. Chem. A, 2011,115, 10078.

[3] A. J. Lopes Jesus and J. S. Redinha, J. Phys. Chem. A. 2011, 115, 14069.

[4] M. Vakili, A-R. Nekoei, S. F. Tayyari, A. Kanaani and N. Sanati, J. Mol. Struc., 2012, 1021, 102.

[5] E. Espinosa, E. Molins and C. Lecomte, Chem. Phys. Lett., 285, 1998, 170.



Feb 27–28, 2019

Estimating the intramolecular hydrogen bonds strength in the O-H…O=C systems

using experimental 1H NMR results and QTAIM calculations

Hadi Zare a, Mohammad Vakili a*, Vahidreza Darugar a

a Department of Chemistry, Faculty of science, Ferdowsi University of Mashhad, Mashhad, Iran

Hydrogen bonding is well recognized as one of the major noncovalent forces which play a

prominent role in supermolecular and template chemistry and is a crucial issue in the study of

biologically important molecules [1-2].

Recently, authors reported new equation that allow to quantify the energy of the

intramolecular hydrogen bond (IMHB) [2]. In this work we obtain based on mentioned

equation as EHB(Δδ) =Δδ+(0.4±0.2), the linear correlation between the energy of

intramolecular hydrogen bonds and some selected calculated parameters due to

intramolecular hydrogen bond strength. For this purpose the structure of a series of molecules

containing the intramolecular O‒H···O=C hydrogen bond was studied by NMR

spectroscopy, have been investigated by DFT-B3LYP/6-311++G(d,p) method was used both

for geometry optimization and for QTAIM calculations of the topological parameters. The

results show that the hydrogen bond strength correlate well with some selected parameters

such as the hydrogen-bond distance, electron density at the bond critical points and etc. in the

molecular electron density topography.

Keywords: Intramolecular hydrogen bond strength; AIM; DFT calculations.

References

[1] Gilli, G.; Gilli, P. The Nature of the Hydrogen Bond – Outline of a Comprehensive Hydrogen Bond Theory;

Oxford University Press: New York, 2009.

[2] S. J. Grabowski, Annu. Rep. Prog. Chem., Sect. C, 2006, 102, 131–165.

[3] A.V. Afonin, A.V. Vashchenko, M.V. Sigalov, Org. Biomol. Chem. 2016, 14, 11199-1211



Feb 27–28, 2019

Identification and design of new drug-like compounds for inhibiting HIV-1 Reverse

transcriptase activity

Roya Behazin*a, Ali Ebrahimia a Department of Chemistry, University of Sistan and Baluchestan, P.O. Box 98135-674, Zahedan, Iran

Human immunodeficiency virus type 1 (HIV-1) is the main agent of acquired

immune deficiency syndrome (AIDS) which encodes three important viral enzymes: reverse

transcriptase, protease, and integrase 1. Reverse transcriptase (RT) is responsible for the

transformation of the single-stranded RNA viral genome into double-stranded DNA. Several

biological processes in the HIV life cycle have been identified as targets for the HIV-1

therapy and, the number of target-specific drugs has been daily increased to develop their

activity, and also face to serious challenges about their toxicity emerging drug resistance and

adverse side effects 2. So a novel series of natural compounds were identified and their

analogs were designed to inhibit the RT (wild type=W) and its mutant types (K, Y, KY and

L) using both AutoDock4 and MOE softwares. The inhibitory effects of these molecules were

investigated and with respect to the results of molecular docking, some of the compounds are

not only effective inhibitors, but they can also replace the prescribed drugs, especially the

analog of Calanolide A (C-1-N) which is the best one for W and mutant types. Also,

orientation and interaction energies of this molecule are estimated and suitable interactions

with LYS101, ARG172 and GLN182 amino acids are obtained. The main skeleton in C-1-N

has a significant role on interaction toward enzymes due to strong cation-π interaction

between central ring and tyrosine, and also hydrogen bonding with TYR318 amino acid

which are demonstrated in Fig. 1.

Fig. 1. Molecular docking of the C-1-N in the binding cavity of the HIV-1 RT.

Keywords: HIV-1, Reverse transcriptase, Molecular docking

References

[1] A.L. Perryman, S. Forli, G.M. Morris, C. Burt, Y. Cheng, M.J. Palmer, K. Whitby, J.A. McCammon, C.

Phillips, A.J. Olson, Journal of molecular biology, 2010, 397, 600

[2] A. Gaspar, M.J. Matos, J. Garrido, E. Uriarte, F. Borges. Chemical reviews.2014, 114, 4960



Feb 27–28, 2019

Aqueous acidities of natural tetrahalogenated indoles

Shiva Rezazadeh*, Ali Ebrahimi

Department of Chemistry, University of Sistan and Baluchestan, P.O. Box 98135-674, Zahedan, Iran

Indole is a fascinating constituent in nature, which characterize by biological and

pharmaceutical activities. In 2016, Woolner and coworkers isolated fourteen unusual

tetrahalogenated indole (with three halogens including bromine, chlorine, and iodine) from

the red alga (Table 1). They reported that these compounds exhibit a range of biological

activities such as antibiotic, and radical scavenging 1. In this study, the aqueous acidity (pKa)

of indole derivatives, 1-14, were investigated and compared with indole at PCM/B3LYP/6-

31g(d,p) level. The pKa values are calculated using the proton dissociation method on the

base of the HA → A- + H+ reaction. In this reaction the pKa is calculated as follow:

∆G = G(H+)g + ∆Gsol(H

+) + G(A-)liq – G(HA)liq

Where the experimental value of ∆Gsolv(H+) is equal to -265.9 kcal mol-1, at 298.15 K 2. The

obtained results indicated significant increase in acidity of indole derivatives than the indole.

The molecular electrostatic potential (MEP) plot of indole and 13 compound illustrated in

Fig. 1. The maximum positive region which preferred site for nucleophilic attack as blue

color. The blue region are observed around the hydrogen. Of all compounds, 13 is the most

acidic compound, and the hydrogen atom of 13 is more positive than indole (Fig. 1). The pKa

values are in agreement with the MEP analysis.

Keywords: Indole, Tetrahalogenated indole, Acidity constant, Electrostatic potential.

Table 1. Name and numbering of compounds and pKa values.

R1 R2 R3 R4 R5 R6 Pka

Indole 13

Fig 1. Molecular electrostatic potential (MEP) map of indole and 13

compound.

Indole H H H H H H 18.85

1 Br Br H H Br Br 6.36

2 Br Br H H Br Cl 6.30

3 Br Br H H Cl Br 6.46

4 Br Br H H Cl Cl 6.31

5 Br I H H Cl Cl 6.73

6 Br I H H Cl Br 6.69

7 Br I H H Br Cl 6.37

8 Cl I H H Cl Cl 6.59

9 I H H Cl Cl Cl 5.46

10 I H H Cl Cl Br 5.75

11 H H Br Cl Cl Cl 6.43

12 Br H H Br Br Br 5.36

13 Br H H Br Cl Cl 5.29

14 Br H H Cl Cl Cl 5.54

[1].V. H. Woolner, C. M. Jones, J. J. Field, N. H. Fadzilah, A. B. Munkacsi, J. H. Miller, R. A. Keyzers and P. T.

Northcote, Journal of Natural Product, 2016, 79, 463

[2]. J. Rimarčík, V. Lukeš, E. Klein, and M. Ilčin, Computational Theoretical Chemistry, 2010, 952, 25



Feb 27–28, 2019

The effect of phenolic natural products to inhibit the VEGFR-2 protein kinase

Asiyeh Shahraki*, Ali Ebrahimi

Department of Chemistry, Computational Quantum Chemistry Laboratory, University of Sistan and

Baluchestan, P.O. Box 98135-674, Zahedan, Iran

Vascular Endothelial Growth Factor (VEGF) is the most potent angiogenesis stimulator.1 The

specific action of the VEGF is mainly mediated by two types of receptor tyrosine kinases,

namely VEGFR-1 and VEGFR-2. Of the two receptors, VEGFR-2 plays a more important

role in mediating the mitogenesis and permeability of endothelial cells, which is an important

therapeutic target for cancer anti-angiogenesis therapy.2 Some orally active inhibitors of

VEGFR-2 are now in clinical trials including sunitinib (Su), vandetanib (Va), and sorafenib

(So).3 The hemorrhage, hypertensive crisis, and gastrointestinal perforation are distinct

adverse effects of these agents.4 Therefore, blocking of VEGFR activation by natural

inhibitors is the interesting issue. Many natural phenolic compounds are found possessing

potent anti-cancer properties. In this work, the inhibitory effect of 12 phenolic natural product

including rutin (1), oleuropein (2), catechin (3), chlorogenic acid (4), epicatechin (5),

hesperetin (6), hydroxytyrosol (7), resveratrol (8), 3-hydroxycinnamic acid (9), genistein (10),

estradiol (11), and phenoxodiol (12) were estimated based on in-silico analysis. The

compounds were docked into ATP binding site of VEGFR-2 protein (pdb code: 2XIR) via the

MOE5 program, and the scores are gathered in Table 1. The results show that all of

mentioned ligands have the proper binding features to bind to ATP pocket of VEGFR-2. Of

all ligands, rutin is the most promising candidate to inhibit the VEGFR-2. Six active residues,

i.e., Lys 161, Glu 227, Val 254, Leu 440, Ile535, and Asp 537 at the ATP pocket were

essential for the stable conformation of phenolic ligands for binding to VEGFR-2 protein.

The presence of the bridged water molecules in the active site is the important issue to

improve the binding of the ligand into active site via the hydrogen bonding interaction.

Table 1. The docking score energies (in kcal/mol) of the compounds calculated using MOE

software Co. -S Co. -S Co. -S Co. -S Co. -S

1 37.05 4 25.64 7 19.35 10 16.38 Su 16.26

2 29.14 5 24.28 8 18.88 11 16.25 Va 18.62

3 26.05 6 20.76 9 18.59 12 14.26 So 15.53

Keywords: VEGFR-2 protein, Natural phenolic compounds, Molecular docking, Ligand

protein interaction

References

[1] D.R. Senger, L. Van de Water, L. F. Brown and et al, Cancer Metastasis Reviews, 1993, 12, 303

[2] N. Ferrara, H. P. Gerber, J. LeCouter, Nature Medicine, 2003, 9, 669

[3] J. Lu, K. Zhang, S. Nam, R. A. Anderson and et al, Carcinogenesis, 2010, 31, 481

[4] T. Kamba, D. M. McDonald, British Journal of Cancer, 2007, 96, 1788

[5] MOE (The Molecular Operating Environment), software available from Chemical Computing Group Inc.,

1010 Sherbrooke Street West, Suite 910, Montreal, Canada H3A 2R7



Feb 27–28, 2019

A theoretical study for the Quantum Capacitance Effect of Defects in

Silicene sheet

Zahra Hasanzadeh Tazeh Gheshlagh *a, Javad Beheshtianb, Sakineh Mansouric

a Department of Chemistry, Faculty of Science, Islamic Azad University, Center Tehran Branch,

Tehran; [email protected]

b Department of Chemistry, Faculty of Science, Shahid Rajaee Teacher Training University, P.O.

Box: 16875-163, Tehran, Iran; [email protected]

c Department of chemistry, Faculty of Science,Islamic Azad University, Central Tehran Branch,


Supercapacitors are one of the most interesting electrical energy storage devices because of

their special features such as good stability and high-power density [1]. To obtain high

capacitance for Supercapacitors, the choice on electrod materials is a key factor and limiting

factor in the total capacity of Supercapacitors is their finite quantum capacitance [2]. Silicene

is expected to have potential application of supercapacitor [3]. In this paper, we are focused

on these important issues for silicene-based electrode materials in nano electronic and

supercapacitor applications. We perporm calculations using Dmol3 package. The generalized

gradient approximation (GGA) in the parameterization of Perdew-Burke-Ernzerhof (PBE)

was used [4, 5]. We investigated the effect of vacancies (missing atoms) V1, V2, V3, V4, V5

and V6 on quantum capacitance and electronic structure of silicene sheet than pristine

silicene, in order to improve the quantum capacitance by the way of missing atoms. On the

basis of these results, we analyze the possibility of the way about defects which is adopted to

improve the performance of silicene-based electrodes.

Keywords: Quantum Capacitance, Silicene, Defects.

References [1] Wang, Z. Zhang, X. et al. J Colloid Interface Sci 2013, 396,251–7.

[2] Zhou, M. Tian, T. et al. Chem Phys Lett 2013,581,64–9.

[3] Wood, B. C. Ogitsu, T. et al. J. Phys. Chem. C, 2014,118,4-15.

[4] J. Soler, J. Phys.: Condens. Matter, 2002, 14, 2745.

[5] J. Perdew, Phys. Rev. Lett, 1996, 77, 3865.

mailto:[email protected]





Feb 27–28, 2019

Investigation of adsorption of Li and Na on doped silicenes as a potential

anod material for ion batteries

Zahra Hasanzadeh Tazeh Gheshlagh *a, Javad Beheshtianb, Sakineh Mansouric

a Department of Chemistry, Faculty of Science, Islamic Azad University, Center Tehran Branch,




c Department of chemistry, Faculty of Science,Islamic Azad University, Central Tehran Branch,


With developing of new technologies, we need to rely on progress energy storage systems for

applications such as electric vehicles, portable electronic devices and energy storage [1]. The

Li/ Na ion rechargeable battery are the most promising candidates for these aims due to good

rate capability, long cycle life and high energy density [2]. Silicene with a buckled layer

structure has high surface area and enough space for the adsorption of Li and Na ions [3]. For

this reason, we have investigated theoretically the creation of di-vacancies silicene sheet, as

well as the B, N and F doping of silicene. Our calculations were explored Within the first-

principles density functional theory (DFT) as a part of the Dmol3 package. the generalized

gradient approximation (GGA) in the parameterization of Perdew-Burke-Ernzerhof (PBE)

was used [4,5]. According to the obtained results for doped silicene structure𝑠 with Li and Na

ions, our calculations show that vacancies with dopants can strongly impact on the electronic

structures of silicene and adsorption turns silicene into a narrow gap semiconductor. Using

doped silicenes can be a suitable substrate for Li and Na dispersing. Therefore, it could be

worthwhile strategy as anod material for ion batteries due to more charge storage capability

and better energy density of silicene than the graphene surface.

Keywords: Ion batteries, Doped Silicene, Adsorption.

References [1] F-H. Du.et al. J.Mater. Chem. 2016, A4, 32-50.

[2] M. R. Zamfir. et al. J.Mater. Chem. 2013, A1, 9566-9586.

[3] Grazianetti, C.et al. 2D Materials 2016, 3, 012001.

[4] J. Soler, J. Phys.: Condens. Matter, 2002, 14, 2745.

[5] J. Perdew, Phys. Rev. Lett, 1996, 77, 3865.






Feb 27–28, 2019

Interaction and Diffusion of Na+ and Li

+ with Defective Graphene

A comparative DFT study

Seyedeh Shabnam Daryabari*a, Javad Beheshtian

b, Sakineh Mansouri

c

a Department of Chemistry, Faculty of Science , Islamic Azad University , Center Tehran Branch,




c Department of chemistry , Faculty of Science,Islamic Azad University, Central Tehran Branch,


Graphene is a bidimensional material with remarkable electronic transport properties and

unusual thermal, optical and mechanical characteristics [1]

. Perfect graphene is not suitable for

desalination since it is impermeable. Graphene is an ideal membrane in that it is the thinnest

membrane possible, but perfect graphene is not permeable to any gas molecule. It has been

shown computationally that by creating subnanometer holes in the graphene sheet, the

resulting porous graphene is capable of molecular-sieving-like separation of gas molecules

and cations with high permeance[2,3]

. We investigated the defected graphene for diffusion

Na+,Li

+. Vacancy defected graphene doped with B and N. The properties and reaction these

cases on graphene quantum dot sheet were studied by means of first principles based on

density functional theory. We analyzed the thermodynamic and structural properties of this

defected graphene, and compared interaction between single Na+, Li

+ and this defect. Finally

diffusion and scanning of these cations were performed. All DFT calculations performed

using Gaussian 09 package and the M062X/6-31G* computational level of theory. The

diffusion barrier values, show the advantage of doped graphenes for use in LiBs with respect

to pure graphene. Examples of applications of these defects include supercapacitors, batteries,

sensors, fuel cells, solar cells, and photocatalyst.

Keywords: graphene, quantum dots , defect, Na

+, Li

+, diffusion

References

[1] D. Cohen-Tanugi, J.C. Grossman, Nano Lett. 2012,12 ,3602–3608

[2] J. S. Bunch, S. S. Verbridge, J. S. Alden, A. M. van der Zande, J. M. Parpia, H. G. Craighead and P. L.

McEuen, Nano Lett. 2008, 8, 2458–2462

[3]. D. E. Jiang, V. R. Cooper and S. Dai, Nano Lett., 2009, 9, 4019–4024.




Feb 27–28, 2019

Effect of Electric Field on Defected Graphene Sheet: A DFT Study

Seyedeh Shabnam Daryabari*a, Javad Beheshtian

b, Sakineh Mansouri

c

a Department of Chemistry, Faculty of Science , Islamic Azad University , Center Tehran Branch,




c Department of chemistry , Faculty of Science,Islamic Azad University, Central Tehran Branch,


Graphene has attracted significant experimental and theoretical research attention since its

discovery in 2004 [1,2]

, and the material is predicted to have wide application prospects in

nanoelectronic and spintronic devices because of its many unusual physical properties[3]

.

Defects are often the first concern in the real application of monolayer materials. Vacancy

defects, which are readily induced by laser irradiation and electron beam, are almost

inevitable in the fabrication and processing of monolayers, and sometimes, small defects are

introduced purposively for specific applications [4]

. We designed a porous graphene and

doped them with B and H. we analysed the interaction and properties of Helium on defective

graphene sheet in present of electric field were investigated by means of first-principles based

on density functional theory. All DFT calculations performed using Gaussian 09 package at

the M062X/6-31G* computational level of theory. Our results shows that the He optimized

energy value on doped graphenes decreases and band gap increases when electric field rises.

Keywords: graphene, quantum dots , Defects, Electric Field, DFT

References

[1] K. S. Novoselov, A. K. Geim, S. V. Morozov, Jiang D, Zhang Y, S. V. Dubonos, I. V. Gregorieva and A. A.

Firsov, Science, 306, 666(2004).

[2] M. Y. Han, B. Ozyilmaz, Y. B. Zhang, S. Lee, and H. Dai, Science, 319, 1229 (2008).

[3] K. Wakabayashi, Y. Takane, M. Yamamoto, and M. Sigrist, Carbon, Science, 47, 124 (2009).

[4] Brumfiel, G. Nature ,2013,495, 152–153




Feb 27–28, 2019

Effect of Multiple Hydrogen Bonds on Properties of an Amino Derivative

of D-Mannose: A Computational Study

Seyed Heydar Moraveja, Alireza Fattahia*, Parham Rezaeea

a Department of Chemistry, Sharif University of Technology, P.O. Box 11155-3615, Tehran, Iran.

In this work an amino derivative of D-Mannose (1) was selected as a probe for

investigating the effect of multiple hydrogen bonds on acidity in gas phase and solution, gas

phase basicity, and bond dissociation energy of most acidic OH1, cation complexation with

the most stable conjugate base (2), and anion complexation with conjugate acid. Also kinetic

studies of proton transfer of 1 to methoxy radical were carried out to investigate the

antioxidant ability (absorbing free radicals in body) of 1. Also cyclohaxanol (3) and

cyclohexylamine (4) were used as the references compound. Calculations were performed at

B3LYP/6-311++G(d,p) density functional theory (DFT) level and ground states were

confirmed by the absence of any imaginary frequencies[1]. For pKa calculations in solvent,

conductor-like polarizable continuum (CPCM) model with direct method and experimental

value for proton free energy solvation was used[2,3]. For calculations of rate constants,

TS(Berny) method was used and the accuracy of calculations was confirmed by computing

intrinsic reaction coordinate (IRC) curve.

Gas-phase acidity (ΔHacidity) was calculated to be 339.609, 341.283, 359.532, 345.351

and 342.997 kcal mol-1 for H1, H2, H3, H4 and H5, respectively and 373.277 kcal mol-1 for 3.

Thus H1 is the most acidic proton in 1 and its conjugate base is stabilizing 33.668 kcal mol-1

with respect to the conjugate base of 3, due to multiple hydrogen bonds. In solution, pKa

values are 11.913, 14.801, 29.097, 15.575 and 14.589 for H1, H2, H3, H4 and H5, respectively

and 24.313 for 3 in DMSO solvent, which shows a similar trend as the gas-phase. Gas-phase

basicity (-ΔHPA) was calculated to be 227.219 and 223.850 kcal mol-1 for 4. Bond

dissociation energy (ΔHBDE) of the O-H1 in 1 is 99.576 and is 99.467 kcal mol-1 for O-H in 3,

which indicates that the radical product, unlike the conjugate base, is not stabilized by

hydrogen bonds.

O OH1

OH2

NH2

3

H4O

H5O

O O-

OH2

NH2

3

H4O

H5O

OH

NH2

1 2 3 4

Keywords: Computational Chemistry, DFT, Acidity and Basicity, Hydrogen Bonding, Metal and

Anion Complexation, Kinetic of Hydrogen transfer.



Feb 27–28, 2019

References

[1] A. Shokri, A. Abedin, A. Fattahi and S. R. Kass, J. Am. Chem. Soc., 2012, 134, 10646–10650.

[2] S. Feng, C. Bagia and G. Mpourmpakis, J. Phys. Chem. A, 2013, 117, 5211-5219.

[3] C. P. Kelly, C. J. Cramer and D. G. Truhlar, J. Phys. Chem. B, 2007, 111, 408-422.



Feb 27–28, 2019

A Thermodynamic and Kinetic Insight into the Pathways Leading to

quinoline Derivatives: A Computational Study

Bahareh Mostafa*a, Sayyed Mostafa Habibi-Khorassanib)

a Department of Chemistry, University of Sistan and Baluchestan, P.O. Box 98135-674, Zahedan,

Iran

Bridgehead nitrogen heterocycles are of interest because they constitute an important class of

natural and non-natural products, many of which exhibit useful biological activity. Quinoline

derivatives, have attracted much synthetic attention. Many derivatives of quinoline have been

studied for different biological activities, such as antimicrobial, anti-inflammatory,

antileishmanial ,antituberculosis, antimalaria, cytotoxicity, and HIV-1 integrate inhibitors [1].

In the past years, the pharmaceutical industry has focused more and more on diversity-

oriented and biased combinatorial libraries. Furthermore, the discovery of novel MCRs can

be consider as an interesting topic for academic research that also satisfies a practical interest

of applied science [2]. Multi-component reactions (MCRs) are extremely popular owing to

their facile execution, high atom-efficiency and the high diversity of products. This reaction

tool allows compounds to be synthesized in a few steps and usually in a one-pot operation. A

typical organic reaction proceeds in a specific mechanism. There may be many proposed

mechanisms for each reaction. Experimental methods have many instrumental limitations

such as trapping the intermediates or transition states (TSs) in confirming the mechanism that

reactions proceeded from it. But computational methods resolve this limitation and make

confirming the mechanism of reactions eases and exacter. During past few years, density

functional theory (DFT) based methods have been widely accepted by computational

chemistry community as a reliably practical tool for the study of chemical reactions,

especially, for large systemsTheoretical study for the reaction between methyl isocyanide,

quinoline, malononitrile, and acetaldehyde for the generation of quinoline derivatives were

reported using quantum mechanical calculation. Three speculative proposed mechanisms for

this reaction were investigated and all steps of three mechanistic pathways have been

thermodynamically and kinetically evaluated.

Keywords:. Quinoline, Multi-component reactions, computational chemistry

References

[1] Mohammed, I. A.; Subrahmanyam, E. V. S. Acta Pharm Sciencia. 2009, 51, 163.

[2] Pellerano, C.; Savini, L.; Massarelli, P.; Bruni, G.; Fiaschi, A. I. Farmacol. 1990, 45, 269.



Feb 27–28, 2019

Theoretical investigation of SERS Enhancement of p-Mercaptoaniline Intracting with

Silver Clusters

Mojtaba Esmaeilia, Zahra Jamshidib*

a b Chemistry and Chemical Engineering Research Center of Iran, P.O. Box 14335-186,

Tehran, Iran

It is been a lifelong dream for chemists to detect and characterize the single molecules and

to monitor their structural changes. Observing single molecules and their unique properties as

well as structural changes can provide useful insights into the nature of processes that cannot

be studied in an averaging manner. One of the spectroscopic techniques that can be very

effective in this way is the surface-enhanced Raman spectrometry. This technique amplifies

spectral responses using the surface plasmonic properties of noble metals, and in comparison

to other analytical methods provides optical detection with high sensitivity. In this project, we

analyzed the surface-enhanced resonance (SERS) Raman of neutral silver cluster in

interaction with the para-aminothiophenol and di-mercaptoazobenzene compounds to

determine the abnormal vibrational modes of the SERS spectrum and to determine the the

underlying mechanism[1,2].

In this study, we used excited state gradient approximation to simulate the resonance Raman

spectrum. Finally, comparing the results of the simulated and the experimental spectra[2],

which are obtained in low-power lasers, we concluded that the computational spectra of the

charge transfer transition fit consistently with the experimental spectrum. Therefore, the

mechanism of enhancement of the SERS spectrum of the para-aminothiophenol compound

was identified as a charge transfer type. In addition, in the experimental SERS spectrum of

para-aminothiophenol with high-power laser, there are three abnormal vibrational modes that

are believed to be the results of dimerization of para-aminothiophenol to

di-mercaptoazobenzene3. In the next step, the SERS spectrum of the di-mercaptoazobenzene

complex was simulated. In this case, the computational spectra of the charge transfer

transitions were consistent with the experimental spectrum. Therefore, it became clear that

the origin of the abnormal vibrational modes is the dimerization of the para-aminothiophenol

compound, which is enhanced by the mechanism of charge transfer.

Keywords: para-aminothiophenol, di-mercaptoazobenzene, TDDFT, SERS

References:

[1] Masatoshi Osawa,*Naoki Matsuda; Katsumasa Yoshii, and Isamu Uchida. J. Phys. Chem. 1994, 98, 12702

2Yi-Fan Huang; Hong-Ping Zhu; Guo-Kun Liu; De-Yin Wu;* Bin Ren,* ; Zhong-Qun Tian. J. Am.Chem.

Soc. 2010, 132, 9244

3XinRen,EnCao,WeihuaLin,YuzhiSong,WejieLiangc and Jingang Wang .J. RSC Adv, 2017, 7, 31189

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