Peslherbe’s Laboratory Theoretical/Computational Chemistry - Research Interests
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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
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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
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
Abstract
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
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.
Issendorff, Nature, 2000,407, 60.
[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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
Feb 27–28, 2019
Computational study of absorption Naproxen drug on fullerene C20
Foad Buazara*, Mouhammad hussain Sayahi, Khadijeh Sayahi
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
Abstract
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
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.
Issendorff, Nature, 2000,407, 60.
[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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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,
Tehran; [email protected]
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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,
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,
Tehran; [email protected]
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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,
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,
Tehran; [email protected]
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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,
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,
Tehran; [email protected]
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
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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.
Eighth Theoretical and Computational Chemistry Workshop
Isfahan University of Technology, Isfahan
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