Authors:Samira Dadi, Morteza Vahedpour Abstract: Journal of Theoretical and Computational Chemistry, Volume 16, Issue 06, September 2017. The gas-phase reaction mechanism of NO2 with NH2 on the singlet potential energy surface is investigated at the B3LYP, MP2, CCSD(T) and G3B3 levels of calculation in connection with the 6-311[math]G(3df, 3pd) basis sets. Seven different kinds of products have been obtained. The results reveal that P7 [N2[math]2O] is the main product in thermodynamic viewpoint with the Gibbs free energy of [math][math]kcal/mol. The product P2 due to less number of transition states and low level barrier height of transition states is introduced as the kinetic product. The calculation of rate constants in different temperatures confirms our predication for P7 adduct in comparison with other products. In the first step, the reactions without catalytic effects are considered. All of these reactions begin with pre-reactive collision complex CR [NO2–NH2]. This complex has been produced from barrier-less process via collision of reactants. From variation of bond lengths and angles or dissociation of this complex, other species are produced. In the second step, the catalytic effect of water and water dimer molecules on the reaction rate of kinetic path, P2, have been attended. Calculation of the rate constant was done in the temperature range from 500[math]K to 3000[math]K. Our results showed that the rate constant of path P2 increases with temperature and the number of water molecules. So, we can conclude that the number of water molecules corresponding to relative humidity of atmosphere has catalytic effect on the mentioned reaction rate. Seven types of products are purposed. Reaction mechanism of NH2 and NO2 are studied.Watermolecules have catalytic effect on the reaction. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-08-31T07:55:56Z DOI: 10.1142/S0219633617500535

Authors:Hiroyuki Nohira, Toshiyuki Nohira Abstract: Journal of Theoretical and Computational Chemistry, Volume 16, Issue 06, September 2017. For sigmatropic reactions, such as [1,3] and [1,5] hydrogen shifts, the Cope and Claisen rearrangements, and the Berson–Nelson rearrangement, no correlation diagrams consistent with the classical electronic formulas have been reported. Here, we report dynamic correlation diagrams for these sigmatropic reactions based on orbital phase conservation theory. The diagrams are consistent with both the selection rules of sigmatropic reactions proposed by Woodward and Hoffmann and classical electronic formulas. • Previously, no correlation diagrams that are consistent with classical electronic formulas have been reported for sigmatropic reactions. • We report dynamic correlation diagrams for sigmatropic reactions based on orbital phase conservation theory. • The diagrams are consistent with the selection rules of sigmatropic reactions proposed by Woodward and Hoffmann and classical electronic formulas. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-08-31T07:55:55Z DOI: 10.1142/S0219633617500559

Authors:Katarzyna Pustuła, Marcin Makowski Abstract: Journal of Theoretical and Computational Chemistry, Volume 16, Issue 06, September 2017. The performance of exchange-correlation (xc) functionals for the description of electron affinities of atomic and molecular systems is investigated. A benchmark set is constructed and experimental adiabatic electron affinities are compared to Density Functional Theory (DFT) predictions. The results show that although good overall accuracy may be achieved from DFT-based approaches, there still exist outliers for any of the approximations applied. Apart from employing the standard DFT models, the possibility of the optimization of range-separated xc functionals has also been tested, however, no large improvement in accuracy is observed. The performance of exchange-correlation functionals for the description of electron affinities of atomic and molecular systems is investigated. A benchmark set is constructed and experimental adiabatic electron affinities are compared to Density Functional Theory predictions. The results show that although good overall accuracy may be achieved, there still exists outliers for any of the approximations applied. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-08-31T07:55:49Z DOI: 10.1142/S0219633617500523

Authors:Xiao-Fang Su, Bo Zhu, Cai-Xia Wu, Li-Kai Yan, Zhong-Min Su Abstract: Journal of Theoretical and Computational Chemistry, Volume 16, Issue 06, September 2017. The geometrical and electronic structures of [M6O[math]][math] (M [math] Mo, W, [math]; M [math] V, Nb, Ta, [math]) and their derivatives were investigated by using density functional theory methods. The results indicate that the geometrical structure of [V6O[math]][math] is not different from other Lindqvist-type anions. The energy gap between highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) (HOMO[math]LUMO energy gap) of [V6O[math]][math] is smaller than those of same charge anions, [Nb6O[math]][math] and [Ta6O[math]][math]. In addition, the charge density [math] of [V6O[math]][math] is larger when compared with those of other studied clusters. The investigation on the derivatives shows that the valence of V atom (V[math] or V[math]) and the methoxy ligand influence the HOMO[math]LUMO energy gap and the charge density [math] of the studied clusters. For the anion [V6O19]8–, the substitutions of atom W or Nb for atom V and methoxy ligands for bridging oxo ligands enhance the stability of system. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-08-31T07:55:43Z DOI: 10.1142/S0219633617500547

Authors:Ayhan Üngördü, Nurten Tezer Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The most stable structure of 5-substituted uracil base pairs and metal-mediated-5-substituted uracil complexes are determined. Density functional theory (DFT) method is used in the calculations which are carried out both in vacuum and water. LANL2DZ and 6–311[math]G(d,p) basis sets are used for metals and the rest atoms, respectively. Effects on frontier molecular orbitals and energy gaps of substituents in 5-position of uracil base pairs in vacuum and water are found. Conductivity of base pairs or complexes are investigated for single nanowires studied by band theory. It is expected that this study will be an example for future studies that require new nanotechnological applications. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-09-28T05:36:34Z DOI: 10.1142/S0219633617500663

Authors:A. Alsaedi, M. Ijaz Khan, T. Hayat Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. This communication addresses unsteady squeezing flow of second grade liquid. NonFourier heat flux model is implemented to discuss heat transfer features subject to heat generation/absorption. Homogeneous–heterogeneous reactions are addressed. Firstly, the problems are nondimensionalized by suitable variables and then solutions for strong nonlinear systems are presented. Convergence region is particularly determined for obtained solutions. Statistical declaration and probable error for drag force are computed. Velocity is found to decay for larger estimation of fluid parameter while thermal and concentration fields are enhanced for higher heat generation and squeezing parameters. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-09-22T02:14:54Z DOI: 10.1142/S021963361750064X

Authors:Kahina Sidi Said, Madjid Nait Achour Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. This work consists of an investigation, using current methods of quantum chemistry and, at first, on the basis of the available experimental results, about the new mechanisms of the reaction between ozone and hydrogen cyanide (HCN) in gaseous phases. Three possible reaction pathways which we have determined as the most probable and, all three, leading exactly to the same products, are proposed here. For each of these pathways, several steps for which we performed a kinetic study were identified in the singlet potential energy surface. To confirm the proposed mechanisms, we have achieved a study including the intrinsic reaction coordinate (IRC), the topological analysis of atoms in molecule and the harmonic vibrational frequencies calculations. The obtained results reveal that the final products have considerable thermodynamic stability and this reaction is exothermic in standard conditions. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-09-20T02:38:02Z DOI: 10.1142/S0219633617500638

Authors:Sumedha Mukherjee, Gaurav Kumar, Ranjana Patnaik Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Poly (ADP-ribose) polymerase-1 (PARP-1) reverses DNA damage by repairing DNA nicks and breaks in the normal cellular environment. However, during abnormal conditions like stroke and other neurological disorders, overactivation of PARP-1 leads to neuronal cell death via a caspase-independent programmed cell death pathway. Strategies involving inhibition or knockout of PARP-1 have proved beneficial in combating neuro-cytotoxicity. In this study, we performed in-silico analysis of 27 phytochemicals of Withania somnifera (Ashwagandha), to investigate their inhibition efficiency against PARP-1. Out of 27 phytochemicals, we report 12 phytochemicals binding to the catalytic domain of PARP-1 with an affinity higher than FR257517, PJ34 and Talazoparib (highly potent inhibitors of the enzyme). Among these 12 compounds, five phytochemicals namely Stigmasterol, Withacnistin, Withaferin A, Withanolide G and Withanolide B show an exceptionally high binding affinity for the catalytic domain of PARP-1 and bind to the enzyme with similar hydrogen bond formation and hydrophobic interaction pattern as their inhibitors. All of these phytochemicals are BBB permeable so that they can be further developed into potential future neuro-therapeutic drugs against neurodegenerative disorders involving neuronal cell death. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-09-12T03:29:48Z DOI: 10.1142/S0219633617500626

Authors:Chunlei Wu, Shuhai Zhang, Fude Ren, Ruijun Gou, Gang Han Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Cocrystal explosive is getting more and more attention in high energy density material field. Different molar ratios of 2,4,6,8,10,12-hexanitrohexaazaisowurtzitane (CL-20)/1-Methyl-4,5-dinitro-1H-imidazole (MDNI) cocrystal were studied by molecular dynamics (MD) simulation and quantum-chemical density functional theory (DFT) calculation. Binding energy of CL-20/MDNI cocrystal and radial distribution function (RDF) were used to estimate the interaction. Mechanical properties were calculated to predict the elasticity and ductility. The length and bond dissociation energy of trigger bond, surface electrostatic potentials (ESP) of CL-20/MDNI framework were calculated at B3LYP/6-311[math]G(d,p) level. The results indicate that CL-20/MDNI cocrystal explosive might have better mechanical properties and stability in a molar ratio 3:2. The N–NO2 bond becomes stronger upon the formation of intermolecular H-bonding interaction. The surface electrostatic potential further confirms that the sensitivity decreases in cocrystal explosive in comparison with that in isolated CL-20. The oxygen balance (OB), heat of detonation [math], detonation velocity [math] and detonation pressure [math] of CL-20/MDNI suggest that the CL-20/MDNI cocrystal possesses excellent detonation performance and low sensitivity. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-09-12T03:29:48Z DOI: 10.1142/S0219633617500614

Authors:A. Hosseinian, E. Vessally, M. Babazadeh, L. Edjlali, M. Es’haghi Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The computational investigations on 1:1 complexes of the nitrogen trifluoride (NF[math] species with the nitroxyl (HNO) species have been carried out, which reveal the existence of the nine complexes on the singlet potential energy surface (PES). The atoms in molecules (AIM) theory and the electron localization function (ELF) along with the identification of noncovalent interaction (NCI) regions and the investigation of electron transfer of all the obtained complexes have been carried out to provide suitable insight into the electronic and structural properties of these complexes. The calculated results reveal that the N-atom of the NF3 species and the O-atom of the HNO species have more key roles compared with the F-atom of the NF3 species and the N-atom of the HNO species in the obtained complexes. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-09-08T02:46:41Z DOI: 10.1142/S0219633617500602

Authors:Sheeraz Ahmad Bhat, Mohd Faizan, Bilal Ahmad Ahanger, Shabbir Ahmad Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In this work, a detailed vibrational analysis of L-(-)-xylose molecule has been carried out. The geometrical parameters and anharmonic spectrum have been calculated and compared with XRD, FTIR (4000–400[math]cm[math]) and FT-Raman (4000–50[math]cm[math]) observed data. The simulated data along with IR and Raman intensities were calculated using DFT/B3LYP level of theory in combination with 6-311[math]G(d,p) basis set. The experimental and theoretical results are found to be in a good agreement with each other. Moreover, thermodynamic properties, molecular electrostatic potential (MEP) and natural bond orbital (NBO) analysis of L-(-)-xylose are also reported. The calculated HOMO and LUMO energies confirm the charge transfer within the molecule. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-08-23T10:02:24Z DOI: 10.1142/S0219633617500596

Authors:Fang-Qin Ren, Fu-Qiang Zhang, Ya-Fen Li, Jin Lv, Wen-Jin Ma Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The equilibrium structures, stabilities, magnetic, and spectroscopic properties of small-sized AlxZry ([math]) alloy clusters have been systematically investigated within the framework of density functional theory. We found that the structures of bimetallic clusters prefer to form the same motif as their corresponding pure Al or Zr clusters and chirality turns up in mixed clusters with [math] and 9. Computations of VCD and VROA spectra confirmed the chirality of these clusters. For a given cluster size, the most favorable mixing occurs when the ratio of Al:Zr is approximatively equal to 1. The total magnetic moments depend not only on the configuration but also on the composition of the clusters. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-08-17T06:04:21Z DOI: 10.1142/S0219633617500584

Authors:R. Bharathi, N. Santhi Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The pyrazole compounds 4-(3-(2-amino-3,5-dibromophenyl)-1-(4-substitutedbenzoyl)-4,5-dihydro-1H-pyrazol-5-yl) benzonitriles (4–6) have been synthesized and characterized by elemental, IR, 1HNMR spectral methods. In addition, the synthesized compounds were subjected to density functional theory for further understanding of the molecular architecture and optoelectronic properties. The optimized geometric parameters were in support of the corresponding experimental values. The FT-IR spectra of 4–6 have been investigated extensively using DFT employing B3LYP/6-31G (d,p) level theory. The molecular electrostatic potential analysis has been utilized to identify reactive sites of title compounds. Natural bonding orbital analysis proved the inter- and intra-molecular delocalization and acceptor–donor interactions based on the second-order perturbation interactions. The calculated band gap energies revealed that charge transfer occurs within the molecule. The polarizability and hyperpolarizability were calculated which show that compounds posses nonlinear optical nature. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-08-14T06:24:39Z DOI: 10.1142/S0219633617500572

Authors:Zhen Zhao, Zhi Li, Linlin Lv Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. To understand how the intermetallic phases of Cu–Sc influence the thermal stability and mechanical strength of Cu–Sc alloys, thermodynamic and mechanical characters of the Cu–Sc alloy have been calculated by first-principles. The lattice parameters of Cu4Sc phase are obtained by calculated and the CuSc phase is found to be the most stable phase based on formation energies. In the binary Cu–Sc alloy, the shear moduli of Cu4Sc and Cu2Sc phases along the [100](001) crystal orientation are easier than those along the [100](010) crystal orientation, respectively. Pure Cu phase acts as the most stiffness phase while [math]Sc phase has the lowest stiffness. Cu4Sc phase possesses the best plasticity while CuSc phase possesses the worst plasticity. Cu4Sc phase is the most ductile phase while [math]Sc phase is the most brittle phase. From the partial density of states, the valence bands of binary Cu–Sc phases are dominated by the Sc-[math] states. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-08-01T06:47:37Z DOI: 10.1142/S0219633617500560

Authors:N. Flores-Gallegos Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In this report, we present three generalized expressions of Shannon’s entropy using the electron densities of position and momentum spaces. Such expressions were obtained using the definition of deformed logarithm introduced by Tsallis. We show that only one expression fulfils the dimensionless criterion, it is strictly positive overall space and follows a growing behavior with respect to the electron number. We also found that by using some values of [math], it is possible to reproduce the general trends of the radial distribution in position space and momentum space of the neon atom. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-07-17T03:25:52Z DOI: 10.1142/S0219633617500511

Authors:O. Yu. Goncharov Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. A technique for constructing the correlation dependencies of the thermodynamic properties of similar compounds was proposed. This technique is based on the Taylor expansion in the supposed analytic relationship between properties. The constructed correlation dependencies were used to estimate the thermodynamic properties of the condensed bromides and iodides of hafnium HfGn (G [math] Br, I and [math], 2, 3, 4) and the compounds formed in the PbO–SiO2 system. Standard formation enthalpy [math], entropy [math], heat capacity [math] and temperature dependencies [math] at temperatures T[math][math]k to 3000[math]k were estimated. The standard estimation error of the thermodynamic properties of the compounds in the PbO–SiO2 system does not exceed 2% for all the estimated properties. For condensed halides, the standard estimation error was (1) [math]% for enthalpy, (2) [math]% for entropy, (3) [math]% for heat capacity. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-07-11T01:52:47Z DOI: 10.1142/S021963361750050X

Authors:Laicai Li, Xiao Chen, Wanfei Cai, Ming Zhang, Xiaoqin Liang, Anmin Tian Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The charge transport properties and the stability of imidazoles with axial-coordinated protoheme molecules have been investigated by the density functional theory (DFT) at B3LYP/6-31[math]G(d) level. With energy of each compound, we find that all heme Fe[math] and Fe[math] complex compounds axially coordinate the imidazoles by strong field in low-spin state. Meanwhile, binding energies were calculated, the structure feature and the frontier orbital distribution of complex compounds were also analyzed. On the basis of Marcus theory, the reorganization energy, matrix element and charge transport rate constant were calculated. The results show that the charge transport rate of the complex compound coordinated imidazole is greater than that of the complex compound coordinated 2-methyl imidazole, which indicates that the charge transfer between the imidazole and the heme iron is more favorable to the heme iron than the 2-methyl imidazole. The results are in good agreement with the experimental ones obtained by Battistuzzi. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-07-03T08:18:42Z DOI: 10.1142/S0219633617500493