Authors:Priya Bhasi, Zanele P. Nhlabatsi, Sanyasi Sitha Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Phosphorus mononitride (PN) shows some interesting chemistry due to its low dissociation energy (compared to N2) and small dipole moment (zero dipole moment for N2). In this work, a reaction between HSi ([math]) and PN ([math]) has been studied using various computational methods. Analysis of the doublet surface of the [math] reaction indicates that the reaction is exothermic in nature leading to the formation of various products. In view of the barrierless association of the reactants and exothermic nature for the product formation, it is suggested that species like HPNSi, cyclic-SiN(H)P (these two most stable isomers have phosphazo linkage) and HSiNP (third most stable isomer has phosphdiazo linkage) can possibly be detected in the interstellar medium. In view of the potential applications of phosphazo compounds in amide synthesis and pervasive nature of amide linkages in the nature, possible interstellar prebiotic applications can be advocated for these compounds. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-11-03T11:55:43Z DOI: 10.1142/S0219633617500754

Authors:Jian Lv, Dapeng Yang Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In this work, we theoretically investigate the properties of excited state process for a novel salicylidene sal-3,4-benzophen (Sal-3,4-B) system, which contains two intramolecular hydrogen bonds (O1-H2[math]N3 and O4-H5[math]N6). Based on the density functional theory (DFT) and time-dependent DFT (TDDFT) methods, we find these two hydrogen bonds should be strengthened in the S1 state, while the O4-H5[math]N6 one could be largely affected upon the excitation process. Analyses about infrared (IR) vibrational spectra about hydrogen bond moieties also confirm this viewpoint. Frontier molecular orbitals (MOs) depict the nature of electronic excited state and support the excited state intramolecular proton transfer (ESIPT) reaction.Two kinds of stepwise potential energy curves of Sal-3,4-B in the S1 state demonstrate that only one proton could be transferred. Also based on constructing potential energy curves, the synergetic situation could be eliminated. Due to the specific ESIPT mechanism for Sal-3,4-B, we successfully explain the previous experiment and provide a reasonable attribution to the second emission peak of experiment. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-10-26T08:38:59Z DOI: 10.1142/S0219633617500730

Authors:Hong-Yu Cao, Wei Guo, Ya-Xian Yu, Hong-Lei Wang, Qian Tang, Shen-Min Li, Xue-Fang Zheng Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. It has been reported that short glucagon-like peptide-1 (sGLP-1), one of glucagon-like peptide 1 (GLP-1) analogues, has the same effect in treating type 2 diabetes mellitus (T2DM) as GLP-1 with increased half-life in human body. Although the high-resolution structure of complex of GLP-1 and its receptor has been achieved, the relationship between the structure of GLP-1 before recognition and its final function is still not clear. As for sGLP-1, few studies attempt to investigate the influences of different conditions on its structure. In present paper, molecular dynamics simulations were applied to explore molecular details of sGLP-1 under various environments. The results demonstrated that in low pH value solvent, the additional helical residue of Pro6 and the flexible N-terminal cannot keep [math] helix biological conformation. At pH 3, the structure has undergone significant changes, resulting in the shortest helical length. Further studies showed that protonation states of Glu21 mainly determined the secondary structure of sGLP-1 when pH values increased from 3 to 7. Interestingly, with ions concentration varying from 0.18% to 0.72%, the fluctuating trend of backbone RMSDs is consistent with that of [math] helix structure of sGLP-1. The structure of sGLP-1 had less helix content and became more flexible when temperatures increased in the range from 305[math]K to 320[math]K. Meanwhile, in mixtures of water and 2,2,2-trifluoroethanol (TFE) sGLP-1 showed a rigid structure with an additional helical residue (Pro6) at the N-terminal of original helix content. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-10-20T11:44:14Z DOI: 10.1142/S0219633617500717

Authors:Lidan Wu, Xiaoyan Meng, Xuejun Wang, Leshu Yu, Siyan Peng, Jianying Xie Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Mechanisms of decomposition reaction of thymine cation radicals (T[math]), 1-methyl substituted T[math] (1-MeT[math]), and 1,3-dimethyl substituted T[math] (1,3-Me2T[math]) generated by ionizing radiation or one-electron oxidation to thymine, 1-methylthymine and 1,3-dimethylthymine in aqueous solution have been investigated by theoretical calculations. Seven reaction paths including H2O or OH[math] addition, and deprotonation were considered. The most likely reaction for T[math] decomposition is N1 deprotonation forming T(-N1H)[math]. When N1 hydrogen is replaced by methyl, T[math] would deprotonate from C5 methyl group generating 1-methyl substituted UCH[math] in neutral solution, and reaction with OH[math] producing 1-methyl substituted T6OH[math] in basic solution. When N1 and N3 hydrogens are both replaced by methyl, T[math] decomposition reaction is similar to 1-MeT[math], indicating that N3 hydrogen barely influences the subsequent reaction of 1-MeT[math]. These results can provide theoretical support for experimental observations. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-10-19T09:15:28Z DOI: 10.1142/S0219633617500705

Authors:Mojgan Bandehpour, Shahrzad Ahangarzadeh, Fatemeh Yarian, Arezou Lari, Poopak Farnia Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Nowadays antibody engineering is an important approach in the design and manufacture of therapeutic and diagnostic antibodies. The study of interactions between antibodies and antigens is the critical step in the design of antibodies with desirable properties. Computational docking is a useful tool for structural characterization of bimolecular interactions. Docking is the process of predicting bound conformations and binding enthalpy of antibody–antigen complexes. In this study, the three-dimensional structures of two ribosome displayed-selected scFv antibodies were constructed by Kotai Antibody Builder. By using ClusPro 2.0 web server, the ESAT-6 antigen (a tuberculosis-specific antigen) structure was docked to both scFv models to obtain the structures of the binding complexes and molecular dynamics (MD) simulations were performed using GROMACS 4.5.3 package. By analyzing of the ESAT-scFv complexes, important amino acids involved in antigen–antibody interactions were identified which were Asn164 in VL3, Ser164 in VL7 and Asn55 in VH7. All three amino acids belonged to the CDRs. In conclusion, results achieved from this bioinformatics study can help in the design and development of novel antibodies with improved affinities for tuberculosis diagnosis. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-10-19T09:15:28Z DOI: 10.1142/S0219633617500699

Authors:Fatemeh Pakzad, Ali Ebrahimi, Abolfazl Azizi Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The misfolding and aggregation of amyloid-[math] (A[math] peptides into amyloid fibrils is regarded as one of the possible causes of Alzheimer’s disease (AD). Aromatic interactions (i.e. [math]–[math] interactions) between tanshinone drugs extracted from Chinese herb Salvia Miltiorrhiza (SM) and aromatic residues of A[math] peptides have been shown to prevent further growth of amyloid aggregates. In this work, the effects of isomerization, complexation and polarity of environment on the strength of [math]–[math] stacking interactions of tanshinone I (TS1) and isotanshinone I (IS1), as the two diterpenoid quinones in the SM herb, and their complexes with Mg[math] cation, IS1-Mg[math] and TS1-Mg[math], with phenylalanine (PHE), as an aromatic amino acid in A[math] structure have been investigated using the quantum mechanical calculations in the gas-phase, ether, acetone, DMSO, and water solvent. Molecular electrostatic potential (MEP), which are used to predict the nucleophile active sites, electron densities calculated at the bond critical points ([math] and ring critical points ([math] by the atoms in molecules (AIM) method and the donor–acceptor interaction energies ([math] calculated using the natural bond orbital (NBO) method were used to investigate the interplay between [math]–[math] stacking and complexation. The results show that the IS1/TS1-Mg[math] compounds have a more protective role compared to TS1/IS1-Mg[math] compounds due to the stronger interaction with PHE of A[math] in antiaggregation for further development of A[math] inhibitors to prevent and disaggregate amyloid formation. Complexation with Mg[math] increases the interaction diterpenoid drugs with PHE and makes notable changes in structural and electronic properties of diterpenoids. Also, the interactions between diterpenoid and PHE in less polar environment are more than other environments. Low-polarity environments have the best mimics of the A[math] binding site. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-09-29T09:14:50Z DOI: 10.1142/S0219633617500675

Authors:Nand Kishor Gour, Plaban Jyoti Sarma, Bhupesh Kumar Mishra, Ramesh Chandra Deka Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. A dual-level quantum chemical calculations have been carried out on the initiation of night-time degradation of 2-chloroethyl ethyl ether (CH3CH2OCH2CH2Cl) via H-abstraction by NO3 radical. Within the scope of density functional theory, the electronic structure of all the species involved in the titled reaction has been optimized at M06-2X functional along with 6-31[math]G(d,p) basis set. A higher level of couple cluster CCSD(T) method in conjunction with 6-311[math]G(d,p) basis set has been used for the refined energy of the species. All minima and saddle states involved in the reaction channel have been characterized on the potential energy surface (PES). From PES, it is confirmed that H-abstraction from methylene (–CH2–) of ethyl (CH3CH2–) part of CH3CH2OCH2CH2Cl follows the minimum energy path. The rate constants (individual and overall) of the titled reaction are obtained using Canonical Transition State Theory (CTST) over the temperature range of 250–350[math]K. The atmospheric lifetime and radiative efficiency of the titled molecule have also been estimated, amounting to 0.23 years and 0.024 years, respectively. The Global Warming Potentials of the 2-chloroethyl ethyl ether in 20 years, 100 years and 500 years time horizon were found to be 0.13, 0.04 and 0.01, respectively. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-09-29T09:14:50Z DOI: 10.1142/S0219633617500687

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:Feng Mei, Xinguo Ma, Yeguang Bie, Guowang Xu Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The hydrogen adsorption properties of Ti and Ni atoms as media on single-walled carbon nanotube (SWCNT) have been studied by density functional theory (DFT) incorporating a pragmatic method to correctly describe van der Waals interactions. The results show that both Ti and Ni atoms can reliably adhere to single-walled carbon nanotube, respectively, making strong TM[math]C bonds. Meantime, it is found that the average adsorption energies of H2 by Ti and Ni atoms are decreased with the increase of the amount of H2 adsorption. Ti or Ni atoms can bind up to no more than six H2 molecules on a carbon nanotube. It is inferred that these transition metals (TMs) can adsorb molecular hydrogen through likely Kubas-type interaction. By comparing the interaction energies among TM and H atoms, it can be identified that the hydrogen adsorption properties of Ti atoms are superior to those of Ni atoms at certain conditions. The present investigation is useful in the wider development of carbon-based nanomaterials as potential high-capacity H2 storage media. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-09-22T02:14:54Z DOI: 10.1142/S0219633617500651

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