Abstract: Journal of Theoretical and Computational Chemistry, Volume 16, Issue 02, March 2017. Using complete orthogonal [math]-Self-Friction Polynomials ([math]-SFPs) introduced by one of the authors, the analytical and power series formulas for SF atomic nuclear attraction integrals over [math]-noninteger Slater type orbitals ([math]-NISTOs) and [math]-noninteger Coulomb–Yukawa-like potentials ([math]-NICYPs) are presented, where [math] are the integer ([math] or noninteger ([math] SF quantum numbers and [math]. As an application, the computer calculations for dependence of the atomic nuclear attraction integrals over [math]-NISTOs and [math]-NICYPs functions are presented. • The Self-Friction Power Series derived by the use of one-center one-range addition theorems are applied to determine the atomic nuclear attraction integrals with non-integer indices of Slater Type Orbitals and Coulomb–Yukawa-Like Potentials. • Series expansion solutions of these integrals are compared with analytical results. • Convergence behaviour of the Self-Friction Power Series is shown up. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-04-04T09:27:51Z DOI: 10.1142/S0219633617500171

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The possible paths of dimethyl ether (DME) synthesis from methanol over hydrated [math]-Al2O3(110) in vacuum and liquid paraffin have been investigated by using density functional theory (DFT). Over hydrated [math]-Al2O3(110), the three possible paths of methanol dehydration to DME have been investigated by the DFT method in vacuum and liquid paraffin. DME synthesis from methanol is carried out along the same pathway 2CH3OH(g) [math] 2* [math] 2CH3OH* [math] 2CH3O* [math] 2H* [math] CH3OCH3* [math] H2O* in vacuum and liquid paraffin, and the step of highest energy barrier is the reaction of 2CH3O* [math] CH3OCH3* [math] O*. The energy barrier of the step in liquid paraffin is higher than that in vacuum by 0.33[math]eV. The surface acid strength in liquid paraffin decreases over [math]-Al2O3(110) surface comparing with vacuum, showing that stronger surface acid strength benefits to DME synthesis. Our result is in consistent with the experiment results. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-04-28T07:14:26Z DOI: 10.1142/S0219633617500298

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Antibodies play a significant role in the immunotherapy, basic research and the pharmaceutical industry. Nowadays, both DNA recombinant technology and antibody engineering technology are widely used in many fields such as diagnostics, therapeutics, drug targeted delivery, and research reagents. Computational docking of antigen-antibody complexes and analysis of atomic interactions are important to find effective B-cell epitopes and new antibodies with appropriate properties. In the present study, by using ClusPro 2.0 webserver, docking the antigen (factor H binding protein (fHbp)) to the novel-selected scFv antibody was performed. By analyzing the fHbp-scFv complexes, important amino acids were identified. After docking, peptides Ala192-His198, Asp 211-216, and Gly229-Ser228 of the fHbp antigen were recognized as essential interactive regions to the scFv antibody. Results obtained from our bioinformatics study are important and give us the basis for the favored designs of new molecules such as effective B-cell epitopes targeted by neutralizing antibodies for vaccine design. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-04-19T06:36:48Z DOI: 10.1142/S0219633617500213

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Ionic liquids (ILs) especially their mixtures are of high interest within the different scientific societies due to their amazing properties. In this regard, a number of attempts have been made to measure, correlate, estimate and calculate the properties of ILs in the neat or mixture forms. Among the different possible predictive methods, artificial neural networks (ANNs) are widely used because of their unique and amazing capabilities for prediction of different parameters. With respect to this paper, a feed-forward ANN model is proposed to model the densities of different binary mixtures of ILs/ethanol. The proposed network is trained and tested with 1078 binary data points gathered by mining into the different published literatures. The data gathered from previously published literatures are separated into two different subsets namely training and testing. The statistical error analysis has shown that the proposed neural network correlated the binary densities with the overall mean absolute percentage error (MAPE), average relative deviation percentage error (ARD%), minimum relative deviation percent (RDmin%), maximum relative deviation Percent (RDmax%) and correlation coefficient ([math] of 1.5%, [math]0.1%, [math]13.0%, 15.0% and 0.9712, respectively. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-04-17T11:00:26Z DOI: 10.1142/S0219633617500316

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In this work, the reaction mechanisms for the selective catalytic reduction (SCR) of nitrogen oxides (NOx) with NH3 on a (MnO)[math]/ZSM-5 catalyst were investigated based on the density functional theory (DFT) method. Our calculations showed that the NH3 could strongly adsorb on the (MnO)[math]/ZSM-5 catalyst as compared to NO. The proposed reaction pathway, NH3(ads)[math]NH[math]H[math]NH2(ads) [math] NO(ads)[math] NH2NO[math]NHNO [math] H[math]N[math]H2O, was more favorable with smaller activation barrier (1.40[math]eV) of the rate-determining step. The compared reaction process that the adsorbed NH3 reacted directly with adsorbed NO was difficult to happen for the higher activation barrier. Meanwhile, the framework oxygen participated in the oxidation process from ammonia to NH2, thereby increasing its availability for the reaction. In addition, the regeneration process of active site in the presence of NH3 and NO2 was explored, and the rate-limiting step possessed an activation barrier of 1.46[math]eV. The NH2NO species was formed as the crucial intermediate and subsequently decomposed into the N2 and H2O. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-04-17T11:00:25Z DOI: 10.1142/S0219633617500304

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Conformational, structural, vibrational spectroscopic properties and nuclear magnetic chemical shift values of 4-acetoxyphenethyl acrylate (4APA) were investigated using spectroscopic and theoretical approaches including FT-IR and NMR spectroscopes and quantum chemical calculations. FT-IR spectroscopic measurement was carried out between 3500[math]cm[math]–400[math]cm[math]. Geometric parameters, vibrational wavenumbers and nuclear magnetic chemical shift values were estimated using B3LYP hybrid density functional theory method with 6-311[math]G(d, p) basis set. 1H, [math]C, APT and HETCOR NMR experiments of 4APA were obtained in DMSO solution. For a quantitative description of vibrational wavenumbers, total energy distribution (TED) values with scaled quantum mechanical (SQM) method were calculated. Moreover, molecular docking study of title molecule was theoretically carried out using Auto Dock Vina Program. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-04-05T06:47:05Z DOI: 10.1142/S0219633617500250

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Here, we have proposed a new scheme of the computational combinatorial design approach to identify potential inhibitor peptides. It consists of four steps: (i) using “multiple copy simultaneous search” (MCSS) procedure to locate specific functional groups on the protein surface; (ii) the peptide main chain is constructed based on the location of favored N-methylacetamide (NMA) groups; (iii) molecular dynamics simulations of the complex formed between the constructed peptides with the target protein in explicit water molecules are carried to select the peptides with strong binding to the protein and (iv) the sequences of the stable peptides selected from (iii) are aligned and the frequencies of the amino acids at each position of peptide are calculated. Sequence patterns of potential inhibitors are determined based on the frequency of amino acids at each position. It was applied to design peptide inhibitors that bind to the E2 protein of HPV16 so as to disrupt its transcriptional regulator of E1–E2 complex formation. The sequence pattern of these potential inhibitors is in agreement with known inhibitors obtained from phage display, and the MCSS calculations indicate that a hydrophobic pocket on HPV16 E2 plays a significant role in E1–E2 formation and inhibitor-E2 binding. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-04-05T06:47:05Z DOI: 10.1142/S0219633617500262

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The gas phase studies on the electronic stabilities and thermochemical properties of metastable AC mismatches have been performed and the results are analyzed to explain the features of experimentally available AC mismatches. The hydrogen bonding patterns observed in these mismatches are relevant to the formation of stable AC mismatches. In these AC pairs, the H migration mechanism to generate other tautomeric forms is not observed, which shows the compatibility of H bonding capacity of the sites involved in H bonds. The presence of hydrogen bond type –N[math]H–N– may contribute to better AC pairing, hence cisA1-1cisC2, transA2-cisC1 and transA1-1cisC2 are found to be more favorable pairs compared to other AC pairs. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-04-05T06:47:05Z DOI: 10.1142/S0219633617500274

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Employing density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations in combination with the semiclassical nuclear ensemble method, we have simulated the photoabsorption spectra of the four canonical DNA nucleobases in aqueous solution. In order to model the effects of solvation, for each nucleobase, a number of solvating water molecules were explicitly included in the simulations, and additionally, the bulk solvent was represented by a continuous polarizable medium. We find that the effect of the solvation shell in general is significant, and its inclusion improves the realism of the spectral simulations. The involvement of lone electron pairs in the hydrogen bonding with the solvating water molecules has the effect of systematically increasing the energies of vertical excitation into the [math]-type states. Apart from a systematic blue shift of around [math][math]eV observed in the absorption peaks, the calculated photoabsorption spectra reproduce the measured ones with good accuracy. The photoabsorption spectra are dominated by excited states with [math] and partial [math] character. No low-energy charge transfer states are observed with the use of the CAM-B3LYP and M06-2X functionals. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-04-05T06:47:05Z DOI: 10.1142/S0219633617500286

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The vibrational structure of 2-ethyl-1-hexanol is of great interest because of its industrial and military applications. However, detailed spectral analysis is challenging due to its flexibility. This paper reports a detailed analysis of the gas and liquid phase vibrational spectra of 2-ethyl-1-hexanol using the Fourier transform infrared spectroscopy and Raman experimental data. By performing a detailed exploration of the conformational space in this work, the theoretical spectra reproduced almost all experimental details observed, and assigned internal valence coordinates to all of the experimentally observed bands in the floppy 2-ethyl-1-hexanol molecule. Relative contributions from the various internal valence coordinates to the experimental vibrational bands are directly compared between the liquid phase Raman band and the gas and liquid phase infrared band. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-03-31T07:47:34Z DOI: 10.1142/S0219633617500237

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The structure of a potential bioactive agent namely, 3-[([math]-methylanilino)methyl]-5-(thiophen-2-yl)-1,3,4-oxadiazole-2(3[math]-thione was characterized by proton and carbon-13 nuclear magnetic resonance (NMR) chemical shifts, Fourier transform infrared (FT-IR) and Laser-Raman spectroscopic techniques. The quantum chemical computations of molecular structures (disorder I and disorder II forms), vibrational wavenumbers, carbon-13 and proton chemical shifts and UV-Vis spectroscopic parameters have been performed with DFT/B3LYP method at 6-311[math]G(d,p) basis set. The highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), nonlinear optical (NLO) properties and natural bond orbital (NBO) analyses have been theoretically examined with the mentioned calculation level. The calculated values have been compared with the recorded experimental data. The computed molecular geometric parameters, vibrational wavenumbers, NMR chemical shifts, and UV-Vis wavelengths have been found to be in a good harmony with the experimental values and spectral results of similar structures in the literature. We believe that the work will be of considerable interest to anyone working in the area of theoretical chemistry, whether in industry or academics. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-03-31T07:47:33Z DOI: 10.1142/S0219633617500249

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. This article communicates the study of magnetohydrodynamic (MHD) stagnation point flow of Casson liquid towards a stretched surface. Chemical reaction model involving both heat and mass transfer is established. Effects of viscous dissipation and Joule heating are also considered. Appropriate transformations yield strong nonlinear ordinary differential system. The obtained nonlinear systems have been solved through built-in shooting method. Velocity field shows decreasing behavior for higher estimation of magnetic parameter while temperature field shows increasing behavior for larger homogeneous heat parameter. Graphical behaviors of velocity, temperature and concentration are analyzed comprehensively corresponding to various pertinent parameters. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-03-22T02:41:30Z DOI: 10.1142/S0219633617500225

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Carbodiimides have been widely used for different purposes, such as an intermediary to form peptides bonds and esters, which have generated industrial, organic and biological applications. Diisoproylcarbodiimide (DIC), (3-(dimethylamino) propyl)ethylcarbodiimide (EDC) and N,N′-dicyclohexylcarbodiimide (DCC) are the most common carbodiimides, however, there exist other carbodiimides that are not normally used. Twelve carbodiimides including the above mentioned were chosen to study their chemical reactivity as well as their nucleophilic and electrophilic attack sites. Geometry optimization in gas and solution phases was obtained using Density Functional Theory (DFT) through B3LYP with 6-31G(d) and 6-311[math]G(d,p) level. Global and local reactivity descriptors were calculated and analyzed such as chemical hardness, ionization potential, electron affinity, Fukui functions, dual descriptor and hypersoftness. The results obtained for geometrical parameters do not have significant differences for gas and solution phase. The introduction of diffuse functions has great impact in electron affinity, modifying notably the values of reactivity descriptors, but didn’t show qualitative differences, since the results found for both basis set calculations show that Cyanamide or CD1 is the most stable and CD11 present greater reactivity of all studied molecules. Also, the hypersoftness results obtained with 6-31G(d) are in agreement with the general affirmation that carbodiimides are easily attacked by nucleophiles and electrophiles in the central carbon–nitrogen double bond. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-03-02T08:06:20Z DOI: 10.1142/S0219633617500195

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Alkali-metal hydrazinidoboranes have been recently investigated as a new stable high-capacity material for hydrogen storage, necessitating an exploration of the dehydrogenation mechanism for further developments in this field. Herein, we present a first systematic study of the structure and dehydrogenation mechanism of sodium hydrazinidoborane (NaHB) with three possible pathways considered: pathway A, corresponding to unimolecular dehydrogenation; pathway B, featuring dehydrogenation of the (NaHB)2 dimer via two different sub-pathways, and pathway C, corresponding to direct dehydrogenation (as compared to B). The calculated rate of the most probable dehydrogenation pathway (B, 3.28[math]min[math] is similar to that obtained experimentally (12.26[math]min[math], supporting the validity of our findings. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-03-02T08:06:20Z DOI: 10.1142/S0219633617500201

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The present work aims at a better and deeper insight into the forces that govern the intramolecular charge transfer (ICT) and photo injection processes in dyes for dye sensitized solar cells (DSSC). The geometry, electronic structure, electron density distribution, and absorption spectra, for a selected donor-[math]-acceptor (D-[math]-A) dye for DSSC were computed and analyzed at a high level of DFT theory. The coplanar geometry of the studied dye (D1) indicates a strong conjugation which facilitates ICT. NBO analyses reveal that this ICT amounts to 0.8e, which is localized on the acceptor and anchoring groups resulting in a marked total delocalization interaction energy. The origin of this stabilization is two-fold; first the [math]-charge transfer (CT) interaction from donor to acceptor orbitals and the hyperconjugative interactions involving Rydberg states. The effect of fluorine substituents, in the [math]-spacer, on the quantum efficiency of DSSCs was investigated. Gibb’s free energy values, redox potentials, excited state life time, non-linear optical properties (NLO) and driving forces for D1 and its fluorinated derivatives were computed. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-02-24T10:35:13Z DOI: 10.1142/S0219633617500183

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In this paper, some geometrical models such as Kohler, Muggianu, Toop, and Hillert have been used to estimate the molar volume of Au–Bi–Sn ternary systems based on the data of sub-binary systems over a wide temperature range (673–973[math]K). The density of Au–Bi–Sn alloys was calculated from the calculated molar volume and using theoretical equation along three cross-sections [math]/[math]/2, 1/1 and 2/1. In addition, the viscosity of Au–Bi–Sn alloys was calculated by using Seetharaman–Sichen equation over a wide temperature range (673–1273[math]K). The density of these alloys show linear dependence on temperature for all investigated compositions, while the molar volumes increase with increasing temperature and Sn compositions. The results show, as a function of temperature, that the increase in concentration of tin influences the viscosity of the Au–Bi–Sn alloys. The calculated values of density of Au–Bi–Sn alloys are compared with the experimental values reported in the literature, and a good agreement was observed. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-02-10T06:27:19Z DOI: 10.1142/S0219633617500158

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In this work, we applied a definition of informational energy and informational temperature using 1865 molecules and showed that such definitions can classify molecules with similar chemical properties such as hardness, softness and chemical potential. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-02-10T06:27:18Z DOI: 10.1142/S021963361750016X

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. A density functional theory (DFT) based multi-step simulation method is used to characterize the detailed molecular structure and inter/intra- molecular interactions of two benchmark liquid crystals (LC) 5CB, 8CB and a novel tri-biphenyl ring bent core LC material. The method uses hybrid DFT at the B3LYP/6-31G* level to obtain molecular structure and Raman data. These results are fed to a crystal packing simulation to find possible crystal structures. A pico-second quantum mechanics/molecular mechanics (QM/MM) simulation model is built for the selected structures with lower overall energy as well as optimal density. The stabilized crystal structures are then extended into a super cell, heated and simulated using a mixed force field and nano-second molecular dynamics (MD). The described simulation process sequence provides predictions of molecular Raman spectrum, LC density, isotropic depolarization ratio, ratio of differential polarizability, order parameters, molecular structures, and rotating Raman spectrum of the different mesophases. The Raman spectra, order parameters and depolarization ratios all agree well with existing experimental and previous simulation results. The study of the novel tri-biphenyl ring bent core LC system shows that the ratio of differential polarizability depends on intra-molecular interactions. The findings presented in this manuscript contribute to the on-going efforts to establish links between LC molecular structures and their properties, including optical behavior. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-01-26T09:19:48Z DOI: 10.1142/S0219633617500122

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Lubricating additives can improve the lubricant performance of base oil in reducing friction and wear and minimizing loss of energy. It is of great significance to study the relationship between chemical structures and lubrication properties of lubricant additives. This paper reports a quantitative structure–property relationship (QSPR) model of the maximum nonseizure loads ([math]) of 79 lubricant additives by applying artificial neural network (ANN) based on the algorithm of backward propagation of errors. Six molecular descriptors appearing in the multiple linear regression (MLR) model were used as vectors to develop the ANN model. The optimal condition of ANN with network structure of [6-4-1] was obtained by adjusting various parameters by trial-and-error. The root-mean-square (rms) errors from ANN model are [math] ([math]) for the training set and [math] ([math]) for the test set, which are superior to the MLR results of [math] ([math]) for the training set and [math] ([math]) for the test set. Compared to the existing model for [math], our model has better statistical quality. The results indicate that our ANN model can be applied to predict the [math] values for lubricant additives. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-01-26T09:19:48Z DOI: 10.1142/S0219633617500146

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Adsorption and interaction mechanisms of fullerene-based complex systems for possible drug delivery vehicles have been at the center of increasing attention. In the scope of this work, the interaction mechanism between an important antiviral drug favipiravir and silicon-doped/undoped C60 fullerenes have been investigated using density functional theory (DFT). Calculations were carried out in both gas phase and water media to see the possible solvent effects. The effect of adsorption of the favipiravir on the SiC59 fullerene system and the nature of interaction were examined by analyzing the band shifts in the carbonyl stretching vibrations and natural bond orbital (NBO) properties of the examined complexes. Some important structural and electronic properties were reported and discussed as well. It was observed that doping the C60 fullerene nanocages with silicon atom enhanced the adsorption mechanism and calculations performed in water media gave rise to more stable complexes for silicon-doped systems compared to the results obtained for the gas phase. Results and parameters found in the present search reveal further insights into the drug delivery systems. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-01-26T09:19:47Z DOI: 10.1142/S0219633617500110

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Two-dimensional optical catalysis materials have a wonderful potential application. Here, a new two-dimensional material consisting of the supported single-atom Au on a graphite carbon nitride (g-C3N[math] single layer has been designed and its electronic and optical properties have been characterized by density functional calculations. The bandgap of 1.82[math]eV calculated by the hybrid functional HSE06 shows that the Au/g-C3N4 is an indirect semiconductor, and the electron can easily be excited from the single-atom Au to the bottom of the conduction band. This material therefore has relatively strong optical properties in the visible region. Moreover, the process of Au insertion into the cavity of g-C3N4 single layer is energy-favorable. This work may provide insights and a new avenue for fabricating supported Au catalysts with high stability. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-01-26T09:19:47Z DOI: 10.1142/S0219633617500134

Authors:Lidan Zhang, Jiguang Du, Gang Jiang Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Density functional theory (DFT) calculations were used to investigate the gas phase reaction of U[math] with COS to produce US[math]CO and UO[math]CS. It is shown that the two reactions are exothermic and the formation of UO[math]CS has the lower energy barrier which agrees with the experimental result that UO[math] is the main product. The reaction mechanisms and the potential energy profiles (CPEPs) considering different spin states were presented in detail. Diverse analyses including atoms in molecules, natural bond orbital were used to study the bonding properties of all the involved species. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-01-17T11:31:38Z DOI: 10.1142/S0219633617500109

Authors:Marilena Carbone Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In the current study, the NO adsorption on the Si(100) surface was investigated by DFT including van der Waals forces (vdW). Stable molecular and dissociative configurations were found and compared to previous studies. Furthermore, additional states were investigated where NO adsorbs across dimers. The transformation of NO from molecular adsorbate into a dissociated adsorbate migrated into the subsurface was investigated by nudged elastic band. Several pathways were explored, either multi-staged, or direct from molecular into subsurface migrated configurations, both including and excluding vdW forces. The energy barriers of the single steps of multi-staged pathways never exceed 0.15[math]eV and are, in general, smaller when NO is adsorbed across dimers rather than bridged on a single dimer and when including vdW. Furthermore, the oxygen-bridged configurations are kinetically more accessible than the nitrogen-bridged ones. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-01-10T06:29:17Z DOI: 10.1142/S0219633617500092