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:Vijay M. Miriyala, Priya Bhasi, Zanele P. Nhlabatsi, Sanyasi Sitha Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Using computational calculations, we have revisited the potential energy surface (PES) of the reaction between OH and SO2, which is believed as the rate-limiting step in the atmospheric formation of H2SO4. In this work, we report for the first time the presence of a pre-reaction hydrogen-bonded complex between OH and SO2 in the reaction PES. Based on this finding, it has been shown that the reaction can be considered as a two-step process in which the first step is the formation of the pre-reaction complex and the second step is the transformation of this complex to the product. It was observed that due to the presence of this pre-reaction complex as a potential well in the reaction PES, the barrier height got increased by around two-fold for the second step. Based on this observation, it has been proposed that the kinetics of the reaction is going to be affected. Also based on the analysis of the geometries of this pre-reaction complex and the transition state, it has been argued that the step involving the transformation of this pre-reaction complex to the product via the transition state is going to be the slowest step as this transformation involves large structural changes of the stationary points involved. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-07-05T07:42:05Z DOI: 10.1142/S0219633617500468

Authors:Mohammad Mostafanejad Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. We review the fundamental ideas of free complement (FC) method through its application on both ground and first excited states of helium atom. We have found that lower energies can be obtained with fewer number of terms in the FC expansion of the ground state wavefunction. In this case, the optimization of orbital exponents was not necessary for achieving spectroscopic accuracy, especially at higher orders where the structure of the FC wavefunction converges to that of the exact one. We have discovered that permanents naturally appear in the FC expansion of the first triplet excited state wavefunction. Including permanents in the FC expansion is shown to be energetically important for the first triplet excited state of helium atom whereas it is not computationally favorable at higher orders. Finally, considering the group theoretical properties of the symmetric group [math] and using immanants, a compact and more elegant form for the FC expansion of the first triplet excited state of the helium atom is achieved. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-07-03T08:18:43Z DOI: 10.1142/S0219633617500481

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

Authors:Jia Fu, Jie Zhan, Qun Chao Fan, Hui Dong Li, Zhi Xiang Fan, Yong Gen Xu Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Full vibrational energies and corresponding analytical potential energy functions (APEFs) for [math] of ClF, [math] of ICl, [math] of IBr, and [math]of IF are obtained by four-term variational algebraic energy-consistent method [VAECM(4)]. Three major methods are used to handle the regularization problems and make the results more reliable: (1) physical constraints like progressive dissociation behavior are used to overcome overfitting problems; (2) reasonable variational method is used to expand the experimental dataset and make the model optimization much faster; and (3) validation dataset is used to further enhance the reliability. After these treatments, our results agree well with experiment and have a good physical converged behavior in molecular dissociation and asymptotic region. This study provides important reference data for the related molecules. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-06-22T04:13:31Z DOI: 10.1142/S021963361750047X

Authors:Tasawar Hayat, Faisal Shah, Ahmed Alsaedi, Muhammad Ijaz Khan Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The objective here is to analyze the influence of homogeneous and heterogeneous reactions in flow induced by convectively heated sheet with nonlinear velocity and variable thickness. Porous medium effect is characterized by Darcy–Forchheimer consideration. A simple isothermal model of homogeneous–heterogeneous reactions is used to regulate the temperature of stretched surface. Thermodynamics processes of homogeneous–heterogeneous reactions analyze the effect of temperature phase changes. Resulting problems are computed for the convergent solutions of velocity, temperature and concentration. Analysis for the influential variables on the physical quantities is graphically examined. Our computed results interpret that velocity field decays for larger magnetic parameter while temperature field enhances for higher estimation of Biot number. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-06-13T09:25:33Z DOI: 10.1142/S0219633617500456

Authors:Alex Brown, E. Pradhan Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In this paper, the use of the neural network (NN) method with exponential neurons for directly fitting ab initio data to generate potential energy surfaces (PESs) in sum-of-product form will be discussed. The utility of the approach will be highlighted using fits of CS2, HFCO, and HONO ground state PESs based upon high-level ab initio data. Using a generic interface between the neural network PES fitting, which is performed in MATLAB, and the Heidelberg multi-configuration time-dependent Hartree (MCTDH) software package, the PESs have been tested via comparison of vibrational energies to experimental measurements. The review demonstrates the potential of the PES fitting method, combined with MCTDH, to tackle high-dimensional quantum dynamics problems. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-06-13T09:25:32Z DOI: 10.1142/S0219633617300014

Authors:Zhengcheng Wen, Mengmeng Du, Yuan Li, Zhihua Wang, Jiangrong Xu, Kefa Cen Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The detailed mechanism of NO oxidation catalyzed by ZSM5 supported Mn/Co–Al/Ce is investigated and revealed by Quantum Chemistry Calculation. A three-step catalytic mechanism for NO oxidation is proposed and studied. Theoretical results show that, the activate energies of reactions catalyzed by ZSM-5 supported Mn/Co (71.1[math]kJ/mol/80.6[math]kJ/mol) are much lower than that obtained from the direct NO oxidation. This indicates that the ZSM-5 supported Mn/Co has an obvious catalytic effect. When the active center Si is replaced by Al and Ce, the activation energies are further decreased to about 40[math]kJ/mol. This indicates that the doping of Al and Ce can obviously improve the catalytic effect. The theoretical study illustrates that the catalysts for NO oxidation not only relate to the supported transition metal such as Co and Mn, but also highly relate to the activity centers such as Al and Ce. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-06-13T09:25:32Z DOI: 10.1142/S0219633617500444

Authors:Mohammed I. Alomari, Taher S. Ababneh, Tareq M. A. Alshboul Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In this study, geometrical optimizations, infrared spectroscopic analysis and relative stabilities of 1-methylcyclobutene and methylenecyclobutane tautomers were investigated by utilizing high-level ab initio and DFT calculations. The thermodynamic data showed that 1-methylcyclobutene is the more stable isomer with enthalpy [math][math]kcal/mol and Gibbs energy [math][math]kcal/mol lower than that for methylenecyclobutane at the M06/aug-cc-PVTZ level of theory. These results are in good agreement with the available experimental data. Additionally, the geometrical parameters and vibrational frequencies agree well with the recorded results in literatures. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-05-26T08:11:13Z DOI: 10.1142/S0219633617500419

Authors:Gaurav Kumar, Pankaj Paliwal, Nishant Patnaik, Ranjana Patnaik Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Neuronal nitric oxide synthase (nNOS or NOS1) is an important therapeutic target for the treatment of various neurological diseases. A major challenge faced in the design of nNOS inhibitors emphasizes on potency in humans and selectivity over other NOS isoforms — eNOS and iNOS. The present structural-based in silico study was carried out to search potent and selective inhibitor for human nNOS from a set of 40 Withania somnifera phytochemicals structure. Ten phytochemicals appear as dual-selective inhibitors of nNOS over both iNOS and eNOS. Here we report five potent and selective human nNOS inhibitors, namely, Chlorogenic Acid, Withanolide B, Withacnistin Pelletierine, and Calystegine B2 based on their selectivity, binding energy and nNOS active site residues interaction profile. These phytochemicals have nNOS selectivity higher than 4-methyl-6-(2-(5-(3-(methylamino)propyl)pyridin-3-yl)-ethyl)pyridin-2-amine inhibitor and have potential as an oral neurotherapeutic agent to combat neurological disorders mediated by nNOS activation. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-05-26T08:11:13Z DOI: 10.1142/S0219633617500420

Authors:Rachida M’chaar, Abdelaziz Sabbar, Mouloud El Moudane, Ahmed Ghanimi Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Some physicochemical properties such as surface tension, molar volume, density and viscosity of liquid Sn–Ag–Cu alloys have been calculated using Kohler, Muggianu, Toop and Hillert geometrical models along three cross-sections namely [math]/[math], 1/1 and 2/1. Indeed, Guggenheim, Kozlov–Romanov–Petrov and Kaptay equations have also been extended to estimate the surface tension and viscosity based on the thermodynamic data of the investigated system over wide temperature ranges of 823–1123[math]K and 773–1173[math]K, respectively. The results show that the three investigated properties, surface tension, density and viscosity, decrease with increasing tin for all studied models. On the other hand, a different behavior of these properties as a function of the temperature was noted. This evolution depends on the composition of the studied alloys. On the contrary, the molar volume increases with increase of temperature and tin compositions. It should be noted that the surface tension, density and molar volume show a linear dependence on temperature for all the investigated compositions. For viscosity, a curvilinear dependence has been observed. The calculated surface tensions and densities were compared with those reported experimentally for Sn–Ag–Cu alloys along the cross-section [math]/[math][math]1/1. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-05-26T08:11:12Z DOI: 10.1142/S0219633617500407

Authors:Arezoo Tahan, Neda Ahmadinejad Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In the present study, density functional theory was employed to analyze the structure and nuclear magnetic resonance (NMR) — nuclear quadrupole resonance (NQR) spectra of hallucinogenic harmine in monomeric, dimeric, trimeric, and tetrameric states in the gas phase. Furthermore, the effects of hydrogen and resonance interactions on the values of NMR and NQR parameters of nitrogen nuclei in the four states mentioned above were investigated. The computations at the B3LYP/6-311[math]G** level of theory indicated that NQR — NMR parameters of nitrogen nuclei varied for each of the four states and were strongly affected by chemical environment, molecular cluster size and molecular interactions. Accordingly, by increasing the participation of lone pair electrons in resonance interactions and aromaticity development, the values of NMR chemical shielding around them increased, whereas their NQR parameters ([math] and [math] decreased. In contrast, it could be observed that resonance interaction was not the only effective factor influencing changes in values and trends of NMR — NQR parameters by passing from monomeric state to other ones. Moreover, the negative charge on nitrogen atoms and the possibility of hydrogen bond formation were other important factors influencing NMR — NQR parameters. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-05-26T08:11:12Z DOI: 10.1142/S0219633617500432

Authors:Yusuf Sert, Mehmet Gümüş, Volkan Kamaci, Halil Gökce, İbrahim Kani, İrfan Koca Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In this present study, the experimental and theoretical vibrational frequencies of an important pharmacological molecule 2-(4-benzoyl-1,5-diphenyl-1[math]-pyrazol-3-yl)-4[math]-naphto[2,3-[math]][1,3]oxazin-4-one have been researched. The experimental FT-IR and laser-Raman spectra of the title compound have been taken in the region (4000–400[math]cm[math]) and (4000–100[math]cm[math]), respectively. The vibrational modes and optimized structure parameters have been computed by using DFT/B3LYP methods with 6-311[math]G(d,p) basis set. In our calculations, Gaussian 09W software program has been used. Assignments of theoretical vibrations have been obtained by potential energy distribution analysis using VEDA 4 software program. This program is important because it performs assignments with 10% precision. We have obtained a fairly good agreement between experimental and theoretically obtained results, and these results have supported the literature. Additionally, we have examined the highest occupied molecular orbital and the lowest unoccupied molecular orbital energies, the other related molecular energy values, nuclear magnetic resonance ([math]C and 1H-proton) chemical shifts, and UV–Vis wavelengths (electronic absorption wavelengths of the title compound) by using the mentioned calculation level. The nonlinear optical properties of the title compound have also been determined by using DFT/B3LYP/6-311[math]G(d,p) level. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-05-24T06:21:46Z DOI: 10.1142/S0219633617500390

Authors:Abolfazl Barzegar, Hossein Hamidi Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Human immunodeficiency virus-1 (HIV-1) integrase appears to be a crucial target for developing new anti-HIV-1 therapeutic agents. Different quantitative structure–activity relationships (QSARs) algorithms have been used in order to develop efficient model(s) to predict the activity of new pyridinone derivatives against HIV-1 integrase. Multiple linear regression (MLR) and combined principal component analysis (PCA) with MLR have been applied to build QSAR models for a set of new pyridinone derivatives as potent anti-HIV-1 therapeutic agents. Four different approaches based on MLR method including; concrete-MLR, stepwise-MLR, concrete PCA–MLR and stepwise PCA–MLR were utilized for this aim. Twenty two different sets of descriptors containing 1613 descriptors were constructed for each optimized molecule. Comparison between predictability of the “concrete” and “stepwise” procedure in two different algorithms of MLR and PCA models indicated the advantage of the stepwise procedure over that of the simple concrete method. Although the PCA was employed for dimension reduction, using stepwise PCA–MLR model showed that the method has higher ability to predict the compounds’ activity. The stepwise PCA–MLR model showed highly validated statistical results both in fitting and prediction processes ([math] and [math]). Therefore, using stepwise PCA approach is suitable to remove ineffective descriptors, which results in remaining efficient descriptors for building good predictability stepwise PCA–MLR. The stepwise hybrid approach of PCA–MLR may be useful in derivation of highly predictive and interpretable QSAR models. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-05-12T06:15:22Z DOI: 10.1142/S0219633617500389

Authors:Xiyuan Sun, Jiguang Du Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The structures, electronic properties, bonding characters and UV–Vis spectra of [math] ([math]–[math]) transition-metal phthalocyanines (TMPcs) molecules have been studied with different density function theory (DFT) methods. The calculated structural parameters agree well with previous experimental or theoretical values. Natural Population Analysis (NPA) charge revealed that [math]–[math] hybridizations occur when [math] TM atoms are involved in chemical bondings. The spin magnetic moments of TMPcs are mainly from the contribution of [math] electrons. Conceptual density functional theory (CDFT) results indicate that [math] TMPcs molecules are willing to accept further electrons. The TM–N chemical bonds show very weak covalent nature, and are consistent with bond order analyses. Time-dependent density function theory (TD-DFT) calculations were carried out to simulate the UV–Vis spectra, and corresponding electronic transfers for dominant peaks were also obtained. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-05-08T06:19:33Z DOI: 10.1142/S0219633617500365

Authors:Hajar Hassani-Ardekani, Hanieh Niroomand-Oscuii, Ehsan Nikbin, Amir Shamloo Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Interactions between P-selectin, expressed on activated endothelium, and its counterpart P-selectin glycoprotein ligand-1 (PSGL-1), expressed on leukocytes, play a pivotal role in adhesive events that recruit circulating leukocytes toward inflamed or injured tissues. Atomistic understanding of the association and dissociation of these bonds under blood flow is necessary to define the underlying mechanism. In this study, steered molecular dynamics (SMD) simulations were applied to investigate the conformational changes of P-LE/SGP-3 construct (an effective binding unit of the P-selectin/PSGL-1 complex) under stretching with constant velocity. In the present simulations, a self-built force field parameterization was developed for sulfated tyrosine by using force field toolkit of Visual Molecular Dynamics (VMD) program. A dissociation mechanism was represented by analyzing the nonbonded energies between interface residues. The results indicate that the salt bridges between P-LE and SGP-3 and the hydrogen bonds between ion Ca[math] and residue fucose of glycan group of PSGL-1 and also between sulfated tyrosine residues are the most effective bonds in binding. Finally, potential of mean force (PMF) was calculated by averaging the outcomes of eight independent runs and the results were discussed. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-05-08T06:19:32Z DOI: 10.1142/S0219633617500353

Authors:Djaffar Kheffache, Ourida Ouamerali Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. We theoretically study, from the thermodynamic point of view, the possibility of the two degradation pathways of antitumor drug of imexon. According to the theoretical results obtained at DFT level in both gas and aqueous phases, the two degradation pathways of imexon are characterized by negative reaction Gibbs free energies. It has been found that 4-imino-5-methylene-imidazolidin-2-one is the favored degradation product of imexon. Herein, the focus of this work has been on calculating the geometries, relative energies and electronic properties of all possible prototropic tautomers of 4-imino-5-methylene-imidazolidin-2-one using the DFT and MP2 levels. The bulk water environment has been simulated by continuum model using Solvation Model based on Density (SMD). The UV spectra of two dominant tautomers of 4-imino-5-methylene-imidazolidin-2-one are also predicted using time-dependent density functional theory and the results are compared with the available experimental data. The comparison of the simulated and the experimental absorption spectra has allowed us to accurately characterize the predominant tautomer of the degradation product in aqueous medium. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-05-08T06:19:32Z DOI: 10.1142/S0219633617500377

Authors:Kolsoom Shayan, Alireza Nowroozi Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In the first part of this paper, a comprehensive theoretical study of molecular structure, stability, intramolecular hydrogen bond (IMHB) and [math]-electron delocalization ([math]-ED) of the enol and thiol tautomers of 3-thioxopropanal (TPA) in the ground state is performed. In this regard, all of the plausible conformations of TPA at M06-2X/6-311[math]G(d,p) are optimized and a variety of theoretical levels are employed to identify the global minimum. Our calculations show that E1 is the most stable form that is in contrast to the results of Gonzalez et al. [J Phys Chem 101: 9710, 1997]. In order to elucidate this duality, the IMHB and [math]-ED of chelated forms (E1 and T1) have been extensively investigated. So, it is found that both of the IMHB analysis and [math]-ED concepts emphasize on the E1, as the global minimum. In the second part of this study, a set of simple electron-withdrawing and electron-donating substituents such as CN, F, Cl, CH3 and NH2 have been considered to evaluate their effects on the IMHB of the first singlet excited state of E1 and T1 at TD-DFT/6–311[math]G(d,p) level of theory. According to our analysis, it was found that the IMHB strength of the excited states are much weaker than the ground states. Surprisingly, the IMHB of thiol derivatives is stronger than the enol ones in contrast to the ground state. Furthermore, the substitution effects in the ground and excited states are significantly different. Finally, various linear correlations between the IMHB energies with geometrical, topological and molecular orbital parameters are obtained. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-05-02T09:19:38Z DOI: 10.1142/S0219633617500341

Authors:Yuan You Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. We investigate the effects of vacancies on the electronic and magnetic properties in fully-hydrogenated boron nitride sheet by performing first-principles calculation. Our results reveal that this sheet fosters magnetic materials with finite magnetic moment under certain vacancies. This phenomenon can be explained by the charge redistribution in which the unpaired electrons in bands determine the magnitude of magnetic moment and thus the ground state of the systems. The magnetic moment can be tuned from 0 to 2 by introducing different vacancies. This picture explicitly demonstrates that the type of vacancy plays an important role in determining nonmagnetic or magnetic materials of fully-hydrogenated boron nitride sheet, indicating their functionalities and possible applications in spintronics. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-04-28T08:52:53Z DOI: 10.1142/S021963361750033X

Authors:Xiao-Yu Gao, Wei-Hong Jiao, Zhi-Jun Zuo, Zhi-Hua Gao, Wei Huang 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

Authors:Wen Liu, Fan-Hua Meng, Jian-Hua Zhao, Xiao-Hui Jiang Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The electronic transport properties of hybrid nanoribbons constructed by substituting zigzag graphane nanoribbons (ZGaNRs) into zigzag graphene nanoribbons (ZGNRs) are investigated with the non-equilibrium Green’s function method and the density functional theory. Both symmetric and asymmetric ZGNRs are considered. The electronic transport of symmetric and asymmetric ZGNR-based hybrid nanoribbons behave distinctly differently from each other even in the presence of the same substitution positions of ZGaNRs. Moreover, the electronic transport of these hybrid systems is found to be enhanced or weakened compared with pristine ZGNRs depending on the substitution position and proportion. Our results suggest that such hybridization is an effective approach to modulate the transport properties of ZGNRs. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-04-25T10:13:33Z DOI: 10.1142/S0219633617500328

Authors:Mostafa Lashkarbolooki 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

Authors:Xiaochuan Zhao, Xingying Li, Zile Liu, Wentao Mu, Jing Zhu, Liqing Su, Zhe Li, Wei Huang 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

Authors:Martina Pola, Michal A. Kochman, Alessandra Picchiotti, Valentyn I. Prokhorenko, R. J. Dwayne Miller, Michael Thorwart 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