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

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

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

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

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

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

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. 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

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