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:Min Ji, Xinlu Cheng, Weidong Wu Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The density functional theory (DFT) was used to investigate some toxic derivatives of aromatic hydrocarbons adsorption on perfect graphene (pG) and graphene-doped with B/Al/Ga (BG/AlG/GaG). And the parallel and vertical adsorptions were considered for the position relation between the adsorbent and adsorbate. The adsorption energy, adsorption distance, charge transfer and density of states (DOS) were discussed in optimized structures. The greater adsorption energy, shorter adsorption distance and more charge transfer were found in AlG by studying the four kinds of molecules (phenol/m-cresol/PCP/p-NP) adsorption on pG/BG/AlG/GaG. Then, 10 derivatives adsorption on AlG were reported, and the adsorption energy increased in the order of pentachlorophenol [math] 2,4,6-trichlorophenol [math] 2,4-dichlorophenol [math] p-cresol [math] m-cresol [math] phenol [math] o-chlorophenol [math] o-cresol [math] 2,4,6-trintrotoluene [math] para-nitrophenol. The interaction between these derivatives and the substrate was chemisorption for AlG and physisorption for pG. The oxygen atom in nitro group was more closer to the substrate than in hydroxyl group about optimized structures. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-01-25T08:46:31Z DOI: 10.1142/S0219633617500043

Authors:Amirali Abbasi, Jaber Jahanbin Sardroodi Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Over the past years, an interest has arisen in resolving the problems of the increased carbon monoxide and carbon dioxide emissions, leading to the serious air pollution and many detrimental effects. A convenient solution would be a process that could utilize metal oxide nanoparticles such as TiO2 to control the concentration of atmospheric pollutants. The chemisorption of CO and CO2 molecules over the semiconductor titanium dioxide (TiO[math] is such a process. In this way, density functional theory (DFT) calculations were performed to investigate CO and CO2 adsorptions on undoped and N-doped TiO2 anatase nanoparticles. The supercell approach is conducted to construct the considered nanoparticles and the adsorption of COx molecule was simulated by use of these chosen nanoparticles. By including van der Waals (vdW) interactions between COx molecule and TiO2 nanoparticle, we found that both CO and CO2 molecules can bind strongly to the N-doped nanoparticles. The adsorption on the five-fold coordinated titanium site of TiO2 nanoparticles including the bond lengths, bond angles, adsorption energies, density of states (DOSs), Mulliken population analysis and molecular orbitals has been broadly studied in this work. Based on the obtained results, it can be concluded that the adsorption on the N-doped nanoparticle is more energetically favorable than the adsorption on the pristine one, representing the higher tendency of N-doped nanoparticles for COx detention, compared to the undoped ones. Therefore, the results indicate that the N-doped TiO2 would be an ideal COx gas sensor in the environment. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-01-25T08:46:30Z DOI: 10.1142/S0219633617500055

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

Authors:S. Ali Beyramabadi, Tina Khadivjam, Atoosa Gonabadi, Ali Morsali, Azar Gharib, Maryam Khashi, Mahdi Khorsandi-Chenarboo Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The Mepivacaine drug is used as a local anesthetic in dentistry, which could exist as three different tautomers. Herein, geometry, energy behavior as well as tautomerization of these tautomers have been investigated by employing density functional theory (DFT) and considering the solvent effects with the polarizable continuum model (PCM) model. The most stable tautomer of the Mepivacaine has a carbonyl and an –NH amine groups in its structure. The frontier orbitals and the energy gap of the molecule have been computed using the natural bond orbital analysis (NBO). Also, the armchair (5,5) single wall carbon nanotube (SWCNT) was used for investigation of the noncovalent interactions of the Mepivacaine molecule with the pristine SWCNT and the –COOH functionalized SWCNT in several forms. Geometries of the possible forms have been optimized. The most stable form for noncovalent interactions of the drug with each of the pristine and functionalized SWCNTs have been determined. The intermolecular H-bonds have essential role in energy behavior of the noncovalent interactions between the Mepivacaine drug and the investigated SWCNTs. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-01-10T06:29:17Z DOI: 10.1142/S0219633617500080

Authors:Reza Ghiasi, Nasrin Sadeghi Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. This study used mpw1pw91 quantum chemical calculations in gas and solution phases to clarify the interaction between C20 and Cr(CO)5 fragment. It also sought to clarify the effects of solvent polarity on dipole moment, structural parameters, and frontier orbital energies of the complex. Energy decomposition analysis (EDA) was applied to analyze the bonding interaction between the C20 and Cr(CO)5 fragment. Percentage composition in terms of the defined groups of frontier orbitals for the complex was evaluated to characterize the metal–ligand bonds. The Cr–C bonds within the complex were examined using quantum theory of atoms in molecules (QTAIM) analysis. In order to determine the back-bonding effects in these bonds, QTAIM analysis was applied to calculate of the quadrupole polarization of the carbon atom. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2017-01-10T06:24:57Z DOI: 10.1142/S0219633617500079

Authors:Juan Frau, Francisco Muñoz, Daniel Glossman-Mitnik Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The validity of the “Koopmans in DFT” (KID) procedure have been assessed by means of the calculation of several Conceptual DFT reactivity descriptors calculated through a [math]SCF procedure compared with the results of the HOMO and LUMO energies of the neutral system. Three resveratrol derivatives were considered: cis- and trans-piceid and resveratrone-6-O-[math] glucoside. The Minnesota latest family of density functionals have been considered for the calculations in connection with water as a solvent simulated with the SMD parametrization. It is shown that the range-separated hybrids MN12SX and N12SX fulfill the KID procedure with great accuracy. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-12-23T03:59:10Z DOI: 10.1142/S0219633617500067

Authors:Jitrayut Jitonnom, Wijitra Meelua Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Group 4 metallocene-mediated cationic ring-opening polymerizations of a series of lactones and cyclic carbonates, with different ring sizes ([math]–8) have been theoretically studied. Using the “naked cation” approach in combination with density functional theory, the activated chain-end mechanism and the influence of transition metals, solvent and monomer ring size on the polymerizability were explored in detail. The results showed that the cationic metallocene–monomer complex, [catalyst][monomer][math], is formed, generating cationic (carbocation ion) species responsible for polymer chain growth. We found that poor polymerizability of five-membered lactone and six-membered ring carbonate depends not only on the nature of the monomer ring size but also the relative stability of the complex, which was found to correlate well with the ring strain. Subsequently, several propagation steps take place through an SN2 reaction which involves ring opening of an active monomer, via alkyl–oxygen bond cleavage. Based on the computed activation energies of all metallocene systems, the first propagation was found to be the rate-determining step of the overall propagation and the hafnocene was found to be most active with the energy barrier of 17.6[math]kcal/mol, followed by zirconocene (18.6[math]kcal/mol) and titanocene (19.5[math]kcal/mol), respectively. The mechanistic study may be applicable to the cationic ROP of lactides and other related monomers. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-12-22T07:04:57Z DOI: 10.1142/S0219633617500031

Authors:Yuan Zhang, Huanjie Wang, Weiren Xu, Fancui Meng Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Martini coarse-grained force field simulations have been carried out to estimate the free energy profiles of the spontaneous membrane-translocating peptide TP2 and one negative control peptide ONEG with POPC as the model bilayer. The results show that the free energy minimum of TP2 is [math]20[math]kJ/mol lower than that of ONEG. In addition, the minimum of TP2 shifts slightly to the bilayer center compared with ONEG. The translocation barrier height for TP2 and ONEG are 119.0[math]kJ/mol and 155.7[math]kJ/mol, respectively. The lower central energy barrier of TP2 facilitates the transition between two leaflets of POPC. Both translocating peptides induce the formation of funnel-shaped structures at the bilayer center, but TP2 has a more compact structure and brings less perturbation compared with ONEG. Subsequently all atom molecular simulations testify the findings. It is indicated that compared with its negative control ONEG, TP2 binds better with lipid and penetrates deeper into bilayer with less perturbation to the bilayer structure. Our findings may shed light on the design and virtual screening of spontaneous membrane-translocating peptides. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-12-05T09:33:23Z DOI: 10.1142/S021963361750002X

Authors:Ahmed Taki Eddine Ardjani, Sidi Mohamed Mekelleche Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. A theoretical study of the antioxidant behavior of N[math]-(2-hydroxy-3-methoxy-benzylidene)-4-tert-buty-lenzohydrazide (1), N[math]-(5-bromo-2-hydroxy-benzylidene)-4-tert-butyl benzohydrazide (2) and N[math]-(2-hydroxy-3-methoxybenzylidene)-4-methyl-benzene-sulfonohydrazide (3) and their tautomers 1 [math] –3 [math] have been carried out at B3LYP/6-31[math]G(2d,2p). The numerical values of descriptors, namely, bond dissociation enthalpy, proton affinity (PA), electron transfer enthalpy (ETE), ionization potential, and proton dissociation enthalpy (PDE) have been calculated in gas phase and media solution (EtOH, DMSO and water). The obtained results show that the hydrogen atom transfer (HAT) mechanism is more favored thermodynamically in gas phase, whereas the sequential proton loss electron transfer (SPLET) mechanism is more preferred in solvents. Moreover, the couple (3,3[math]) is found to be the most potent antioxidant as expected experimentally. Furthermore, the BDE values of compound 3 [math] is much lower than that of ascorbic acid (AA), indicating that the tautomerization of compounds 1–3 has great influence on the antioxidant activity of these compounds. The antioxidant power of compounds (3.3[math]) was also rationalized by the calculation of the atomic spin density. In addition, the molecular docking study of compounds 1–3 and 1[math] –3[math] on xanthine oxidase (XO) as the protein target revealed important interactions between active compounds and amino acids. Moreover, compound 3 is predicted to be a potential inhibitor with higher activity. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-11-17T02:10:23Z DOI: 10.1142/S0219633617500018

Authors:Marilena Carbone Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The adsorption of [math]-AminoTiophene on Si(100)2[math][math][math]1 was investigated by van der Waals corrected DFT and climbing image nudged-elastic band, in view of potential applications in silicon-based technologies. The overall scenario indicates that dissociative states are more favorable than the molecular ones, the one occurring through N–C bond breakage and Si–N and Si–C bond formation, having the largest adsorption energy (2.71[math]eV). Furthermore, this configuration is also kinetically easily accessible, being connecting to one of the physisorbed states (Phys1) by a nearly barrierless transition. Also the molecular states are relatively easily kinetically accessible, with transition barriers from the corresponding physisorbed states in the 0.05–0.30[math]eV range. At variance with this, the transitions to the dissociative state characterized by N–H bond breakage and Si–N and Si–H bond formation (N–H Diss) either from physisorbed or from molecular states are all significantly higher, i.e. in the 0.63–2.70[math]eV range. Finally, the effects of the coverage on the adsorption energy were evaluated for the N–H Diss configuration and indicating a gain, whose extent depends both on the coverage and on the surface arrangement, i.e. whether cis or trans. The trend is different if the vdW forces are excluded. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-11-17T02:10:21Z DOI: 10.1142/S0219633617400016