Authors:Anbang Li, Kaifu Gao Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Poisson–Boltzmann (PB) model is a widely used implicit solvent approximation in biophysical modeling because of its ability to provide accurate and reliable PB electrostatic salvation free energies ([math] as well as electrostatic binding free energy ([math] estimations. However, a recent study has warned that the 0.5[math]Å grid spacing which is normally adopted can produce unacceptable errors in [math] estimation with the solvent excluded surface (SES) (Harris RC, Boschitsch AH and Fenley MO, Influence of grid spacing in Poisson–Boltzmann equation binding energy estimation, J Chem Theory Comput 19: 3677–3685, 2013). In this work, we investigate the grid dependence of the widely used PB solver DelPhi v6.2 with molecular surface (MS) for estimating both electrostatic solvation free energies and electrostatic binding free energies. Our results indicate that, for the molecular complex and components the absolute errors of [math] are smaller than that of [math], and grid spacing of 0.8[math]Å with DelPhi program ensures the accuracy and reliability of [math]; however, the accuracy of [math] largely relies on the order of magnitude of [math] itself rather than that of [math] or [math]. Our findings suggest that grid spacing of 0.5[math]Å is enough to produce accurate [math] for molecules whose [math] are large, but finer grids are needed when [math] is very small. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-11-17T02:10:16Z DOI: 10.1142/S0219633616500711

Authors:Ana María Mendoza-Wilson, Francisco Javier Carmelo-Luna, Humberto Astiazarán-García, Bertha I. Pacheco-Moreno, Iván Anduro-Corona, María Lucila Rascón-Durán Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The objective of this study was to determine the physicochemical properties of the oligomers of procyanidins (PCs) including PA1, PA2, PB1, PB2, PC1 and a B-type tetramer, taking into account of their conformations related to the interflavan links using the density functional theory (DFT). This information may provide useful insight into the potential effect of physicochemical properties on the absorption of PCs. The results indicate that A-type and B-type PCs in all of their conformations tend to be more stable in water than in octanol, showing a hydrophilic character due to their negative log [math] values, which increase with the degree of polymerization (DP). The studied PCs, including the B-type tetramer, can achieve an appropriate molecular size (i.e. width and length) that can allow them to pass through the pores in the paracellular route in the human small intestine. The factor that could limit the absorption of the PC oligomers with increases in size is the higher number of hydroxyl groups exposed to the outside of the molecule due to their potential to interact with other molecules, which is based on electrostatic potential maps. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-11-03T06:16:29Z DOI: 10.1142/S0219633616500693

Authors:Xin Zhang, Yuan Zhao, Xinli Duan, Hui N. Zhang, Zexing Cao, Yirong Mo Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The deamination reaction of 8-oxoguanine (8-oxoG) catalyzed by 8-oxoguanine deaminase (8-oxoGD) plays a critically important role in the DNA repair activity for oxidative damage. In order to elucidate the complete enzymatic catalysis mechanism at the stages of 8-oxoguanine binding, departure of 2-hydroxy-1H-purine-6,8(7H,9H)-dione from the active site, and formation of 8-oxoxanthine, extensive combined QM(PM3)/MM molecular dynamics simulations have been performed. Computations show that the rate-limiting step corresponds to the nucleophilic attack from zinc-coordinate hydroxide group to free 8-oxoguanine. Through conformational analyses, we demonstrate that Trp115, Trp123 and Leu119 connect to O8@8-oxoguanine with hydrogen bonds, and we suggest that mutations of tryptophan (115 and 123) to histidine or phenylalanine and mutation of leucine (119) to alanine could potentially lead to a mutant with enhanced activity. On this ground, a proton transfer mechanism for the formation of 8-oxoxanthine was further discussed. Both Glu218 and water molecule could be used as proton shuttles, and water molecule plays a major role in proton transfer in substrate. On the other hand, comparative simulations on the deamination of guanine and isocytosine reveal that, for the helping of hydrogen bonds between O8@8-oxoguanine and enzyme, O8@8-oxoguanine is the fastest to be deaminated among the three substrates which are also supported by the experimental kinetic constants. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-10-25T03:37:09Z DOI: 10.1142/S0219633616500668

Authors:Dating Wu, Hui Zhang Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. We present results of a detailed numerical investigation of the phase separation kinetic process of the macromolecular microsphere composite (MMC) hydrogel. Based on the Flory-Huggins-de Gennes-like reticular free energy, we use the time-dependent Ginzburg–Landau (TDGL) mesoscopic model (called MMC-TDGL model) to simulate the phase separation process. Domain growth is investigated through the pair correlation function. Then we obtain the time-dependent characteristic domain size, which reflects the growth kinetics of the MMC hydrogel. The results indicate that the growth law based on the MMC-TDGL equation is consistent with the modified Lifshitz–Slyozov theory. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-10-14T09:52:05Z DOI: 10.1142/S0219633616500644

Authors:Narges Khatoon Attaran Toosy, Heidar Raissi, Maryam Zaboli Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The density functional theory (DFT) method with 6-311[math]G[math] basis set has been used to calculate the intramolecular hydrogen bond, molecular structure, vibrational frequencies, nuclear quadrupole resonance (NQR) parameters, 1HNMR, and resonance parameters of 2-Amino-2, 4, 6-cycloheptatrien-1-one (2-amino tropone) and its 18 derivatives in 5 positions. The natural bonding orbital (NBO) and quantum theory of atoms in molecules (QTAIM) analyses have been studied. The strongest and weakest hydrogen bonds exist for NO2 substituent in R3 position and OH in R7 position, respectively. In general, the substituted systems in position 3 indicate the stronger hydrogen bond in comparison with the parent molecule (R[math]H), while, it is comparatively weaker for position 5. The energy of the N-H[math]O interaction is found to be medium in strength ([math][math]kJ mol[math] to [math][math]kJ mol[math]). The low [math], positive [math] values and [math] show that the nature of O [math] H bonding is electrostatic. Also, our theoretical results show that the hydrogen bond strength in solution phase and the first singlet excited state is weaker in comparison with the gas phase ground state. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-10-14T09:52:05Z DOI: 10.1142/S0219633616500632

Authors:Rachida M’chaar, Mouloud El Moudane, Abdelaziz Sabbar, Ahmed Ghanimi Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In this paper, the surface tension, molar volume and density of liquid Ag–Cu–Sn alloys have been calculated using Kohler, Muggianu, Toop, and Hillert models. In addition, the surface tension and viscosity of the Ag–Cu–Sn ternary alloys at different temperatures have been predicted on the basis of Guggenheim and Seetharaman–Sichen equations, respectively. The results show that density and viscosity decrease with increasing tin and increasing temperature for the all studied models. While the surface tension shows a different tendency, especially for the Kohler and Muggianu symmetric models. On the other hand, the molar volume increases with increase of temperature and tin compositions. The calculated values of surface tension and density of Ag–Cu–Sn alloys are compared with the available experimental values and a good agreement was observed. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-09-23T09:03:41Z DOI: 10.1142/S0219633616500620

Authors:Jingjing Xia, Ping Wu Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Alkyl methyl di(tri)thiocarbonates can be thermally decomposed into alkenes. In this paper, theoretical calculations were used to calculate the thermal decomposition procedures. Six compounds, including ethyl, isopropyl and [math] dithiocarbonate and trithiocarbonate, were examined. For each decomposition, nine possible paths were considered, including the paths leading to the desired alkene products, as well as rearrangement and elimination reactions. This calculation was performed with the MP2/6-31G(d) method. Wiberg bond indices were also calculated to further reveal the reaction progress. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-09-23T09:03:41Z DOI: 10.1142/S0219633616500619

Authors:Ahmad Irfan, Abdullah G. Al-Sehemi, Aijaz Rasool Chaudhry, Shabbir Muhammad Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The isoxazole derivatives gained significant attention in our daily life from better biological activity to the semiconducting materials. This study deals in depth investigation of two isoxazole derivatives, i.e. 2-[(E)-(3,4-Dimethylisoxazol-5-yl)iminomethyl]phenol (1) and 1-[(E)-(3,4-Dimethylisoxazol-5-yl)iminomethyl]-2-naphthol (2) with respect to the geometric, charge transport, optoelectronic and nonlinear optical properties by density functional theory (DFT) and time-dependent DFT. The comprehensible intra-molecular charge transfer (ICT) was conceived from HOMOs to LUMOs. Strength of the electron donor groups was investigated on the absorption wavelengths, emission wavelengths, ionization potentials (IPs), electron affinities (EAs), total/partial densities of states and structure-property relationship. The smaller hole reorganization energies and superior transfer integrals of isoxazole derivatives (1 and 2) than the electron ones are leading to higher hole intrinsic mobility values as compared to the electron mobility exhibit that these systems would be good hole transport contenders. The first hyperpolarizability values are about 19 and 21 times larger than that of urea suggesting that 1 and 2 can also be considered as potential contestants for NLO applications as well. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-09-16T06:04:23Z DOI: 10.1142/S0219633616500607

Authors:Erik J. Alred, Malachi Phillips, Manikanthan Bhavaraju, Ulrich H. E. Hansmann Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Alzheimer’s Disease is characterized by the formation of amyloid beta (A[math] fibril plaques in the brain. These fibrils can be probed by solid state NMR (ssNMR), which leads to an ensemble of configurations that are compatible with the NMR signals. Typically, only the lowest energy conformer is considered in computer simulations that probe the stability of fibrils and their binding with drug candidates. This restriction could produce data that are not physiologically relevant if the NMR entries differ significantly in stability or binding affinities. In order to study this effect, we have investigated the variance in stability between members of NMR ensembles. Our test cases are a patient-derived A[math]-fibril model and two in vitro A[math]-fibril models from a previous study we performed on comparative stability. The latter two models allow us also to compare different staggering patterns. We observe significant variations in molecular flexibility, compactness and secondary structure, suggesting that the full NMR ensemble must be considered for a physiologically relevant description of A[math] fibrils. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-09-14T06:20:23Z DOI: 10.1142/S0219633616500590

Authors:Benfei Ye, Longhua Yang, Jianqi Sun, Chao Luo, Hongming Wang Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. DFT calculations have been carried out to study the detailed mechanisms of the carboxylative cyclization reaction between propargylic alcohols and CO2 catalyzed by N-Heterocyclic Olefins (NHO), as well as the molecular orbital theory. Results indicated that this type of reaction prefers a three steps mechanism controlled by free NHO rather than to be catalyzed by the NHO–CO2 adducts. For the first step, CO2 promotes the hydrogen transfer from alkynol to NHO to form the carboxylate, in which propargylic alcohols was deprotonated by the free NHO acted as the catalyst precursor to form the alkynol anion; meanwhile, alkynol anion captures carbon dioxide to form the carboxylate. We found this CO2 promoting Hydrogen abstraction mechanism would decrease the reaction energy barrier and increase releasing heat of this reaction. Secondly, a five-membered-ring intermediate is easily formed to generate carboxylate via an intramolecular ring-closing reaction. Finally, the production generated through a protonating process. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-09-09T07:13:51Z DOI: 10.1142/S0219633616500589

Authors:Xiao-Yan Hou, Ablikim Kerim Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The local aromaticity of fullerene C[math] ([math] was studied using the bond resonance energy (BRE) method. The global aromaticity of all 349 possible isomers of C[math]H2 based on [math] symmetry was investigated using the topological resonance energy (TRE) method. The TRE results show that most of the C[math]H2 isomers have greater stability than C[math] ([math]. Based on the BRE results, the preferred addition sites of hydrogen atoms are discussed. The relationship between the addition sites and BREs is analyzed and discussed. We found that the addition sites of hydrogen atoms are strongly dependent on the magnitude of the parent cage BRE values. The most stable isomers of C[math]H2 are often produced by diminishing of the [math]-bonds from those sites in the parent cage at which are located the two carbon atoms with the lowest BRE values. Based on this rule, the preferred addition patterns for non-IPR fullerene cages can be easily predicted. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-09-09T07:13:50Z DOI: 10.1142/S0219633616500577

Authors:Keyumars Hassanzadeh, Keivan Akhtari, Sara Sheikh Esmaeili, Azin Vaziri, Hedyeh Zamani, Mobina Maghsoodi, Shamim Noori, Atefeh Moradi, Pardis Hamidi Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The encapsulation of Altretamine (ALT) and Thiotepa (THI) as neurotoxic anticancer drugs in Cucurbit[[math]]uril (CB[[math]]) family of macrocycles ([math],8) have been investigated and their potential in drug delivery, ability to provide physical and chemical stability, improving water solubility and decreasing the side effects have been studied using density functional theory (DFT) approach with B3LYP and the dispersion corrected functional WB97XD methods by employing the 3-21G* basis set. All the calculations were evaluated for gas phase and water as a pharmaceutical and biological solvent according to the polarizable continuum model (PCM). The non-covalent inter-molecular interactions between the host and guest parts were visualized using reduced density gradient analysis. The molecular characteristics for drugs, CB[[math]] and their complexes calculated and the global and local descriptors were employed to study the chemical stability of the host–guest complexes. The results show that the encapsulation of THI and ALT for both CB[7] and CB[8] energetically favorable and this can decrease the central nervous system (CNS) neurotoxicity, and increase the stability of THI in electrophilic and nucleophilic. Beside the CNS neurotoxicity reduction and increasing the stability in electrophilic and nucleophilic attacks, the solubility in water for ALT was improved. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-09-02T03:12:09Z DOI: 10.1142/S0219633616500565

Authors:Isaac J. Sugden, David F. Plant, Robert G. Bell Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The effect of radiative impacts on the structure of boron carbide has been studied by both classical and ab initio simulations. As a part of this study, a new forcefield was developed for use in studying boron carbide materials. Impact scenarios in boron carbide were simulated in order to investigate the exceptional resistance of this material, and other icosahedral boron solids, to high-energy impact events. It was observed that interstitial defects created by radiative impacts are likely to be quenched locally, utilizing the high substitutional disorder of chains and cages in the boron carbide structure, rather than via impacted atoms recombining with their vacated lattice site. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-08-29T08:17:58Z DOI: 10.1142/S0219633616500553