Authors:Atanu Basak, Kuheli Chakrabarty, Animesh Ghosh, Gourab Kanti Das Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Biosynthesis of polyterpenoid and related molecules are largely accomplished via mevalonate pathway. One of the vital steps in this pathway is the inter-conversion of two intermediates isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP) catalyzed by IPP:DMAPP isomerase (IDI). The crystal structure of the enzyme, bound to the substrate analogues and inhibitors, revealed possible mechanism of this inter-conversion; however, none of them could affirm the true nature of the transition state through which the process is taking place. Our DFT study on the pathway of this isomerization reaction at the active site of the enzyme suggests a favorable concerted mechanism that occurs through a single transition structure without generating any carbocation intermediate. In this mechanism, the Cys-67 residue acts as proton donor whereas Glu-116 acts as proton acceptor. The mechanism also reveals the active involvement of other two components present at the active site. A crystallographic water molecule (Wat508) and Glu-87 assist to reprotonate the conjugate base of cysteine residue through a proton shuttle mechanism while forming the transition structure of the isomerization reaction. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-03-15T10:38:48Z DOI: 10.1142/S0219633616500255

Authors:Qing-Hai Hao, Qian Chen, Zhen Zheng, Li-Yan Liu, Tie-Ju Liu, Xiao-Hui Niu, Qing-Gong Song, Hong-Ge Tan Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Molecular dynamics simulations are applied to investigate the cylindrical polyelectrolyte brushes in monovalent and multivalent salt solutions. By varying the salt valence and concentration, the brush thickness, shape factor of grafted chains, and distributions of monomers and ions in the solutions are studied. The simulation results show that the single osmotic pressure effect in the brush leads to changes in conformation in the presence of monovalent salt, while the ion exchange effect induces the collapse of the brushes in the multivalent salt solutions. Furthermore, the snapshots combined with the distributions of the end-monomers and the mean bond angles demonstrate a nonuniform stretching picture of the grafted chains, which is different with the chains tethered on the planar surface. The charge ratios between the ions trapped in the brush and the monomers are also calculated to elucidate the details of ion exchange process. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-03-15T10:38:48Z DOI: 10.1142/S0219633616500267

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. A variety of organic donor–acceptor–donor materials based on thienylbenzothiadiazole (BTD[math]–5) combined with different [math]-conjugated systems are studied by density functional theory (DFT) and time-dependent DFT (TD-DFT) for the ground- and excited-state properties, respectively, using B3LYP and the 6-31G(d, p) basis set. The effect of different electron-donor groups on the structural, electronic and optoelectronic properties is studied. To provide for the bandgap and to guide the synthesis of novel low bandgap materials, we applied quantum chemistry techniques to calculate the difference in the highest occupied molecular orbital (HOMO) and lowest occupied molecular orbital LUMO energies. However, we have studied the effect of the reduction and oxidation properties on the electronic excitation transitions for all compounds. The emission energies have been obtained from TD-DFT calculations performed on the excited-state optimized S1 geometries. The theoretical results suggest that both the introduction of electron-donor groups and the doping process contribute significantly to the electronic and optoelectronic properties of the alternating donor–acceptor–donor conjugated systems studied. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-03-09T08:01:26Z DOI: 10.1142/S0219633616500231

Authors:Kenneth Osondu Monago, Charles Otobrise Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. This work describes a procedure for the numerical calculation of third virial coefficients of simple linear molecules. The method is applied to nitrogen using a site–site model pair-potential and the triple dipole term. Values of volumetric and acoustic second and third virial coefficients of nitrogen are reported over a wide range of temperature and compared with experimental data of several authors. The effect of including the quadrupole–quadrupole energy to the pair potential is investigated and the results suggest that the contributions of the quadrupole moment to second and third virial coefficients are non-negligible at low temperatures. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-03-07T04:24:20Z DOI: 10.1142/S0219633616500243

Authors:Ming-Xia Zhang, Bing-Fei Yan, Wen-Zuo Li, Qing-Zhong Li, Jian-Bo Cheng Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The addition reaction of germylenoid H2GeFMgF with ethylene (C2H4) was first investigated in this work. All of the stationary points were optimized using the M062X method in conjunction with the 6-311[math]G (d, p) basis set and the corresponding energies were calculated using the QCISD method with the 6-311[math]G (d, p) basis set. The calculated results demonstrated that there are two different channels in the addition reaction of H2GeFMgF with C2H4, while only the channel I is feasible once the C2H4 approaches H2GeFMgF in the proper conditions. The solvent effect upon the addition reaction was also investigated using PCM model. The results demonstrated that the tetrahydrofuran (THF) solvent could accelerate the addition reaction. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-03-02T11:55:27Z DOI: 10.1142/S021963361650022X

Authors:M. G. Khrenova, B. L. Grigorenko, J.-P. Zhang, P. Wang, A. V. Nemukhin Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The all-atom model of the photosynthetic core complex composed of the light-harvesting system (LH1) and the reaction center (RC) from a thermophilic purple bacterium Thermochromatium tepidum is constructed. We compare the structural parameters of this complex embedded into the lipid bilayer to those reported for the recently resolved crystal structure of the LH1–RC. We focus on the local structure of the binding sites of the calcium ions regulating stability and optical spectra of the core complex. We show the differences between the computationally derived model and the crystal structure at the extramembrane region of the LH1 polypeptides where the calcium binding sites are located. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-02-22T08:53:32Z DOI: 10.1142/S0219633616500206

Authors:Priyanka, Sanjay Kumar Srivastava, Diksha Katiyar Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The FTIR, UV–Vis and NMR spectra of 4-(2-hydroxy-3-morpholin-4-yl-propoxy)-chromen-2-one (4-HMPC) have been recorded and analyzed. The optimized geometry and harmonic vibrational frequencies of 4-HMPC were obtained by the Hartree–Fock (HF) and density functional theory (DFT) using B3LYP functional with 6-311[math]G basis set. The 1H and [math]C NMR chemical shifts were calculated by the GIAO method in chloroform. The absorption spectra of 4-HMPC were computed in ethanol and water solutions using TD-B3LYP/6-311[math]G(d,p) approach. The correlation of theoretical and experimental results provides a detailed description of the structural and physicochemical properties of the molecule. The results obtained from the studies of HOMO and LUMO were used to calculate the conceptual-DFT-based global reactivity descriptors such as electronic chemical potential, electronegativity, chemical hardness, global softness and electrophilicity index of the compound. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-02-22T08:53:26Z DOI: 10.1142/S0219633616500176

Authors:Mohammad Solimannejad, Behnia Sadat Mirhoseini, Mehdi D. Esrafili Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In the present study, microsolvation and interaction of the CH[math] cation with He[math] clusters are investigated by means of ab initio calculations at MP2/aug-cc-pVTZ and QCISD/aug-cc-pVTZ levels. Stabilization energies of the studied complexes including basis set superposition error (BSSE) and zero point energy (ZPE) corrections are in the range of [math][math]kJ/mol and [math][math]kJ/mol. A good linear correlation is found between the stabilization energy and stretching frequency shift ([math]) in the studied complexes. According to energy decomposition analysis, it is found that polarization effects are the major source of the attraction in these complexes. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-02-22T08:53:09Z DOI: 10.1142/S0219633616500188

Authors:Toufik Salah, Salah Belaidi, Nadjib Melkemi, Ismail Daoud, Salima Boughdiri Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Current knowledge about Chagas disease, the potentially life-threatening illness caused by the protozoan parasite (Trypanosoma cruzi), has led to the development of new drugs and the understanding of their mode of action. The Conceptual Density-Functional Theory was applied to determine the active center sites of trypanocidal compounds, extended by the Molecular Docking analysis to identify the most favorable ligand conformation when bound to the active site of cruzain. Results such as CHELPG charges, Fukui function, MESP, and Molecular Docking analysis are reported and discussed in the present investigation. Whereas, a close agreement with experimental results was found to explain the possibility of studying the receptor-binding mode using these different axes. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-02-18T07:08:15Z DOI: 10.1142/S0219633616500218

Authors:Qingxi Meng, Peiying Su, Fen Wang, Shuhua Zhu Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Density functional theory (DFT) was used to investigate the reaction mechanisms of ruthenium(II)-catalyzed hydroacylation of isoprene with benzaldehyde, and o-methoxyl, m-methoxyl and p-methoxyl benzaldehyde. All intermediates and transition states were entirely optimized at the B3LYP/6-31G(d,p) level (LANL2DZ(f) for Ru). The results demonstrated that the hydroacylation had two different catalytic cycles (path I and II), path II was more favorable than path I. Ru(II)-catalyzed hydroacylation began from the first catalytic cycle, and the nucleophilic reaction was the rate-determining step. The activation barriers of hydrogen migration were the highest in two catalytic cycles, so the hydrogen migration was the rate-determining step. The activation barrier of hydrogen migration could be broken down to two parts: the free energy of exchange ([math]) and the relative free energy of transition state ([math]). The ligand exchange energy ([math]) had more contribution to the activation barrier than the relative free energy of transition state ([math]), so the ligand exchange would control these hydroacylation. Furthermore, our calculations also described the substituent effect, and the results indicated that four aldehydes showed different chemical reactivity, and benzaldehyde and m-methoxyl benzaldehyde were predicted to have the best reactivity in ruthenium hydride-catalyzed hydroacylation. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-02-18T07:08:14Z DOI: 10.1142/S021963361650019X

Authors:Saeedeh Kazemi, Aliasghar Sarabi Daryani, Majid Abdouss, Zahra Shariatinia Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The hydrogen bonding interactions between letrozole (Let) anticancer drug and three copolymers of methacrylic acid-trimethylolpropane trimethacrylate (M1–M3 as molecular imprinted polymers) were studied using density functional theory (DFT) at both B3LYP and B3PW91 levels. The binding energies were corrected for the basis set superposition error (BSSE) and zero-point vibrational energies (ZPVE) so that the most negative [math] were measured for compounds 7 and 8 formed between M1 copolymer and endocyclic N1 and N2 atoms of drug, respectively. Also, among complexes 13–15 in which two copolymers were contributed in the formation of O–H[math]N bonds with the drug, compound 13 (containing two M1 copolymers) showed the highest [math] value. The interactions of all copolymers with drug were exergonic (spontaneous interaction) and exothermic. The QTAIM data supported the covalent character of the C–N, C–H, N–N, C–O, O–H and O–H[math]N bonds, the intermediate nature of C[math]N and C[math]O bonds while the electrostatic character of C–H[math]O, HC[math]HC and CH[math]N interactions. According to the [math], [math] and [math] values, it was suggested that t complexes 7 and 8 (among two particles systems) as well as complex 13 (among three particles systems) can be the most promising drug delivery systems. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-02-16T09:36:12Z DOI: 10.1142/S0219633616500152

Authors:Arvids Stashans, Alexander Chamba Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Density functional theory and generalized gradient approximation using a Hubbard-like term was employed to study tin dioxide material containing an oxygen vacancy as an intrinsic defect and being codoped simultaneously with Fe and Ni atoms. Results on atomic displacements, electronic and magnetic features are obtained and discussed for different configurations taking into consideration relative impurity–impurity as well as impurity–vacancy positions. It appears that Fe atom addition to the system enlarges considerably a local magnetic moment due to the strong magnetic coupling between the Fe [math] and O 2p states for the [math] spin subsystem. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-02-16T09:36:11Z DOI: 10.1142/S0219633616500164

Authors:Chun Guo Zhang, Qun Chao Fan, Zhi Xiang Fan, Hui Dong Li, Jia Fu Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The full vibrational spectra especially those high-lying vibrational energies in the dissociation region of the electronic state [math] of [math], the [math] state of [math], the [math] and [math] states of [math] are obtained using the variational algebraic method (VAM). Then, an analytical potential energy function (APEF) with adjustable parameter [math] for each electronic state is determined by the 4-terms variational algebraic energy consistent method (VAECM(4)) based on the VAM vibrational energies. The full vibrational energies, the vibrational spectroscopic constants, the force constants [math], and the expansion coefficients [math] of the potential are tabulated. Compared with experimental and other calculated results, accurate APEFs, vibrational energy levels and spectroscopic parameters are obtained with the VAECM(4) for the four electronic states of diatomic ions. The results show that the VAECM(4) method also applies to diatomic ion systems. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-02-16T09:36:10Z DOI: 10.1142/S0219633616500140

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The photodissociation of water on rutile (110) is studied from first principles. Using an embedded cluster approach, the motion of one hydrogen atom with a fixed OH group served as a model system. The ground and an electronically excited state are calculated on a CASSCF level of theory, explicitly accounting for the multi-reference character of the wave function during bond breaking. The dynamics is simulated by solving the time-dependent Schrödinger equation for a wave packet moving on the electronic potential energy surface. Photodissociation probabilities of water are calculated for hydrogen, deuterium and tritium, thereby revealing significant isotope effects. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-01-29T07:54:08Z DOI: 10.1142/S0219633616500139

Authors:Xinliang Yu, Xianwei Huang Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The glass transition temperature (Tg) is the most important parameter of an amorphous polymer. A quantitative structure-property relationship (QSPR) was developed for Tgs of 82 polyacrylates, by applying stepwise multiple linear regression (MLR) analysis. Molecular descriptors used to describe polymer structures were, for the first time, calculated from the motion units of polymer backbones, which are chain segments with 20 carbons in length (10 repeating units). After internal validation with leave-one-out (LOO) method, external validation was carried out to test the stability of the MLR model of Tgs. Compared to the models already published in the literature, the MLR model in this paper was accurate and acceptable, although our model was based on bigger data sets. The feasibility of calculating molecular descriptors from the motion units of polymer backbones for developing Tg models of polyacrylates has been demonstrated. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-01-21T07:47:45Z DOI: 10.1142/S0219633616500115

Authors:S. S. Setayandeh, A. Lohrasebi Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Using molecular dynamics simulation method, the effects of external electric fields of 900[math]MHz and 2450 frequencies on [math]-tubulin dimer stabilized by paclitaxel, have been modeled. Due to this purpose, two systems, (A) [math]-tubulin dimer and (B) [math]-tubulin dimer stabilized by paclitaxel, were exposed to an external electric field of 0.01[math]V/nm with frequency values of 900[math]MHz and 2450[math]MHz. It was found that application of these fields, which are in the range of cell phone and microwave frequencies, increased the flexibility of each system. Since paclitaxel, as chemotherapy drug, is used to increase the rigidity of dimer, application of such fields may disturb the effect of paclitaxel on the dimer. Consequently, negative side effects on the chemotherapy process may be observed. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-01-21T07:47:44Z DOI: 10.1142/S0219633616500103

Authors:Jiping Cao, Yali Liu, Aijuan Shi, Yuan Yuan, Mingliang Wang Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The reaction mechanisms between 2, 4-Diisocyanatotolune (2, 4-TDI) and cellulose have been investigated using the density functional theory at the B3LYP/6-31[math]G (d, p) level. The calculations show that the direct addition of 2, 4-TDI and cellulose possesses an unrealistically high barrier of 32–34[math]kcal[math]mol[math]. With a neighboring [math]-d-glucose serving as a proton transporter by forming a flexible six-membered ring transition state, the energy barrier of the reaction is significantly reduced to 16–18 kcal[math]mol[math], which is in a good accordance with the experimental activation energy of 13.9–16.7[math]kcal[math]mol[math]. It is indicated that the reaction between 2, 4-TDI and cellulose is auto-catalyzed with a neighboring [math]- d-glucose acting as a reactive catalyst. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2016-01-14T11:28:14Z DOI: 10.1142/S0219633616500127