Authors:Muhammad Haneef, Bakhtawar, Suneela Arif, Jehan Akbar, Nasrullah Shah Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The detached electron flux and photodetachment cross section are derived using the theoretical imaging method and quantum approach for system comprising of hydrogen negative ion (H[math]) placed near a surface having spherical dent. The dent is modeled like a spherical concave surface. It is observed that the spherical dent generates additional oscillatory and smooth structure in the detached electron flux and photodetachment cross section, respectively. The radius of curvature, inter-ion surface distance and the dent factor strongly manipulate the results. When the inter-ion surface distance is equal to the focal length of the concave surface, the detached electron flux and photodetachment cross section are not well behaved. The photodetachment cross section is also not well behaved for the inter-ion surface distance equal to the radius of curvature. The focus and center of curvature of the concave surface act as a spherical singularity. This study gives new understanding on the photodetachment of negative ions in the vicinity of concave surfaces. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2015-12-01T03:42:48Z DOI: 10.1142/S0219633615500637

Authors:Ghader M. Sukker, Nuha Wazzan, Ashour Ahmed, Rifaat Hilal Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Carbidopa (CD) is a drug used in combination with L-dopa (LD) in treatment of Parkinson’s disease (PD). CD is an inhibitor for enzyme decarboxylase, yet its mode of action is not entirely known although it is believed to involve enzyme shape recognition. The present work attempts to investigate the conformational preferences of CD. Tight geometry optimization at the density functional theory (DFT)/B3LYP/6-311[math]G** level of theory has been carried out. The shallow nature of the potential energy surface (PES) and the presence of several local minima within a small energy range necessitate the launching of DFT-based molecular dynamics (MD) simulations. Two MD experiments were submitted for 35,000 points each. The complete trajectory in time domain of 10.5 ps is analyzed and discussed. The global minimum energy structure of CD is localized and identified by subsequent frequency calculations. The quantum theory of atom in molecules (QTAIMs) is used to extract and compare the quantum chemical topology features of the electron density distribution in CD and LD. Bonding characteristics are analyzed and discussed within the natural bond orbital (NBO) framework. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2015-12-01T03:42:47Z DOI: 10.1142/S0219633616500024

Authors:Kenji Mishima, Takumi Kinoshita, Michitoshi Hayashi, Ryota Jono, Hiroshi Segawa, Koichi Yamashita Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. In the present paper, we theoretically reinvestigate structural properties, and photo-physical and chemical characteristics and electronic absorption spectra of three kinds of ruthenium polypyridyl complexes [Ru(tpy)[math], [Ru(tpy)(bpy)(H2O)][math], and [Ru(tpy)(bpy)(Cl)][math] complexes in acetone (tpy[math]2,2[math],2[math]-terpyridine and bpy[math]2,2[math]-bipyridine). In particular, the experimental absorption spectra of these complexes are revisited theoretically in detail and are simulated using the first-order perturbation theory based on time-dependent density functional theory (TD-DFT) where the first-order perturbation term is the spin–orbit (SO) coupling Hamiltonian, and quantum chemistry calculations based on various functionals and basis sets. It was found that in general the theory including SO coupling can reproduce experimental data better than the simple quantum chemistry calculation neglecting SO coupling, which indicates that SO coupling is very important to understand the optical features of these complexes and that therefore the mixing between singlet and triplet states is strong due to the large SO coupling constant of Ru atom involved in these complexes. This suggests the fact that the disagreement between the experimental and calculated absorption spectra was found in TDB3LYP/(SDD with triple-[math] for Ru and 6-31G* for others) [Jakubikova EJ et al., Inorg Chem 48:10720, 2009] can be tracked down to the neglect of SO couplings. It was also found that the choice of the DFT functionals and basis sets is crucial for a good theoretical reproduction of experimental data. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2015-12-01T03:42:42Z DOI: 10.1142/S0219633616500012

Authors:Erbin He, Weitong Ren, Jun Wang, Wenfei Li, Wei Wang Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Many proteins contain cofactors, such as heme, ATP and metal ions. Binding of cofactors is not only essential for their biological functions, but also can reshape the intrinsic energy landscape of protein molecules and modulate the folding and stability. However, the molecular mechanism of cofactor coupled protein folding is not well understood. In this work, we study the cofactor coupled folding of myoglobin, which is a typical cofactor (heme) containing protein, by performing molecular dynamics simulations with a structure-based protein model developed based on the energy landscape theory. We showed that the heme binding increases the stability of the myoglobin. More importantly, the heme binding tends to increase the protein folding cooperativity, and switch the folding process from a “three-state” mechanism to a “two-state” mechanism. We also showed that the folding pathways of the myoglobin can be modulated by the heme binding. By performing comparative simulations, we revealed that the above effects of heme binding are resulted from the heme induced folding of F-helix, which is otherwise unstructured at apo state, and the heme mediated contacting interactions around the heme binding site. The simulation results are consistent with available experimental data, and provide insights into the molecular mechanism of the effects of cofactor binding on the protein folding and stability. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2015-11-02T03:25:42Z DOI: 10.1142/S0219633615500595

Authors:Mohammed Shkir, V. K. Jain, S. AlFaify, M. M. Abutalib, I. S. Yahiya, M. Ajmal Khan Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Dichlorobis(L-proline) zinc(II) (DCBLPZ) is an excellent nonlinear optical (NLO) material because of its ability to exhibit high second harmonic generation and having significant optical transparency. In this work, electro-optical properties of the titled material has been thoroughly investigated by Hartree–Fock (HF) and Density functional theory using different basis sets in C1 symmetry. The calculated geometrical parametres and vibrational frequencies were found to be in good agreement with reported experimental results. Highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) studies were carried out to understand the intramolecular charge transfer within the molecule. Total dipole moment ([math]), polarizability ([math]), anisotropy of polarizability ([math] and first hyperpolarizability ([math]) values were calculated. The static first hyperpolarizability value is found to be six times higher than urea. Ultra violet-visible spectrum of DCBLPZ molecule was calculated by time-dependent density functional theory (TD-DFT) in gas phase using different functionals. The calculated value of absorption wavelength was found at 234[math]nm using TD-B3LYP/[math]* level of theory and was in good experimental value (230[math]nm) than other applied methods. Our results give us flexibilty to predict about possible intramolecular charge transfer from both the chlorine atoms toward both the proline units through zinc atom in the studied metallic complex. The other important parametres such as frontier molecular orbital’s (FMO), global reactivity descriptors and molecular electrostatic potential have also been calculated and discussed. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2015-11-02T03:25:42Z DOI: 10.1142/S0219633615500613

Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Twisted conformations of ethylene molecule have diradical character and the second hyperpolarizability of these conformations is best described by the multiconfigurational self consistence field theory (MCSCF) wave function. Present calculation indicates that unrestricted density functional theory (UDFT) predicts second hyperpolarizability which is qualitatively correct for the intermediate diradical region. However, for the two extremities, i.e. rear diradical region and near diradical region, the second hyperpolarizability obtained by UDFT methods differ significantly from the MRCISD result. The BHHLYP and LC-BLYP ([math]) results of [math] are found to be in good agreement with the MRCISD result. Using the spin-projected UDFT methods almost similar results are obtained. The reasonably fair agreement between the calculated results of second hyperpolarizability obtained at the MRCISD and CASSCF(4,4) levels demonstrates that static electron correlation is the dominant feature of twisted ethylene. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2015-10-27T07:23:47Z DOI: 10.1142/S0219633615500601

Authors:Wei Gao, Bin-Bin Wang, Yong-Chang Han, Shu-Lin Cong Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. This work explores the vibrational state-selective photoassociation (PA) in the ground state of the HX ([math], Cl, I) molecule by solving the time-dependent Schrödinger equation. For the three systems, the vibrational level of [math] is set to be the target state and the PA probability of the target state is calculated and compared by considering different initial collision momentums. It is found that the PA probabilities are in accordance with Franck–Condon overlap integral for the HI and HCl systems, but it is not the case for the HF system. Moreover, for the HF system, it is shown that the PA probability of the target state is largest and the multiphoton transition is more likely to occur. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2015-10-27T07:23:47Z DOI: 10.1142/S0219633615500625

Authors:Faranak Dastineh, Sadegh Salehzadeh, Mehdi Bayat, Yazdan Maghsoud Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. A theoretical study on the selectivity of a series of [M(12C4)][math] (M = Li[math], Na[math], K[math], 12C4 = 12-crown-4) complexes for F[math], Cl[math] and Br[math] anions and a number of neutral molecules (CH3CN, CH3OH, NH3, H2O, py, and 12C4) is reported. At first, it was shown that in the gas phase among all studied halide anions and neutral molecules, halides have much more bonding interaction with all [M(12C4)][math] cations. Calculated interaction energies of above anions and [M(12C4)][math] cations decrease from F[math] to Br[math]. Also the interaction energy of halide anions with [M(12C4)][math] complexes, decreases from [Li(12C4)][math] to [K(12C4)][math]. The electron decomposition analysis showed that the bond between [M(12C4)][math] complexes and both the neutral and anion guests is mainly electrostatic in nature. Then the selectivity of [M(12C4)][math] complexes for studied anions and neutral molecules are compared in methanol, acetone, acetonitrile, and nitromethane solutions. It was shown that both the desolvation process of reactants and the strength of host–guest interactions have significant effect on the selectivities. Thus the selectivity of [Li(12C4)][math] cation for NH3 and H2O neutral molecules in solution, in contrast to the gas phase, is higher than that for bromide anion. The results of calculations showed that all [M(12C4)][math] complexes, specially [Li(12C4)][math], have high selectivity for F[math] over other halide anions and neutral molecules. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2015-10-12T02:12:10Z DOI: 10.1142/S0219633615500571

Authors:Wei Liu, Huanjie Wang, Fancui Meng Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Aspalathin and nothofagin are the major dihydrochalcones found in rooibos (Aspalathus linearis), which display anti-diabetic activities, but the mechanism is still unclear. In this paper, hSGLT2 (human sodium dependent glucose co-transporter 2), a target for diabetes mellitus, was built using homology modeling method. Molecular docking and dynamics simulations were carried out on aspalathin, nothofagin and SGLT2 complexes with dapagliflozin as positive control. The results show that both the binding energies and binding modes of aspalathin and nothofagin are similar to dapagliflozin, indicating that either component of rooibos may exhibit anti-diabetic effects through inhibiting SGLT2 receptor. However, the predicted permeability value of aspalathin and nothofagin is low, which may cause poor absorption, resulting in weak SGLT2 inhibition. Calculation results elucidate the possible inhibiting mechanism of aspalathin and nothofagin against SGLT2, and therefore enhance our understanding of anti-diabetic activities of rooibos. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2015-10-07T02:55:05Z DOI: 10.1142/S021963361550056X

Authors:Yingbin Ge, Douglas DePrekel, Kui-Ting Lam, Kevin Ngo, Phu Vo Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Titanium dioxide (TiO2) nanoparticles are widely used in contaminant remediation, photocatalysis and solar cell manufacturing. The low-cost production of TiO2 nanoparticles via the combustion of titanium tetrachloride (TiCl4) in oxygen is thus an important industrial process. To accurately model the flame synthesis of TiO2 nanoparticles, reliable thermodynamic data of Ti–O–Cl species are indispensable but often unavailable. We therefore carried out benchmark calculations, using the left-eigenstate completely renormalized singles, doubles and perturbative triples (CR-CC(2,3), aka CR-CCL) method with the cc-pVTZ basis set, to obtain the equilibrium structures and vibrational frequencies of selected Ti–O–Cl species; we then performed single-point CCSD(T)/aug-cc-pVLZ ([math]–5) calculations to extrapolate the CCSD(T)/CBS energies. After analyzing the experimental and calculated enthalpy of selected Ti–O–Cl species, the standard enthalpy of formation of the TiOCl2 molecule is determined to be [math]600.5[math]kJ/mol at 298[math]K. The standard enthalpy of all other Ti–O–Cl species are determined accordingly. Finally, we assessed the accuracy of 42 popular density functionals for the Ti–O–Cl species. Among these assessed functionals, the B98 functional, tightly followed by B97-1 and B3LYP, exhibits the best overall performance in the prediction of the thermochemistry of the Ti–O–Cl species. Citation: Journal of Theoretical and Computational Chemistry PubDate: 2015-10-07T02:55:04Z DOI: 10.1142/S0219633615500558