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 Journal of Theoretical and Computational Chemistry   [SJR: 0.364]   [H-I: 17]   [10 followers]  Follow         Hybrid journal (It can contain Open Access articles)    ISSN (Print) 0219-6336 - ISSN (Online) 1793-6888    Published by World Scientific  [120 journals]
• Theoretical exploration to the cation effect on the second-order nonlinear
optical properties of Strandberg-type polyoxometalates
• Authors: Ting Zhang, Wei Guan, Shizheng Wen, Tengying Ma, Likai Yan, Zhongmin Su
Abstract: Journal of Theoretical and Computational Chemistry, Volume 14, Issue 01, February 2015. The combination of cations with octahedral coordinated d0 transition metal ions has been proved to be an effective way for designing new polar materials. So we investigate the second-order nonlinear optical (NLO) properties of Strandberg-type polyoxometalates (POMs) with alkali metal cations M6Mo5X2O23 (M = K+, Rb+, Cs+; X = P, As) and M4Mo5X2O21 (M = K+, Rb+, Cs+; X = S, Se, Te) by density functional theory (DFT) method. The calculated results show that this kind of Strandberg-type POMs possesses remarkably large molecular second-order NLO polarizability, especially for the Cs6Mo5P2O23 (system Ic), which has a computed β0 value of 12526 a.u. and might be an excellent second-order NLO material. Moreover, the cations have important impact on the second-order NLO polarizabilities. Therefore, a careful choice of appropriate cations may allow the control of the second-order NLO response on these Strandberg-type POMs, which may provide a new route to design efficient NLO materials. • This is the first theoretical report on an anion topology in Strandberg-type POMs. • The work reveals the general rules to design the large optical nonlinearity system. • A careful choice of appropriate cations may allow the control of the NLO response.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Mon, 09 Mar 2015 09:23:13 GMT
DOI: 10.1142/S0219633615500078

• Electronic structures of hexane isomers studied using quantum mechanics
and graph theory
• Authors: Subhojyoti Chatterjee, Feng Wang
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Electronic and topological properties of hexane (C6H14) and its five geometric isomers are systematically studied quantum mechanically using several techniques such as positron–electron annihilation gamma-ray spectra, C1s binding energy spectra and carbon nuclear magnetic resonance (NMR) spectra, as well as information derived from graph theory. It is revealed that the Doppler-shift in the gamma-ray spectra of the hexane isomers is in the vicinity of the n-hexane molecule with small structural dependency, in agreement with the fact that the measured Doppler-shifts of other linear alkanes are in the vicinity of hexane. The present study further reveals the electronic structures of hexane isomers, which are deeply rooted into the carbon core electrons, more than mere properties in the valence space. The calculations show that the highest occupied molecular orbitals (HOMOs) of the isomers exhibit less important roles in gamma-ray spectra; whereas the electron–positron annihilation is dominated by the electrons of the lowest occupied valence orbitals (LOVOs) and other valence electrons underneath the HOMO electrons, in agreement with previous findings. The present study further reveals that the C1s binding energies of the isomers exhibit association with the nodes of the isomers using graph theory. That is, more branched carbons likely engage with larger chemical shift, which is indicated by the largest eigenvalues (LEVs) of the adjacency matrix (AM) from graph theory. The chemical shift of the carbon NMR spectra is revealed by the LEVs of the Laplacian matrix (LM) obtained from chemical graph theory.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Fri, 06 Mar 2015 01:41:11 GMT
DOI: 10.1142/S0219633615500145

• Effect of electronic excitation to intermolecular proton transfer in bulk
nitromethane: Tuned parameter SCC-DFTB and first principles study
• Authors: Feng Guo, Hong Zhang, Chao-Yang Zhang, Xin-Lu Cheng, Hai-Quan Hu
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. To understand the reaction mechanism involving hydrogen transfers through hydrogen-bond bridge, we carried out both Self-Consistent Charge Density Functional Tight-Binding (SCC-DFTB) calculations of bulk nitromethane and Density Functional Theory (DFT) calculations of singlet ground state/triplet excited state molecular nitromethane using B3LYP functional. Firstly, we tuned the repulsive parameters of the SCC-DFTB method for nitromethane with dataset calculated from DFT at B3LYP/6-311g level. The molecular dynamics simulations are carried out with tuned parameters to get the dynamical properties of the bulk nitromethane, and the static calculations are intended to give energy profile of the reaction process. These calculations indicate the excitation of nitromethane molecule making the proton transfer reactions possible, and lowering the reaction barrier.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Wed, 04 Mar 2015 07:09:41 GMT
DOI: 10.1142/S0219633615500133

• Water molecules response to an external GHz electric field in KcsA
potassium channel: A molecular modeling approach
• Authors: M. Sajadi, A. Lohrasebi, S. S. Setayandeh, H. Rafii-Tabar
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. KcsA potassium channel is a membrane protein that allows the passage of potassium ions and water molecules across the cellular membrane. Using molecular dynamics (MD) simulation method, the effect of an applied GHz oscillating electric field of strength 0.004 V/nm on the dynamics of K+ and water molecules in a KcsA channel was modeled. It was found that the application of GHz range electric field caused a change in the potential energy profile of the water molecules in the filter sites, causing an increase in the delay time of the water molecules in these sites. Therefore, exposing the channel to the GHz fields can perturb the dynamics of the water molecules in the filter, and consequently, the channel operation may be disturbed. Furthermore, the results show that the applied field has no major effects on the dipole orientation of water molecules in the channel.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Thu, 26 Feb 2015 02:44:02 GMT
DOI: 10.1142/S0219633615500121

• Adsorption of 2-vinyl thiophene on Si(100)2 × 1: A van Der Waals
corrected DFT study
• Authors: Marilena Carbone
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Oligo- and polythiophenes on surfaces play a fundamental role in building molecular circuits and organic-based electronics and may be assembled via interaction of the monomer units with the surface. In this framework, the nature of interaction of 2-vinyl thiophene (2VTP), a conjugated heteroaromatic monomer unit, with the Si(100) surface was studied by means of density functional theory (DFT). In particular, structural optimizations were performed comparing the effects of the inclusion of van der Waals (VdW) forces. It came out that the adsorption through the double bond is energetically favored, if VdW forces are included, whereas the adsorption through both aromatic ring and double bond simultaneously is more stable, if they are excluded. Physisorbed states were singled out and the barriers between two of them and the corresponding chemisorbed states were calculated along with the imaginary frequencies of the transition states. Also the transition energies have different values if the VdW forces are included.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Wed, 11 Feb 2015 07:12:41 GMT
DOI: 10.1142/S021963361550011X

• Theoretical investigation of an atmospherically important reaction between
methyl methacrylate and Cl atom: A mechanistic and kinetic approach
• Authors: Partha Biswas
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. A theoretical investigation of the mechanism, kinetics and probable product analysis of the Cl-initiated oxidation reaction of methyl methacrylate (MMA) is presented in this paper. The major degradation pathway of MMA is the Cl-addition to the terminal carbon of the olefinic bond. Beside this, energetic and mechanism of other possible reaction pathways are discussed in detail. In addition, the mechanism for the secondary reactions in presence of O2 and NO has also been presented. Cl-addition to the double bond takes place via formation of the pre-reactive complex as these reaction channel passes through negative activation barrier. Energetics and thermochemical analysis have been studied at the MP2=Full/6-311++g(d,p) level of theory. The rate constant of the Cl-addition reaction has been calculated using conventional transition state theory (CTST) at 1 atm pressure and 250–350 K temperature range.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Fri, 06 Feb 2015 01:40:33 GMT
DOI: 10.1142/S0219633615500108

• Computational comparison of reactions of CS2 with CHX•- (X = F, Cl,
and Br): Do F, Cl, and Br substitutions effect differently?
• Authors: Junxi Liang, Qiong Su, Shijie Zheng, Jing Yu, Zhiyuan Geng
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Calculations based on density functional theory (DFT) have been carried out for the gas-phase ion-molecule reactions of CS2 with CHX•- (X = F, Cl, and Br) to investigate the effect of the halogen-substituent on the reaction mechanism. The doublet potential energy surfaces (PESs), involving two striking reaction patterns named by the middle-C attack and the end-S attack in terms of anion attack on the C and S atoms of CS2, have been explored and characterized in detail. Compared with the results of the end-S attack, reaction with the middle-C attack pattern displays more efficiency on PES. For a given reaction pattern, the reactions of CHCl•- and CHBr•- occur with similar efficiencies and reactivity trends. The CHF•- anion displays remarkably different reactivity, which is traced to its lower electron binding energy and the effect of the electronegative fluorine substituent. This is in good agreement with the experimental observation. According to the property of the product branching ratios in experiment, dynamical effect is used to evaluate the reason that the end-S attack with less energetically favorable obtained in our theoretical studies is comparable to the middle-C attack.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Wed, 04 Feb 2015 07:15:17 GMT
DOI: 10.1142/S0219633615500091

• The mechanisms of α-H and proton transfers of glycine induced by Mg2+
• Authors: Qing Zhang, Xiang-Jun Meng
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. A MP2/6-31++G(d,p)//B3LYP/6-31++G(d,p) method was used to investigate the mechanisms of α-H and proton transfers of glycine induced by Mg2+. Eight complexes were obtained, six of which were neutral and the other two were zwitterionic. Among them, the zwitterion with a binding energy of 159.4 kcal/mol was the most stable structure. Conformation transformations of the complexes caused by the rotation of single bond and the transfers of α-H and proton were completed via seven transition states. The inductive effect of Mg2+ made the electron cloud of glycine deviate to Mg2+, which activated the covalent bond involving the transferred proton. The neutral complex can be turned into the zwitterionic one by the transfers of both carboxyl hydrogen and α-H, and the energy barrier of each reaction was less than 9.2 kcal/mol. After the transfer of α-H, a delocalized π bond was formed in glycine skeleton and the α-C atom took 0.19 positive charges. So the chemical activity of the glycine enhanced, and glycine was readily available for addition and nucleophilic substitution reactions. The path from the most stable glycine conformer G1 to the zwitterionic conformation I is G1 → G1–G3 → G3 → G3–G4 → G4 → G2–G4 → G2 → VI → I–VI → I, and the highest energy barrier of this path is 9.2 kcal/mol.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Fri, 30 Jan 2015 09:16:02 GMT
DOI: 10.1142/S021963361550008X

• Computational characterization of organometallic ligands coordinating
metal: Case of azopyridine ligands
• Authors: Sopi Thomas Affi, Kafoumba Bamba, Nahossé Ziao
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Azpy (2-phenylazopyridine), Nazpy (2-pyridylazonaphtol), Mazpy (2,6-diméthyl-2-phenylazopyridine) and Dazpy (2-phenylazo-4,6-dimethylpyridine) are four pyridylazo ligands that are characterized by density functional theory (DFT) theoretical investigation either in gas or in condensed phases. As they display at least three heteroatoms donors of electrons, hydrogen bond basicity has been experimented via energy and geometrical descriptors to determine which of the donors will link to metal so as to form metallic complexes. The pyridinic Nitrogen (Npy) and that close to the substituent linked to azo group (N2) are the most available with almost the same energy to authorize coordination with metal. Before, prediction of Azpy synthesis was undertaken. 1H NMR was also performed. They showed that the conformational trans or E2-azpy was the most stable existing ligand. Nonetheless, this structure undergoes a modification on behalf of the conformational cis or E1-azpy that is the suitable ligand to provide with two nitrogen atoms with the same energy. Regarding this observation, all calculations were undertaken on the conformational E1 of each pyridylazo ligand. Therefore, the results obtained were consistent with the experimental analysis confirming that all of the four ligands are bidentates. In consequence, all the pyridylazo ligands can be assumed to connect to the metal by two nitrogen atoms forming five membered ring regardless the azo group's substituent nature.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Wed, 14 Jan 2015 03:02:28 GMT
DOI: 10.1142/S0219633615500066

• Gate-modulated electronic transport through a graphene nanoribbon composed
of nanoribbons of different widths
• Authors: Wen Liu, Jie Cheng, Jian-Hua Zhao, Cai-Juan Xia, De-Sheng Liu
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Based on the non-equilibrium Green's function (NEGF) method combined with the density functional theory (DFT), we have studied the gate-modulated electronic properties of a graphene nanoribbon (GNR) which is composed of two GNRs of different widths. The results show that the charge transport is greatly modulated by the applied gate. Negative differential resistance (NDR) behaviors is found in such a system. With the increase in the gate, the NDR behaviors will disappear and reappear. Furthermore, under certain gate voltages multiple NDR behavior is found, the origin of which is attributed to the change of the number of effective transport channels and the variation of delocalization degree of the orbitals within the bias window. Interestingly, low bias NDR behavior is obtained which is desirable for integrated circuits from the point view of power consumption.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Tue, 06 Jan 2015 09:25:48 GMT
DOI: 10.1142/S0219633615500054

• Structure of H2GeFMgF and its insertion reactions with RH (R = F, OH, NH2)
• Authors: Ming-Xia Zhang, Ming-Jun Zhang, Wen-Zuo Li, Qing-Zhong Li, Jian-Bo Cheng
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The structures of the germylenoid H2GeFMgF and its insertion reactions with RH (R = F, OH, NH2) were studied using the DFT B3LYP and QCISD approaches for the first time. The geometries of all of the stationary points were optimized at the B3LYP/6-311+G (d, p) level of theory. And then the QCISD/6-311++G (d, p) single-point energies were calculated. The solvent effects on the geometries and insertion reactions were also computed using the PCM model. The calculated results suggested that H2GeFMgF had three equilibrium configurations, in which the p-complex structure had the lowest energy and was the most stable structure. The isomerization reactions among the three complexes had been studied. For the insertion reactions of H2GeFMgF with RH (R = F, OH, NH2), along the potential energy surface, there were one transition state and one intermediate which connected the reactants and the products. For the three insertion reactions the mechanisms are identical. However, under the same conditions the insertion reactions should occur easily in the order of H-F > H-OH > H-NH2. The solvent effect calculations suggested the larger the solvent polarity is, the easier the reaction will be.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Mon, 05 Jan 2015 02:12:26 GMT
DOI: 10.1142/S0219633615500042

• Possible use of BN-modified fullerene as a nano-biosensor to detect
adenine–thymine Watson–Crick base pair in mutagenic tautomeric
form: Theoretical approach
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The present work deals with the theoretical investigation of electronic structure features and stability of adenine–thymine (AT) and rare tautomer of adenine–thymine (rAT) base pairs along with their complexes with Cu2+ cation and their interactions with BN doped fullerene (C58BN). All the calculations have been performed with density functional theory using B3LYP functional. Electronic structures of the two base pairs are almost identical. Hence, it is rather difficult to distinguish between the two base pairs on the basis of their electronic properties. As per our theoretical calculations, we have observed that, BN modified fullerene could act as a nano-biosensor for detection of mispairing between these two complementary bases as well as their Cu2+ complexes.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Tue, 30 Dec 2014 11:26:51 GMT
DOI: 10.1142/S0219633615500030

• Benchmark of electronic structure methods for protein–ligand
interactions based on high-level reference data
• Authors: Nusret Duygu Yilmazer, Pascal Heitel, Tobias Schwabe, Martin Korth
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The accurate prediction of the strength of protein–ligand interactions is a very difficult problem despite impressive advances in the field of biomolecular modeling. There are good reasons to believe that quantum mechanical methods can help with this task, but the application of such methods in the context of scoring is still in its infancy. Here we benchmark several wave function theory (WFT), density functional theory (DFT) and semiempirical quantum mechanical (SQM) approaches against high-level theoretical references for realistic test cases. Based on our findings for systematically generated model systems of real protein/ligand complexes from the PDB-bind database, we can recommend SCS-MP2 and B2-PLYP-D3 as reference methods, TPSS-D3+Dabc/def-TZVPP as the best DFT approach and PM6-DH+ as a fast and accurate alternative to full ab initio treatments.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Fri, 12 Dec 2014 03:18:45 GMT
DOI: 10.1142/S0219633615400015

• Second hyperpolarizability of multimetallocenes [Cp–Mn–Cp] of
Be, Mg and Ca
• Authors: Kaushik Hatua, Prasanta K. Nandi
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Multimetallocene complexes (Cp–Mn–Cp) of Be, Mg and Ca have been considered for the theoretical study of static second hyperpolarizability using a number of DFT functionals. Owing to the cooperative effect in bonding, beryllium forms multiberyllocene complexes (Cp–Ben–Cp) which have sufficient thermal stability with respect to dissociation into neutral fragments up to n = 10. On the other hand, multimetallocene complexes of Mg and Ca are found to be stable for n ≤ 5 which may be due to the weaker covalent bonding interaction between the larger metal atoms. The rather small variation of linear and cubic polarizabilities of Cp–Ben–Cp complexes beyond n = 5 arises from the rather weaker charge transfer transitions. The difference in NLO property among the investigated metal complexes arises from the extent of charge transfer from the terminal metal atoms and the distance between them. The charge transfer at longer distances in the ground state of Mg and Ca complexes leads to more intense electronic transition — the spectroscopic parameters of which strongly favors the enhancement of second hyperpolarizability.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Thu, 11 Dec 2014 08:07:03 GMT
DOI: 10.1142/S0219633615500029

• MP2 and DFT studies on interaction of a halide anion with the fully
protonated form of 1,4,7-triazacyclononane
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Density functional theory (DFT) using PBE, PBE1PBE, B3P86, B97-1, and BHandHLYP functionals as well as MP2 calculations employing the TZVP basis set were used to study the formation of four host–guest complexes with formula [H3L⋯X]2+ (X = F-, Cl-, Br-, and I-). The result of calculations on the structural parameters of [H3L⋯Cl]2+ shows that the calculated data with BHandHLYP functional have the best agreement with the experimental data and all five DFT methods give the better result than MP2. The largest amounts of interaction energies between the halide anions and protonated macrocycle were also calculated by PBE functional. The results show the following trend for the formation of complexes in the gas phase: [H3L⋯F]2+ > [H3L⋯Cl]2+ > [H3L⋯Br]2+ > [H3L⋯I]2+. Formation of the complexes in solution also shows the above trend where the [H3L⋯Br]2+ and [H3L⋯I]2+ complexes have positive $\Delta G_{\rm aq}^{0}$ values and probably cannot be formed.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Tue, 02 Dec 2014 01:31:27 GMT
DOI: 10.1142/S0219633615500017

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