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 Journal of Theoretical and Computational Chemistry   [SJR: 0.286]   [H-I: 16]   [10 followers]  Follow         Hybrid journal (It can contain Open Access articles)    ISSN (Print) 0219-6336 - ISSN (Online) 1793-6888    Published by World Scientific  [114 journals]
• Author Index Volume 13 (2014)
• Abstract: Journal of Theoretical and Computational Chemistry, Volume 13, Issue 08, December 2014.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Tue, 06 Jan 2015 00:29:26 GMT
DOI: 10.1142/S0219633614990016

• 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
• Authors: Shamoon Ahmad Siddiqui, Tabish Rasheed, Nadir Bouarissa, A. Al-hajry
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
• Authors: Yasin Gholiee, Sadegh Salehzadeh
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

• Acyclic and cyclic nitrone cycloadditions to 1-cinnamoyl-1-piperidine: A
DFT study
• Authors: Nivedita Acharjee
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. DFT studies have been carried out for the cycloaddition reactions of a cyclic nitrone, 1-pyrroline-1-oxide and an acyclic nitrone, C,N-diphenyl nitrone to an unsymmetrically disubstituted dipolarophile, 1-cinnamoyl-1-piperidine. These reactions proved to be opposite to each other with respect to the electron demand character predicted by the electronic chemical potentials, electrophilicities and charge transfer at the transition states. The regio- and stereoselectivities have been predicted from DFT based reactivity indices, interaction energy calculations using a perturbative orbital independent theoretical model and the activation parameters of the located transition states. Two different concepts have been used for the evaluation of interaction energies. The selectivities were found to be in conformity with the experimental findings. The time gaps between the formations of C–C and C–O bonds were evaluated from single trajectory simulations. The asynchronicity of bond formation process was analyzed from the wiberg bond indices, atom–atom overlap weighted NAO bond orders and the calculated asymmetry indices of the transition states.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Tue, 25 Nov 2014 02:40:26 GMT
DOI: 10.1142/S0219633614500710

• First-principles study on electronic structure and optical properties of
In-doped GaN
• Authors: Xingxiang Ruan, Fuchun Zhang, Weihu Zhang
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The In-doped GaN is investigated by first-principles calculations of plane wave ultra-soft pseudo-potential method based on the density functional theory (DFT). The band structure, electronic structure, density of states and optical properties are investigated. The results indicate that the band-gap becomes narrower and the absorption edge of optical properties is red-shifted with the increase in In-doped concentration. Meanwhile, the visible region has strong absorption properties, and the significant absorption peaks are observed near 3.0 eV and 6.1 eV. The other peaks correspond to the wavelength of absorption spectra from the ultraviolet portion extending to the infrared portion, which almost covers the entire solar spectrum. The studied results show that In-doped GaN can be applied as solar cell and transparent conductivity material.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Fri, 21 Nov 2014 06:11:02 GMT
DOI: 10.1142/S0219633614500709

• DFT calculations of tin dioxide crystals containing heavily-doped fluorine
• Authors: Freddy Marcillo, Arvids Stashans
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. First-principles calculations based on the density functional theory (DFT) within the generalized gradient approximation have been used in the present research. Fluorine doping in the SnO2 crystals has been carried out considering a number of different defect concentrations. Dopant influence upon structural, electronic and electrical properties of the tin dioxide has been discussed in detail. The system presents n-type electrical conductivity relating our work directly to a number of empirical studies in this area. An experimental fact that n-type conductivity tends to decrease at rather high fluorine impurity rates has been explained at the theoretical level.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Thu, 20 Nov 2014 02:52:30 GMT
DOI: 10.1142/S0219633614500692

• Theoretical calculations of π-type pnicogen bonds in the triad
intermolecular complexes
• Authors: Hui-Ying Xu, Wei Wang, Jian-Wei Zou, Xiao-Lu Xu
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The pnicogen bonding interactions of PCl3 and π-electron systems (acetylene, ethylene, benzene) were calculated by using MP2/aug-cc-pVDZ method and the effect of hydrogen bond on pnicogen bond systems were investigated. It has been indicated that the hydrogen bonding and the pnicogen bonding interactions have influence on each other and the positively cooperative effect has been detected. The interaction energies of pnicogen bonded supramolecular system were also calculated by using DFT method (M06-2X) and some simple comparisons with those by using MP2 method were made. It has been disclosed from natural bond orbitals (NBO) analysis that more the amount of charge transfer of pnicogen bonding interaction, the greater the stability of the corresponding complex. Through AIM topological analysis, it has been revealed that the electron density of pnicogen bond BCP point is positively correlated with the stability of trimeric complex. Electron localization function (ELF) was also adopted to analyze the nature of pnicogen bonding interactions. Furthermore, density difference function (DDF) method was adopted to analyze the variation of electron density of pnicogen bond system because of hydrogen bond.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Tue, 18 Nov 2014 01:46:39 GMT
DOI: 10.1142/S0219633614500680

• Conformational space analysis of neutral and protonated glycine using a
genetic algorithm for multi-modal search
• Authors: B. El Merbouh, M. Bourjila, R. Tijar, R. Drissi El Bouzaidi, A. El Gridani, M. El Mouhtadi
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The genetic algorithm based on the Multi-Niche Crowding (MNC) method is used with the semi-empirical methods AM1 and PM3 in order to scan the potential energy surface (PES) of neutral and protonated glycine. The algorithm is implemented as a package of programs interfaced with MOPAC and piloted by scripts. Both methods AM1 and PM3 located six minima on the PES of neutral glycine and seven on the protonated glycine one, of which three are those of the N-protonated form and four of the O-protonated one.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Fri, 14 Nov 2014 01:22:56 GMT
DOI: 10.1142/S0219633614500679

• Molecular dynamics simulation on the interfacial features of supercritical
1-butene/subcritical water
• Authors: Huidong Zheng, Jingjing Chen, Fangdi Wu, Suying Zhao
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. We studied the interfacial features of 1-butene/water and extraction process of 2-butanol by molecular dynamics (MD) simulations. The infinite dilute diffusion coefficients of 1-butene in water is larger than that of 2-butanol, and one important reason is that 2-butanol molecules can form hydrogen bonds with water molecules. 1-butene is more soluble in water under supercritical condition than that under subcritical condition. 1-butene under supercritical condition can extract more 2-butanol from aqueous solution than that under other conditions. A process of producing 2-butanol by the direct hydration of 1-butene is more competive when it operates under the supercritical conditions of 1-butene which due to a higher solubility of 1-butene in water, a lager diffusion coefficient of 1-butene and a lower 2-butanol concentration in water.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Thu, 13 Nov 2014 02:09:42 GMT
DOI: 10.1142/S0219633614500667

• First principle calculations of hydrogen sulfide adsorption and
dissociation on pure Pd (111) and Au (111), and alloy Pd/Au (111) and
Au/Pd (111) surfaces
• Authors: Na Liu, Xue-Ye Wang, Ya-Li Wan
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. The hydrogen sulfide adsorption and dissociation on pure Pd (111) and Au (111), alloy Pd/Au (111) and Au/Pd (111) surfaces have been investigated using the pseudo-potential plane wave method within the generalized-gradient approximation density functional theory (GGA+DFT). The results show that H2S tends to be adsorbed on top site, HS prefers to locate on bridge site, and the S and H locate on fcc site on various surfaces. Compared the adsorption of sulfur-containing species and hydrogen on pure and alloy metal surfaces, a similar trend of adsorption energies on the metal surfaces (Pd/Au (111) > Pd (111) > Au (111) > Au/Pd (111)) is found. In addition, the dissociation process on the Pd (111) and Pd/Au (111) surfaces is predicted to be exothermic. However, on Au (111) and Au/Pd (111), the dissociation process is endothermic. The work reveals that H2S dissociation is more likely to happen on Pd/Au (111) surface. Finally, the adsorption energies of adsorbate on metal surfaces have strong correlation with the d-band center. The d-band center moves away from the Fermi level, and the adsorption energy decreases. According to the LDOS analysis, the inner Au atoms of Pd/Au (111) can enhance the top-layer d-band intensity, whereas the inner Pd atoms of Au/Pd (111) cause the opposite effect. The further electronic state analysis reveals the interaction between H2S and metal surfaces.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Tue, 21 Oct 2014 03:46:16 GMT
DOI: 10.1142/S0219633614500655

• TD-DFT study on some triphenylamine-based organic dyes as photosensitizers
in DSSCs
• Authors: Ahmed A. Hasanein, Yasser R. Elmarassi, Ahmed M. Ramadan
Abstract: Journal of Theoretical and Computational Chemistry, Ahead of Print. Geometrical and molecular electronic structure calculations on a series of metal free organic dyes based on triphenylamine (TPA) moiety have been performed using the TD-DFT methods. The B3LYP/6-31G, B3LYP/6-31G(d,p), M06-HF/6-31G(d,p) and WB97XD/6-31G(d,p) levels of theory have been utilized to predict the relationships between chemical structure and theoretically calculated molecular electronic properties of the studied dyes which may help in optimizing the properties of TPA-based photosensitizers in DSSCs. The solvation process of these dyes has been taken into account by means of the polarizable continuum model. The light harvesting efficiency, the free energy change for the electron injection process to the surface of TiO2 nanocrystalline semiconductor and the open circuit potential are calculated using all of these methods in different media. Significant charge transfer character of the HOMO → LUMO electronic transition which dominates the So → S1 vertical excitation in these systems facilitates the electron transfer process to the surface of TiO2. The results of the present computations are reported and discussed.
Citation: Journal of Theoretical and Computational Chemistry
PubDate: Tue, 14 Oct 2014 02:27:24 GMT
DOI: 10.1142/S0219633614500643

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