Journal of Computational Chemistry

Cover image for Vol. 36 Issue 14

Early View (Online Version of Record published before inclusion in an issue)

Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner

Impact Factor: 3.601

ISI Journal Citation Reports © Ranking: 2013: 36/148 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

Associated Title(s): International Journal of Quantum Chemistry, Wiley Interdisciplinary Reviews: Computational Molecular Science

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  1. Full Papers

    1. Electronic stress tensor analysis of molecules in gas phase of CVD process for gesbte alloy

      Hiroo Nozaki, Yuji Ikeda, Kazuhide Ichikawa and Akitomo Tachibana

      Article first published online: 23 APR 2015 | DOI: 10.1002/jcc.23920

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      The chemical bonds among Ge, Sb, and Te atoms are analyzed by the electronic stress tensor density and associated energy density. The covalency and metallicity of these bonds are examined in terms of the electronic stress tensor analysis, and they are contrasted with those in the hydrocarbon molecules and alkali metal clusters. Also, the energy density integrated over the “Lagrange surface” between two atoms is found to be proportional to their force constant.

    2. [DBU-h]+ and h2o as effective catalyst form for 2,3-dihydropyrido[2,3-d]pyrimidin-4(1h)-ones: A DFT study

      Haiyan Yuan and Jingping Zhang

      Article first published online: 23 APR 2015 | DOI: 10.1002/jcc.23923

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      DFT invesigations suggest that [DBU-H]+-H2O acts as a high efficency, green catalyst to facilitate the formation of 2,3-dihydropyrido[2,3-d]-pyrimidin-4(1H)-ones. The calculated results open a new insight for the green catalyst model of DBU-H2O.

    3. Electronic, bonding, and optical properties of 1d [CuCN]n (n = 1–10) chains, 2d [CuCN]n (n = 2–10) nanorings, and 3d [Cun(CN)n]m (n = 4, m = 2, 3; n = 10, m = 2) tubes studied by DFT/TD-DFT methods

      Athanassios C. Tsipis and Alexandros V. Stalikas

      Article first published online: 23 APR 2015 | DOI: 10.1002/jcc.23932

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      A series of linear 1-D [CuCN]n (n = 1–10) chains, cyclic 2-D [CuCN]n (n = 2–10) nanorings, and 3-D [Cun(CN)n]m (n = 4, m = 2, 3; n = 10, m = 2) tubes are investigated by means of a multitude of computational methodologies using DFT and time-dependent density-functional theory methods. Particular emphasis was given on the photophysical properties (absorption and emission spectra) of the [CuCN]n chains, nanorings, and tubes.

    4. Inter- and intramolecular CF···c[DOUBLE BOND]o interactions on aliphatic and cyclohexane carbonyl derivatives

      Rodrigo A. Cormanich, Roberto Rittner, David O'Hagan and Michael Bühl

      Article first published online: 23 APR 2015 | DOI: 10.1002/jcc.23918

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      Prototypical inter- and intramolecular CF···C[DOUBLE BOND]O interactions are assessed computationally at the B3LYP-D3 level. The interactions are noticeable in intermolecular complexes 1, where they can amount to stabilizations around about 1 kcal mol, however, they are not strong enough to dominate conformational preferences in organofluorine derivatives such as 2 - 4.

    5. Development of minimized mixing molecular orbital method for designing organic ferromagnets

      Xun Zhu and Yuriko Aoki

      Article first published online: 22 APR 2015 | DOI: 10.1002/jcc.23915

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      Conventional ab initio methods face difficulties when they are applied to huge high-spin open-shell systems such as organic ferromagnets due to the quick increase of CPU time relative to the size of the system. To solve this problem, the minimized mixing elongation (MMELG) method is a linear-scaling quantum chemical method that utilizes minimized mixing and regional localized molecular orbitals to treat the system with constant size at each elongation step. The Lmin method with an index Lmin is combined with the MMELG method to design organic ferromagnets.

    6. Interaction potential models for bulk Zns, Zns nanoparticle, and Zns nanoparticle-PMMA from first-principles

      Sadanandam Namsani, Nisanth N. Nair and Jayant K. Singh

      Article first published online: 21 APR 2015 | DOI: 10.1002/jcc.23912

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      Interaction models for bulk ZnS, ZnS nanoparticles, and ZnS–PMMA systems have been developed using ab initio calculations. Molecular dynamics simulations using the derived empirical force-field show that PMMA and ZnS interact through Zn[BOND]O bond formation. The obtained radial distribution function for Zn[BOND]O is in good agreement with the density functional theory calculations.

    7. Bridging Organometallics and Quantum Chemical Topology: Understanding Electronic Relocalisation During Palladium-Catalyzed Reductive Elimination

      Benoit de Courcy, Etienne Derat and Jean-Philip Piquemal

      Article first published online: 21 APR 2015 | DOI: 10.1002/jcc.23911

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      The proposed computational strategy based on quantum topological analyses allows a deeper understanding of the interactions between the constitutive elements of a reactive organometallic complex. The coupled QTAIM/ELF partitioning used here is able to dissect the electronic rearrangement along a chemical pathway. This methodology was applied here to reinvestigate a classical process in organometallic chemistry, namely the reductive elimination and more specifically the one induced by palladium.

    8. Ab initio calculations of the ground and excited states of the ZrN molecule including spin-orbit effects

      Ayman Farhat and Saleh N. Abdul-Al

      Article first published online: 21 APR 2015 | DOI: 10.1002/jcc.23921

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      The electronic structure of the Zirconium Nitride molecule is studied with the inclusion of spin-orbit effects. The methods of multireference single and double configuration interaction (MRSDCI) are used to analyze the potential energy curves in the ground and excited states of this molecule. The spectroscopic constant for 34 spin-orbit state in ZrN is calculated.

    9. Efficient parametrization of complex molecule–surface force fields

      David Z. Gao, Filippo Federici Canova, Matthew B. Watkins and Alexander L. Shluger

      Article first published online: 16 APR 2015 | DOI: 10.1002/jcc.23904

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      Classical force fields are essential for studying the mobility and self-assembly of molecules on surfaces. This article presents an efficient scheme for parameterizing complex molecule-surface force fields directly from ab initio data. The embedded slab quantum mechanics / molecular mechanics model combined with genetic algorithm methods greatly reduces the computational expense of producing such force fields. This method is efficient enough to be applied routinely to each new molecule-surface combination of interest.

    10. Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations

      Shu-Ching Ou, Di Cui, Matthew Wezowicz, Michela Taufer and Sandeep Patel

      Article first published online: 13 APR 2015 | DOI: 10.1002/jcc.23906

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      GPU-enabled all-atom molecular dynamics simulations were performed to study the assembly of two (10,10) single-walled carbon nanotubes in 3 m NaI aqueous salt solution at different temperatures. The solvent components (water, anions, cations) show distinct responses to the change of temperature, which lead to different contribution to the strength of nanotube assembly.

    11. Theoretical and experimental investigation of crown/ammonium complexes in solution

      Andreas J. Achazi, Larissa K. S. von Krbek, Christoph A. Schalley and Beate Paulus

      Article first published online: 13 APR 2015 | DOI: 10.1002/jcc.23914

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      Gibbs energies of association inline image of monovalent crown/ammonium complexes in solution are calculated with DFT-D3(BJ) and the continuum solvation model COSMO-RS. For comparison, experimental data are obtained by isothermal titration calorimetry. Calculated and measured Gibbs energies of association inline image in solution agree well.

    12. Using bonding to guide transition state optimization

      Adam B. Birkholz and H. Bernhard Schlegel

      Article first published online: 2 APR 2015 | DOI: 10.1002/jcc.23910

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      Bonding information from the reactants and products is used to obtain a better initial guess of the transition state and to improve the efficiency of the transition state optimization.

    13. Toward assessment of density functionals for vibronic coupling in two-photon absorption: A case study of 4-nitroaniline

      Robert Zaleśny, Guangjun Tian, Christof Hättig, Wojciech Bartkowiak and Hans Ågren

      Article first published online: 31 MAR 2015 | DOI: 10.1002/jcc.23903

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      CC2 method and several exchange-correlation functionals are used to predict vibronic two-photon absorption spectra of 4-nitroaniline.

    14. From small fullerenes to the graphene limit: A harmonic force-field method for fullerenes and a comparison to density functional calculations for Goldberg–Coxeter fullerenes up to C980

      Lukas N. Wirz, Ralf Tonner, Andreas Hermann, Rebecca Sure and Peter Schwerdtfeger

      Article first published online: 26 MAR 2015 | DOI: 10.1002/jcc.23894

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      A general force field is introduced which works for all fullerene isomers. It leads to structures and zero-point vibrational energy contributions in very good agreement to more expensive quantum theoretical calculations. The graphene limit is well represented by the growth of Goldberg-Coxeter transforms of C20.

    15. Solvents effects on the mechanism of cellulose hydrolysis: A QM/MM study

      Claudia Loerbroks, Andreas Heimermann and Walter Thiel

      Article first published online: 21 MAR 2015 | DOI: 10.1002/jcc.23898

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      Acid hydrolysis of cellulose yields glucose. This process is investigated computationally in water using two cellulose models (cellobiose and a 40-unit glucose chain) and explicit solvation. Hydrogen bonding is found to have a large impact on the reaction mechanism and on the barriers to hydrolysis. The results are compared to those from to a previous study with implicit solvation.

    16. An anisotropic coarse-grained model based on Gay–Berne and electric multipole potentials and its application to simulate a DMPC bilayer in an implicit solvent model

      Hujun Shen, Yan Li, Peijun Xu, Xiaofang Li, Huiying Chu, Dinglin Zhang and Guohui Li

      Article first published online: 18 MAR 2015 | DOI: 10.1002/jcc.23895

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      The promising performance of an anisotropic coarse-grained model (so-called GBEMP) has been demonstrated in modeling a DMPC lipid bilayer. A 72-DMPC bilayer system was used for testing the performance of the GBEMP model, and it has shown a few important structural properties. In addition, the atomistic and experimental results for electron density profiles and order parameters can be reproduced reasonably well by this GBEMP model.

    17. Prediction of the crystal packing of di-tetrazine-tetroxide (DTTO) energetic material

      Jose L. Mendoza-Cortes, Qi An, William A. Goddard III, Caichao Ye and Sergey Zybin

      Article first published online: 18 MAR 2015 | DOI: 10.1002/jcc.23893

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      The two most stable isomers of Di-tetrazine-tetroxide (DTTO), c1 and c2, were used to predict the most stable polymorphs of DTTO. For the c1 isomer, the most stable polymorph has P212121 space group with a density of 1.96 g/cm3. Conversely, for the c2 isomer, the most stable polymorph has Pbca space group with a density of 1.98 g/cm3. These predicted densities are among the highest of current energetic materials.

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