Journal of Computational Chemistry

Cover image for Vol. 35 Issue 14

30 May 2014

Volume 35, Issue 14

Pages i–iv, 1045–1105

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. You have free access to this content
      Cover Image, Volume 35, Issue 14 (pages i–ii)

      Article first published online: 18 APR 2014 | DOI: 10.1002/jcc.23624

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      Calculations predict very strong oxygen adsorption on hybrid carbon and boron-nitride nanotubes, as compared to pristine materials. In addition, oxygen binding increases the conductivity of the hybrid nanotubes, suggesting the potential to use these materials in sensor applications. On page 1058 (DOI: 10.1002/jcc.23589), Haining Liu and C. Heath Turner use first-principles density functional theory to predict oxygen adsorption on two types of hybrid carbon and boron-nitride nanotubes: zigzag (8,0), and armchair (6,6).

    2. You have free access to this content
      Inside Cover, Volume 35, Issue 14 (pages iii–iv)

      Article first published online: 18 APR 2014 | DOI: 10.1002/jcc.23625

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      On page 1045 (DOI: 10.1002/jcc.23560), Marc Raupach, Stefanie Dehnen, and Ralf Tonner use energy- and density-based analysis methods for a quantitative picture of chemical bonding in ternary Sn/(Sb,Bi)/Zn Zintl anions. They outline the importance of π-bonding contributions, polarized σ-bonding, and significant electrostatic effects. This leads to a quantitative description of the metal-ligand interaction in this interesting compound class and has implications on ligand design for the stabilization of Zintl cages. The cover picture is designed by Marc Raupach.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Quantitative investigation of bonding characteristics in ternary Zintl anions: Charge and energy analysis of [Sn2E152(ZnPh)] (E15 = Sb, Bi) and [Sn2Sb5(ZnPh)2]3− (pages 1045–1057)

      Marc Raupach, Stefanie Dehnen and Ralf Tonner

      Article first published online: 24 FEB 2014 | DOI: 10.1002/jcc.23560

      Thumbnail image of graphical abstract

      Density functional theory based analysis of the chemical bonding in ternary Sn/(Sb,Bi)/Zn Zintl anions outlines the importance of π-bonding contributions, polarized σ-bonding, and significant electrostatic effects. This leads to a quantitative description of the metal–ligand interaction in this interesting compound class and has implications on the ligand design for the stabilization of Zintl cages.

    2. Oxygen adsorption characteristics on hybrid carbon and boron-nitride nanotubes (pages 1058–1063)

      Haining Liu and C. Heath Turner

      Article first published online: 23 MAR 2014 | DOI: 10.1002/jcc.23589

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      Recently, hybrid carbon nanotube and boron-nitride nanotube materials have been synthesized in the lab. Here, DFT calculations indicate that molecular oxygen adsorption is significantly enhanced on these hybrid carbon and boron-nitride nanotube materials, versus on pristine nanotubes. The large change in the band gap upon oxygen adsorption may provide unique sensing capabilities in addition to other catalytic properties, motivating further experimental investigations.

    3. Midpoint cell method for hybrid (MPI+OpenMP) parallelization of molecular dynamics simulations (pages 1064–1072)

      Jaewoon Jung, Takaharu Mori and Yuji Sugita

      Article first published online: 23 MAR 2014 | DOI: 10.1002/jcc.23591

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      A new hybrid (MPI+OpenMP) parallelization scheme is developed for molecular dynamics (MD) simulations, introducing a cell-wise version of the midpoint method named the “midpoint cell method”. This method retains the advantages of the original midpoint method for the message passing interface (MPI) parallelization, and it allows efficient shared memory parallelization by grouping particle data cell-wise and distributing cell pairs over OpenMP threads. The parallel performance of the midpoint cell method on a K computer shows scalability up to 32,768 cores for a system of 1 million atoms. One MD step with long-range interaction can be calculated within 4.5 ms.

    4. Assessment of the orbital-optimized coupled-electron pair theory for thermochemistry and kinetics: Improving on CCSD and CEPA(1) (pages 1073–1081)

      Emine Soydaş and Uğur Bozkaya

      Article first published online: 25 MAR 2014 | DOI: 10.1002/jcc.23592

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      An assessment of the orbital-optimized coupled-electron pair theory (or simply “optimized CEPA(0)”, OCEPA(0)) for thermo-chemistry and kinetics is presented. The results demonstrate that the OCEPA(0) method is helpful for problematic open-shell systems and transition-states, and for closed-shell molecules.

    5. A new perspective of shape recognition to discover the phase transition of finite-size clusters (pages 1082–1092)

      Po-Jen Hsu

      Article first published online: 23 MAR 2014 | DOI: 10.1002/jcc.23593

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      An ultrafast shape recognition technique is applied to analyze the phase transition of finite-size clusters. The shape of clusters is the unique property that distinguishes clusters from bulk systems, and is comprehensive and natural for structural analysis. The probability contour and the implementation of the substructure provide insightful atom/shell-resolved perspectives. The method can considerably simplify the tedious trajectory analysis and is efficient in any type of finite-size system, including polymers and nanostructures.

    6. Reactivity index based on orbital energies (pages 1093–1100)

      Takao Tsuneda and Raman K. Singh

      Article first published online: 17 APR 2014 | DOI: 10.1002/jcc.23599

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      Chemical reactivity depends on the orbital energy gap contributing to the reaction in the initial reaction process. This is because the small orbital energy gap gradient indicates the precursory charge transfer process, while the large gradient implies the initial structural transformation. Analyses using a normalized reaction diagram show that large orbital energy gap gradients are given for specific reactions, including several SN2 reactions, which are experimentally established to get around the optimum reaction pathways.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. ALMOST: An all atom molecular simulation toolkit for protein structure determination (pages 1101–1105)

      Biao Fu, Aleksandr B. Sahakyan, Carlo Camilloni, Gian Gaetano Tartaglia, Emanuele Paci, Amedeo Caflisch, Michele Vendruscolo and Andrea Cavalli

      Article first published online: 27 MAR 2014 | DOI: 10.1002/jcc.23588

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      “Almost” (all atom molecular simulation toolkit) is an open source computational package for the structure determination and analysis of biomolecules. Almost provides tools for the molecular structure determination using various types of experimental measurements as conformational restraints and methods for the analysis of structural and dynamical properties of complex molecular systems.

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