Journal of Computational Chemistry

Cover image for Vol. 36 Issue 16

June 15, 2015

Volume 36, Issue 16

Pages i–iv, 1187–1274

  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 36, Issue 16 (pages i–ii)

      Article first published online: 21 MAY 2015 | DOI: 10.1002/jcc.23954

      Thumbnail image of graphical abstract

      Classical force fields are essential for studying the mobility and self-assembly of molecules on surfaces. The cover depicts one example system: 1,4-bis(cyanophenyl)-2,5-bis(decyloxy)benzene (CDB) molecules adsorbed onto KCl(001). David Z. Gao, Filippo Federici Canova, Matthew B. Watkins, and Alexander L. Shluger present an efficient scheme for parameterizing complex molecule-surface force fields using ab initio molecular dynamics data on page 1187 (DOI: 10.1002/jcc.23904). 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 other molecule-surface combinations of interest.

    2. You have free access to this content
      Cover Image, Volume 36, Issue 16 (pages iii–iv)

      Article first published online: 21 MAY 2015 | DOI: 10.1002/jcc.23955

      Thumbnail image of graphical abstract

      Classical molecular dynamics with empirical force fields is a computational technique to simulate the behaviors of an atomic model. However, insufficient sampling becomes a problem as the system size increases, limiting the application of the technique. In the study on page 1196 (DOI: 10.1002/jcc.23906), Shu-Ching Ou, Di Cui, Matthew Wezowicz, Michela Taufer, and Sandeep Patel utilize Graphical Processing Unit (GPU) resources (FEN ZI) to extend the sampling for molecular simulations to study the thermodynamics of carbon nanotube assembly. This study is relevant in the continuing discourse and interpretations on hydrophobic interactions. The image shows a representative snapshot of the system setup of two parallel single-walled carbon nanotubes in NaI salt solution.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Efficient parametrization of complex molecule–surface force fields (pages 1187–1195)

      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

      Thumbnail image of graphical abstract

      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.

    2. Free energetics of carbon nanotube association in aqueous inorganic NaI salt solutions: Temperature effects using all-atom molecular dynamics simulations (pages 1196–1212)

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

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

      Thumbnail image of graphical abstract

      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 contributions to the strength of nanotube assembly.

    3. Conformational ensembles and sampled energy landscapes: Analysis and comparison (pages 1213–1231)

      Frédéric Cazals, Tom Dreyfus, Dorian Mazauric, Christine-Andrea Roth and Charles H. Robert

      Article first published online: 21 MAY 2015 | DOI: 10.1002/jcc.23913

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      The potential energy landscape (PEL) plays a fundamental role in understanding the meta-stable states of a system as well as transitions between them. Novel methods are presented for modeling a sampled PEL and its associated transition graph (including ruggedness), and for comparing two PELs obtained, for example, from two different simulation runs. Software tools implementing these methods are made available and should prove valuable wherever conformational ensembles and energy landscapes are used.

    4. Development of minimized mixing molecular orbital method for designing organic ferromagnets (pages 1232–1239)

      Xun Zhu and Yuriko Aoki

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

      Thumbnail image of graphical abstract

      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. Introduced 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.

    5. Electronic stress tensor analysis of molecules in gas phase of CVD process for gesbte alloy (pages 1240–1251)

      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.

    6. Ab initio calculations of the ground and excited states of the ZrN molecule including spin-orbit effects (pages 1252–1258)

      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.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. MOLSIM: A modular molecular simulation software (pages 1259–1274)

      Reščič Jurij and Linse Per

      Article first published online: 21 MAY 2015 | DOI: 10.1002/jcc.23919

      Thumbnail image of graphical abstract

      The main features of the modular software MOLSIM for all-atom and coarse-grained simulation are presented. The software is unique in the sense that (1) Monte Carlo, molecular dynamic, and Brownian dynamics capability is integrated in a single software, (2) simulated objects can range from simple noble-gas atoms to complex macromolecules and are constructed through a four-level hierarchical manner, (3) several advanced treatments of electrostatic interactions are available, and (4) statistical uncertainties are evaluated for all calculated observables.

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