Journal of Computational Chemistry

Cover image for Vol. 35 Issue 31

December 5, 2014

Volume 35, Issue 31

Pages i–iv, 2231–2278

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    1. You have free access to this content
      Cover Image, Volume 35, Issue 31 (pages i–ii)

      Article first published online: 25 OCT 2014 | DOI: 10.1002/jcc.23768

      Thumbnail image of graphical abstract

      On page 2272 (DOI: 10.1002/jcc.23752), Jorge Garza and co-workers report an efficient grid-based algorithm to find critical points on the electron density, which scales very well on CPUs and exhibits a high performance on GPUs. The convenience in using this new proposal is evidenced when non-nuclear attractors are found in a molecule and when the code is used on common GPUs, which are nondedicated to high-performance applications. The cover was designed by Alfredo Garza.

    2. You have free access to this content
      Cover Image, Volume 35, Issue 31 (pages iii–iv)

      Article first published online: 25 OCT 2014 | DOI: 10.1002/jcc.23769

      Thumbnail image of graphical abstract

      Damien J. Carter and Andrew L. Rohl investigate the performance of several van der Waals (vdW) functionals at calculating the interactions between benzene and the copper (111) surface. On page 2263 (DOI: 10.1002/jcc.23745), they demonstrate that local orbital methods using appropriate basis sets combined with a vdW functional can successfully model adsorption between metal surfaces and organic molecules.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    1. Melting of icosahedral nickel clusters under hydrostatic pressure (pages 2231–2238)

      Bing Fu, Li Chen, Feifei Wang, Yiqun Xie and Xiang Ye

      Article first published online: 21 SEP 2014 | DOI: 10.1002/jcc.23739

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      The nickel–iron mixture is a dominant component in the terrestrial planet lower mantle, which makes the melting of nickel under hydrostatic pressure of interest. Here the melting behaviors of icosahedral nickel clusters under hydrostatic pressure are studied by constant-pressure molecular dynamic simulation. This work intends to provide a better understanding of the thermal properties of nickel clusters and will aid development of new nanomaterials under hydrostatic pressure.

    2. Impact of Mn on the solution enthalpy of hydrogen in austenitic Fe-Mn alloys: A first-principles study (pages 2239–2244)

      Jörg von Appen, Richard Dronskowski, Aurab Chakrabarty, Tilmann Hickel, Robert Spatschek and Jörg Neugebauer

      Article first published online: 24 SEP 2014 | DOI: 10.1002/jcc.23742

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      Adding a substantial amount of manganese to steels yields a material with extraordinary mechanical properties. A tiny amount of hydrogen in high-Mn steels, however, is already suffcient for the onset of devastating embrittlement effects. Using first-principles methods, an attraction of both elements is revealed, providing a complete analysis of the elastic, chemical, and magnetic origin of this phenomenon. These insights contribute to strategies to better control the hydrogen distribution in steels.

    3. GneimoSim: A modular internal coordinates molecular dynamics simulation package (pages 2245–2255)

      Adrien B. Larsen, Jeffrey R. Wagner, Saugat Kandel, Romelia Salomon-Ferrer, Nagarajan Vaidehi and Abhinandan Jain

      Article first published online: 26 SEP 2014 | DOI: 10.1002/jcc.23743

      Thumbnail image of graphical abstract

      This paper describes the modular architecture of the GneimoSim software package for performing long time scale internal coordinate molecular dynamics simulations. GneimoSim includes advanced dynamics methods, integrators for robust long time scale dynamics, interfaces for all-atom forcefields such as AMBER and CHARMM, and the Generalized Born solvation model. The software is available at no cost for academic use.

    4. Efficient calculation of relative binding free energies by umbrella sampling perturbation (pages 2256–2262)

      Fabian Zeller and Martin Zacharias

      Article first published online: 29 SEP 2014 | DOI: 10.1002/jcc.23744

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      The change of a potential of mean force upon the modification of a system can be estimated by an umbrella sampling perturbation method that does not require additional simulations. Application to computational alanine-scanning of a peptide-protein complex by means of relative separation of potential of mean forces (PMFs) resulted in accurate free energy estimates for a series of peptide modifications. The method yields rigorously derived free energy changes under the condition of sufficiently small perturbations.

    5. van der Waals corrected density functional calculations of the adsorption of benzene on the Cu (111) surface (pages 2263–2271)

      Damien J. Carter and Andrew L. Rohl

      Article first published online: 6 OCT 2014 | DOI: 10.1002/jcc.23745

      Thumbnail image of graphical abstract

      The performance of several van der Waals (vdW) functionals at calculating the interactions between benzene and the copper (111) surface was investigated. Local orbital methods using appropriate basis sets combined with a vdW functional can successfully model adsorption between metal surfaces and organic molecules.

    6. Grid-based algorithm to search critical points, in the electron density, accelerated by graphics processing units (pages 2272–2278)

      Raymundo Hernández-Esparza, Sol-Milena Mejía-Chica, Andy D. Zapata-Escobar, Alfredo Guevara-García, Apolinar Martínez-Melchor, Julio-M. Hernández-Pérez, Rubicelia Vargas and Jorge Garza

      Article first published online: 25 OCT 2014 | DOI: 10.1002/jcc.23752

      Thumbnail image of graphical abstract

      Grid-based methods are quite convenient to search for critical points on systems that exhibit non-nuclear attractors. However, these methods are computationally expensive. An efficient algorithm with good scaling on central processing units is proposed. The algorithm has better performance when implemented on graphics processing units (GPUs), even in GPUs not dedicated for high-performance computing.

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