Journal of Computational Chemistry

Cover image for Vol. 35 Issue 17

30 June 2014

Volume 35, Issue 17

Pages i–iv, 1261–1337

  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 17 (pages i–ii)

      Article first published online: 23 MAY 2014 | DOI: 10.1002/jcc.23647

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      An extension of a multiscale code MBN Explorer is developed by Mikhail Panshenskov, Ilia A. Solov'yov, and Andrey V. Solov'yov on page 1317 (DOI: 10.1002/jcc.23613), providing a universal approach to the study of selfassembly phenomena in biology and nanoscience. In particular, this extension involves a highly-parallelized module of MBN Explorer that allows the simulation of stochastic processes using the kinetic Monte Carlo approach in a threedimensional space. The method permits the study of dynamics of processes occurring on long time scales, for example, milliseconds to hours. Instead of propagating individual atoms in time, as in molecular dynamics, it models the evolution of a molecular coarse-grained system in a probabilistic way.

    2. You have free access to this content
      Cover Image, Volume 35, Issue 17 (pages iii–iv)

      Article first published online: 23 MAY 2014 | DOI: 10.1002/jcc.23648

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      The concept of “electron deformation orbitals” (EDOs) is used by Marcos Mandado and Nicola's Ramos-Berdullas on page 1261 (DOI: 10.1002/jcc.23595) to investigate the electric response of conducting metals and oligophenyl chains. The cover represents the electron transfer and the external electric voltage in a gold cluster (top figure) in an oligophenyl chain, which is attached to gold atoms (bottom figure), and a hybrid structure formed by the same oligophenyl chain, which is linked to gold chains at both sides (central figure). The electron deformation density associated with the main EDOs is shown, indicating positive and negative regions (accumulation and depletion of the electron charge) for the central figure and the direction of the electron transfer.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Analyzing the electric response of molecular conductors using “electron deformation” orbitals and occupied-virtual electron transfer (pages 1261–1269)

      Marcos Mandado and Nicolás Ramos-Berdullas

      Article first published online: 27 MAR 2014 | DOI: 10.1002/jcc.23595

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      Electron deformation orbitals and occupied-virtual electron transfer induced by a constant external electric perturbation provide an orbital picture of the charge transfer process. The proposed methodology is qualitatively related to the band model of conductivity and allows discernment between good and poor unimolecular conductors in terms of their electronic structure.

    2. Moving of fullerene between potential wells in the external icosahedral shell (pages 1270–1277)

      Olga E. Glukhova, Anna S. Kolesnikova, Michael M. Slepchenkov and Vladislav V. Shunaev

      Article first published online: 28 APR 2014 | DOI: 10.1002/jcc.23620

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      The behavior of fullerenes C20 and C60 inside the icosahedral external shell in carbon nanoclusters C20@C240 and C60@C540 is investigated. The movement of fullerene C20 between potential wells is predicted based on topology data of the relative positioning of fullerenes in nanoparticles and an analysis of the relief for the interaction energy surface of fullerenes.

    3. New force field parameters for metalloproteins I: Divalent copper ion centers including three histidine residues and an oxygen-ligated amino acid residue (pages 1278–1289)

      Olivia Wise and Orkid Coskuner

      Article first published online: 28 APR 2014 | DOI: 10.1002/jcc.23622

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      First principles calculations are performed. The structures, the Hessian matrix, and binding affinities of sets of divalent copper ion bound peptides are calculated. First principles calculation results are used to generate the missing force field parameters of sets of metallopeptides. Molecular dynamics simulations are performed to validate the force field parameters and to investigate the structures and thermodynamic properties in an aqueous solution. This study links the quantum level to thermodynamics by providing statistical mechanics information.

    4. Interaction of aromatic units of amino acids with guanidinium cation: The interplay of π···π, X[BOND]H···π, and M+···π contacts (pages 1290–1301)

      Alba Campo-Cacharrón, Enrique M. Cabaleiro-Lago, Jorge A. Carrazana-García and Jesús Rodríguez-Otero

      Article first published online: 25 APR 2014 | DOI: 10.1002/jcc.23623

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      An analysis of the interaction on ternary systems formed by a guanidinium cation and two aromatic species among benzene, phenol, and indole shows that the interaction is dominated by the strength of the cation···π contacts with a given aromatic molecule. Nonadditive effects are only relevant in complexes with the two aromatic units coordinated to guanidinium (anticooperative) and for structures where X[BOND]H···π hydrogen bonds are formed (cooperative).

    5. Ab initio path-integral calculations of kinetic and equilibrium isotope effects on base-catalyzed RNA transphosphorylation models (pages 1302–1316)

      Kin-Yiu Wong, Yuqing Xu and Darrin M. York

      Article first published online: 20 MAY 2014 | DOI: 10.1002/jcc.23628

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      There is a wide range of applications and implications of RNA catalysis, from new biotechnologies to the evolutionary origin of life. A comprehensive study in comparing various levels of theory in isotope-effect calculations on RNA catalysis is desired. This article reports isotope-effect results from a total of eight levels of electronic-structure calculations, including a “gold standard” coupled-cluster theory [CCSD(T)]. A new ab initio path-integral method is also used to compute the anharmonic and tunneling-effect contributions.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Efficient 3D kinetic monte carlo method for modeling of molecular structure and dynamics (pages 1317–1329)

      Mikhail Panshenskov, Ilia A. Solov'yov and Andrey V. Solov'yov

      Article first published online: 22 APR 2014 | DOI: 10.1002/jcc.23613

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      An efficient Monte Carlo extension of a computational suite MBN EXPLORER is developed for the study of self-assembly phenomena in systems of increasing complexity. Among morphologies of various objects in nature, fractal shapes are of key interest. Because of their surface for three-dimensional (3D) structures, or perimeter for 2D structures, they present important possibilities for interaction with the environment. This paper introduces algorithms of the code for the study of silver fractal formation on a graphite surface.

    2. The READY program: Building a global potential energy surface and reactive dynamic simulations for the hydrogen combustion (pages 1330–1337)

      César Mogo and João Brandão

      Article first published online: 24 APR 2014 | DOI: 10.1002/jcc.23621

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      READY is a program for the study of reactive dynamic systems. Starting from existing potential energy surfaces for each of the most important elementary reactions present in the system and from intermolecular forces, READY constructs a global potential to integrate the equations of motion. This is applied to the combustion dynamics of a mixture of hydrogen and oxygen, using accurate potential energy surfaces for all systems involving up to four oxygen and hydrogen atoms.

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