Journal of Computational Chemistry

Cover image for Vol. 34 Issue 13

15 May 2013

Volume 34, Issue 13

Pages i–iv, 1083–1175

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software news and updates
    5. Software News and Updates
    1. You have free access to this content
      Cover Image, Volume 34, Issue 13 (pages i–ii)

      Article first published online: 9 APR 2013 | DOI: 10.1002/jcc.23301

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      The cover portrays the application of the metropolis Monte-Carlo method used by E. Iype, M. Hütter, A. P. J. Jansen, S. V. Nedea, and C. C. M. Rindt on page 1143 to scale-up DFT results to generate an MD reactive force field (ReaxFF). The tedious optimization problem of finding the global minimum in a high dimensional parameter space, often encountered in force field optimization problems, can be solved efficiently by this approach. The stochastic nature of the algorithm enables one to determine the optimum values for the parameters even when one does not have a good starting point.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 13 (pages iii–iv)

      Article first published online: 9 APR 2013 | DOI: 10.1002/jcc.23302

      Thumbnail image of graphical abstract

      Program PHI is a new and powerful program created by Nicholas Chilton, Russell Anderson, Lincoln Turner, Alessandro Soncini, and Keith Murray from Monash and Melbourne Universities, Australia on page 1164. The program is used to fit and analyze magnetic susceptibility and magnetization data for wide ranges of d- and f-block molecular magnetic materials. The image shows typical plots together with contour maps that form part of the fitting routine.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software news and updates
    5. Software News and Updates
    1. Monte Carlo configuration interaction applied to multipole moments, ionization energies, and electron affinities (pages 1083–1093)

      Jeremy P. Coe, Daniel J. Taylor and Martin J. Paterson

      Article first published online: 19 JAN 2013 | DOI: 10.1002/jcc.23211

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      Monte Carlo configuration interaction (MCCI) is shown to be able to generally reproduce full configuration interaction (FCI) multipole moments for equilibrium or stretched geometries, and for ground or excited states using a small fraction of the states required for FCI. MCCI is also demonstrated to be a viable alternative for the calculation of ionization energies using a small fraction of the FCI space, while electron affinities seem more challenging for the method.

    2. Theoretical study of ionization and one-electron oxidation potentials of N-heterocyclic compounds (pages 1094–1100)

      Liudmyla K. Sviatenko, Leonid Gorb, Frances C. Hill and Jerzy Leszczynski

      Article first published online: 19 JAN 2013 | DOI: 10.1002/jcc.23228

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      A generally applicable protocol can successfully predict the gas-phase adiabatic ionization potentials of nitrogen-rich heterocyclic compounds and their standard oxidation potentials in acetonitrile.

    3. First principles study of gallium-cleaning for hydrogen-contaminated α-Al2O3(0001) surfaces (pages 1101–1111)

      Rui Yang and Alistair P. Rendell

      Article first published online: 5 FEB 2013 | DOI: 10.1002/jcc.23236

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      Substrate pretreatments, such as surface-cleaning, are essential for growing electronic device materials, such as group III-V nitride semiconductors. Gallium-cleaning has an advantage over traditional approaches because it avoids additional contaminates. This article considers gallium-cleaning of a hydrogen-contaminated Al2O3 surface at electronic and thermodynamic levels using a first principles simulation.

    4. A multiscale coarse-grained polarizable solvent model for handling long tail bulk electrostatics (pages 1112–1124)

      Michel Masella, Daniel Borgis and Philippe Cuniasse

      Article first published online: 5 FEB 2013 | DOI: 10.1002/jcc.23237

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      A coarse-grained multiscale scheme is proposed to account for long-range electrostatic effects in molecular simulations. This scheme is based on pseudoparticles of diverse sizes, allowing the modeling of a larger and larger portion of the solvent. Here, a protein is embedded in a solvent two-levels scheme. The green particle size corresponds to that of a water molecule, whereas the blue particle size corresponds to a volume comprising eight water molecules.

    5. Could an anisotropic molecular mechanics/dynamics potential account for sigma hole effects in the complexes of halogenated compounds? (pages 1125–1135)

      Krystel El Hage, Jean-Philip Piquemal, Zeina Hobaika, Richard G. Maroun and Nohad Gresh

      Article first published online: 5 FEB 2013 | DOI: 10.1002/jcc.23242

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      Halogenated compounds are gaining importance in medicinal chemistry and materials science. The multipolar contribution of anisotropic molecular mechanics potentials can reproduce the in- and out-of plane angular dependencies of the Coulomb contribution from quantum chemistry energy decomposition analyses, accounting for the impact of the “sigma hole” on the interaction energies without resorting to extraneous, fictitious, off-centered, partial atomic charges.

    6. Molecular dynamics study of DNA binding by INT-DBD under a polarized force field (pages 1136–1142)

      Xue X. Yao, Chang G. Ji, Dai Q. Xie and John Z.H. Zhang

      Article first published online: 5 FEB 2013 | DOI: 10.1002/jcc.23244

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      The combined use of a quantum-based, polarized, protein-specific charge (PPC) for protein and a polarized, nucleic, acid-specific charge (PNC) for DNA is employed in a molecular dynamics simulation to study the interaction dynamics between INTDBD and DNA. The protein-DNA structure is stabilized by polarization, and the calculated protein-DNA binding free energy is in good agreement with the experimental data. The image shows the structure of the INT-DBD-DNA binding complex, in which the secondary structure elements are labeled as L, loop; T, turn; and β, beta strand.

    7. Parameterization of a reactive force field using a Monte Carlo algorithm (pages 1143–1154)

      E. Iype, M. Hütter, A. P. J. Jansen, S. V. Nedea and C. C. M. Rindt

      Article first published online: 19 FEB 2013 | DOI: 10.1002/jcc.23246

      Thumbnail image of graphical abstract

      Parameterization of a reactive force field (ReaxFF) is performed using a robust Metropolis Monte Carlo algorithm for a system of magnesium sulfate hydrates. This new method for optimizing the force field is more efficient than the previous single parameter parabolic search method, especially when one does not have a good initial condition. The stochastic nature of the method enables one to arrive at the global minimum in the parameter space and thereby the best obtainable force field.

  3. Software news and updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software news and updates
    5. Software News and Updates
    1. QMX: A versatile environment for hybrid calculations applied to the grafting of Al2Cl3Me3 on a silica surface (pages 1155–1163)

      Torsten Kerber, Rachel Nathaniel Kerber, Xavier Rozanska, Philippe Sautet and Paul Fleurat-Lessard

      Article first published online: 23 JAN 2013 | DOI: 10.1002/jcc.23225

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      Hybrid calculations with QMX: Just run it! This flexible tool makes it easy to couple (almost) any two computation methods to obtain accurate structures and energies for large systems.

  4. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software news and updates
    5. Software News and Updates
    1. PHI: A powerful new program for the analysis of anisotropic monomeric and exchange-coupled polynuclear d- and f-block complexes (pages 1164–1175)

      Nicholas F. Chilton, Russell P. Anderson, Lincoln D. Turner, Alessandro Soncini and Keith S. Murray

      Article first published online: 5 FEB 2013 | DOI: 10.1002/jcc.23234

      Thumbnail image of graphical abstract

      A new and extensively parallelized code for the calculation of the magnetic properties of large spin systems or complex orbitally degenerate compounds is presented. The program can simulate theoretical systems or fit experimental data with a specific Hamiltonian. PHI is much faster than other commonly employed codes, and its use is very intuitive and approachable for novice users.

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