Journal of Computational Chemistry

Cover image for Vol. 35 Issue 30

Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner

Impact Factor: 3.601

ISI Journal Citation Reports © Ranking: 2013: 36/148 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

Associated Title(s): International Journal of Quantum Chemistry, Wiley Interdisciplinary Reviews: Computational Molecular Science

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Recently Published Articles

  1. Computing pKA values of hexa-aqua transition metal complexes

    Gegham Galstyan and Ernst-Walter Knapp

    Article first published online: 19 OCT 2014 | DOI: 10.1002/jcc.23764

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    Aqueous pKA values for hexa-aqua complexes of first and second row transition metals were computed using a combination of quantum chemical and electrostatic methods. Computed pKA values show very good agreement with measured pKA values with a root mean square deviation of 1 pH unit. Compared to previous approaches from the same lab, the precision of the method was systematically improved.

  2. A spherical harmonic transform spectral analysis of a localized surface plasmon on a gold nano shell (pages 2225–2230)

    Dan Berco and Chin-Kun Hu

    Article first published online: 18 OCT 2014 | DOI: 10.1002/jcc.23741

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    The localized surface plasmon (LSP) modes of a gold nano shell (AuNS) having a silica core by means of discrete dipole approximation (DDA) and spherical harmonics transform for selected wavelengths is studied. An efficient solution is demonstrated for the near and intermediate field terms by the dyadic green function approach and determine the optical extinction efficiency by the far field term. The advantages of a spectral analysis are combined with DDA flexibility to solve an arbitrary-shaped model and demonstrate the LSP dominant mode wavelength dependency.

  3. From orientation disordered to ordered—An ab initio simulation on ammonia borane phase transition within Van Der Waals corrections

    Qi Song, Zhenyi Jiang, Zhiyong Zhang, Yuqing Hou and Xiaodong Zhang

    Article first published online: 18 OCT 2014 | DOI: 10.1002/jcc.23762

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    The phase transition of ammonia borane (NH3BH3), from a tetragonal I4mm ( inline image) phase with disordered orientation of hydrogen to an orthorhombic phase with Pmn21 ( inline image) symmetry, is investigated as a function of temperature, based on density functional theory calculations with semi-empirical dispersion potential correction. A series of substructures are defined and the partially occupied high temperature state can be described as a continuous transformation between these substructures. The total energies with phonon spectrum of each substructure allow the minimal free energy structure at each temperature to be determined explicitly.

  4. Lightweight object oriented structure analysis: Tools for building tools to analyze molecular dynamics simulations

    Tod D. Romo, Nicholas Leioatts and Alan Grossfield

    Article first published online: 18 OCT 2014 | DOI: 10.1002/jcc.23753

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    LOOS is a software library designed to facilitate making novel tools for analyzing molecular dynamics simulations using C++ or Python. LOOS supports reading the native file formats of most common biomolecular simulation packages. A dynamic atom selection language is included and is easily accessible to the tool-writer. LOOS is bundled with over 140 tools. Through modern C++ design, LOOS is both simple to develop with and is easily extensible

  5. Scents and sense: In silico perspectives on olfactory receptors

    Charleen G. Don and Sereina Riniker

    Article first published online: 18 OCT 2014 | DOI: 10.1002/jcc.23757

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    G protein-coupled receptors (GPCRs) compose one of the largest protein membrane family in our body. These refined receptors have a critical function in many essential regulation pathways and thus are involved in several severe diseases. Therefore, many studies are focus to gain insight in their functioning. In this review, Olfactory receptors (ORs), the largest GPCR subfamily, are discussed with main focus on their structural characteristics and the computational techniques that can be used to broaden our current knowledge regarding both GPCRs-malfunctioning diseases and human odor perception.