Journal of Computational Chemistry

Cover image for Vol. 36 Issue 11

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. Robustness in the fitting of molecular mechanics parameters

    Kenno Vanommeslaeghe, Mingjun Yang and Alexander D. MacKerell Jr.

    Article first published online: 31 MAR 2015 | DOI: 10.1002/jcc.23897

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    Automated methods for the parametrization of empirical force fields have attracted renewed interest of the community. However, the robustness issues associated with the often ill-conditioned nature of parameter optimization have been vastly underappreciated. This article discusses these issues and proposes a novel restraining scheme that mitigates ill-conditioned behavior in concerted Linear Least Squares fitting of bonded parameters in a continuous fashion and without affecting the quality of the results.

  2. You have full text access to this OnlineOpen article
    New ways to boost molecular dynamics simulations

    Elmar Krieger and Gert Vriend

    Article first published online: 30 MAR 2015 | DOI: 10.1002/jcc.23899

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    Molecular simulations with empirical force fields were originally a task for experts with huge computer clusters, but have nowadays become easily accessible for all interested scientists on their personal computers. The long simulation time scales needed to draw useful conclusions can be reached with faster hardware or faster software. This article concentrates on the latter and describes algorithms to speed up simulations, implemented in the molecular modeling program YASARA.

  3. From small fullerenes to the graphene limit: A harmonic force-field method for fullerenes and a comparison to density functional calculations for Goldberg–Coxeter fullerenes up to C980

    Lukas N. Wirz, Ralf Tonner, Andreas Hermann, Rebecca Sure and Peter Schwerdtfeger

    Article first published online: 26 MAR 2015 | DOI: 10.1002/jcc.23894

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    A general force field is introduced which works for all fullerene isomers. It leads to structures and zero-point vibrational energy contributions in very good agreement to more expensive quantum theoretical calculations. The graphene limit is well represented by the growth of Goldberg-Coxeter transforms of C20.

  4. Theoretical comparative studies on transport properties of pentacene, pentathienoacene, and 6,13-dichloropentacene

    Xu Zhang, Xiaodi Yang, Hua Geng, Guangjun Nan, Xingwen Sun, Jinyang Xi and Xin Xu

    Article first published online: 24 MAR 2015 | DOI: 10.1002/jcc.23870

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    The hole and electron transport properties are theoretically studied for pentacene, pentathienoacene and 6,13-dichloropentacene. A detailed comparative calculation is carried out to gain insights in the theoretical design of organic transport materials.

  5. Solvents effects on the mechanism of cellulose hydrolysis: A QM/MM study

    Claudia Loerbroks, Andreas Heimermann and Walter Thiel

    Article first published online: 21 MAR 2015 | DOI: 10.1002/jcc.23898

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    Acid hydrolysis of cellulose yields glucose. This process is investigated computationally in water using two cellulose models (cellobiose and a 40-unit glucose chain) and explicit solvation. Hydrogen bonding is found to have a large impact on the reaction mechanism and on the barriers to hydrolysis. The results are compared to those from to a previous study with implicit solvation.

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