Journal of Computational Chemistry

Cover image for Vol. 36 Issue 20

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

Impact Factor: 3.589

ISI Journal Citation Reports © Ranking: 2014: 36/157 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

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

Recently Published Issues

See all

JCCLinks

JCClinksAbout JCCJournal NewsSubmit a PaperKeyword CloudMost Accessed PapersImage Map

Recently Published Articles

  1. Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis

    Junchao Xia, William F. Flynn, Emilio Gallicchio, Bin W. Zhang, Peng He, Zhiqiang Tan and Ronald M. Levy

    Article first published online: 7 JUL 2015 | DOI: 10.1002/jcc.23996

    Thumbnail image of graphical abstract

    We present the ASyncRE methodology to perform large-scale replica exchange molecular dynamics (REMD) simulations asynchronously on grid computing networks consisting of heterogeneous and distributed computing environments as well as on homogeneous high-performance clusters, such as NSF XSEDE clusters and BOINC distributed computing networks at Temple University and Brooklyn College at CUNY. We also propose several ways to improve the efficiency of REMD simulations in the context of the ASyncRE methodology.

  2. A theoretical study of imine hydrocyanation catalyzed by halogen-bonding

    Norah Heinz, Michael Dolg and Albrecht Berkessel

    Article first published online: 7 JUL 2015 | DOI: 10.1002/jcc.23999

    Thumbnail image of graphical abstract

    A mechanistic description of an organocatalysis based on halogen-bonding: Possible reaction pathways of the hydrocyanation of an imine species catalyzed by C[DOUBLE BOND]N activation by four different monodentate halogen-bond donors. The mechanism is evaluated and discussed in detail at the level of scalar-relativistic gradient-corrected density functional theory.

  3. Atomic-resolution dissection of the energetics and mechanism of isomerization of hydrated ATP-Mg2+ through the SOMA string method

    Davide Branduardi, Fabrizio Marinelli and José D. Faraldo-Gómez

    Article first published online: 7 JUL 2015 | DOI: 10.1002/jcc.23991

    Thumbnail image of graphical abstract

    The mechanisms of isomerization of ATP-Mg2+ in solution are examined with three complementary enhanced-sampling simulation methods. The recently developed String Method with Optimal Molecular Alignment is used to identify and characterize the minimum free-energy paths for the major conformational transitions of the complex, in a 48-dimensional space. This analysis reveals the driving forces controlling these isomerization mechanisms at single-atom resolution.

  4. Orthogonal sampling in free-energy calculations of residue mutations in a tripeptide: TI versus λ-LEUS

    Noah S. Bieler and Philippe H. Hünenberger

    Article first published online: 7 JUL 2015 | DOI: 10.1002/jcc.23984

    Thumbnail image of graphical abstract

    λ-LEUS, a combination of λ-dynamics and local-elevation umbrella-sampling, is more efficient than thermodynamic integration, because the dynamical variation of the alchemical variable λ opens up pathways to circumvent barriers in the orthogonal space.

  5. Three-dimensional reference interaction site model self-consistent field analysis of solvent and substituent effects on the absorption spectra of Brooker's merocyanine

    Yuichi Tanaka, Norio Yoshida and Haruyuki Nakano

    Article first published online: 7 JUL 2015 | DOI: 10.1002/jcc.23980

    Thumbnail image of graphical abstract

    Using the three-dimensional reference interaction site model self-consistent field method, the origin of the solvent and substituent effects on the absorption spectra of Brooker's merocyanine are revealed at the molecular level. The analyses reveal that solvent effects are reduced because of the steric hindrance of the t-Bu groups and substituent effects are increased in high-polarity solvents.

SEARCH

SEARCH BY CITATION