Journal of Computational Chemistry

Cover image for Vol. 35 Issue 14

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

Impact Factor: 3.835

ISI Journal Citation Reports © Ranking: 2012: 34/152 (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. Surface electronic structure calculations using the MBJLDA potential: Application to Si(111)2 × 1

    Phillip V. Smith, Marian W. Radny and G. Ali Shah

    Article first published online: 22 APR 2014 | DOI: 10.1002/jcc.23615

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    A general procedure and justification for applying the MBJLDA exchange and correlation potential to the determination of the electronic structure of surfaces is presented. It is shown that this approach predicts an electronic structure for the Si(111)2 × 1 surface which is comparable in accuracy to that resulting from the GW approach, and generally more accurate than the results obtained using hybrid functionals, both of which are far more computationally demanding.

  2. Efficient 3D kinetic monte carlo method for modeling of molecular structure and dynamics

    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 was developed for studying self-assembly phenomena in systems of increasing complexity. Among morphologies of various objects which exist 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 to interaction with environment. The article introduces the algorithms of the code and employs it for studying silver fractal formation on graphite surface.

  3. WATsite: Hydration site prediction program with PyMOL interface

    Bingjie Hu and Markus A. Lill

    Article first published online: 22 APR 2014 | DOI: 10.1002/jcc.23616

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    WATsite identifies hydration sites from a molecular dynamics simulation trajectory and predicts the free energy profile of each hydration site. The results of WATsite can be displayed in PyMOL and be used to estimate the protein desolvation free energies for any bound or docked ligand.

  4. Transferable pseudoclassical electrons for aufbau of atomic ions

    Solen Ekesan, Seyit Kale and Judith Herzfeld

    Article first published online: 21 APR 2014 | DOI: 10.1002/jcc.23612

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    The development of force fields with explicit electrons is motivated by the computational difficulty of quantum simulations of chemical reactions. The present study demonstrates that context-independent, pairwise interactions are able to describe the aufbau of diverse elements, including Hund's rule, the energies of electron transfers between atoms, and the spatial disposition of electrons according to orbital hybridization. In effect, LEWIS• constitutes a pointillist approach to density functional theory, providing an efficient route to reactive simulations.

  5. On the induced-fit mechanism of substrate-enzyme binding structures of nylon-oligomer hydrolase

    Takeshi Baba, Ryuhei Harada, Masayoshi Nakano and Yasuteru Shigeta

    Article first published online: 21 APR 2014 | DOI: 10.1002/jcc.23614

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    Parallel cascade selection molecular dynamics (PaCS-MD) simulation method was applied to the investigation of the induced-fit motion upon the substrate binding of a nylon-oligomer hydrolase, NylB. Free energy change and barrier in relation to the induced-fit of the substrate are estimated the umbrella sampling with weighted histogram analyses method along reactive trajectories taken from PaCS-MD.

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