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. 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.

  2. 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.

  3. Toward the understanding of the environmental effects on core ionizations

    Adèle D. Laurent, Vitaly N. Glushkov, Thibaut Very and Xavier Assfeld

    Article first published online: 18 APR 2014 | DOI: 10.1002/jcc.23604

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    A systematic methodology is used to evaluate core ionization energies of amino acids in the gas phase or in part of the human serum albumin protein. This is performed with the help of QM/MM tools and, more precisely, with the asymptotic projection formalism, accounting for orthogonality constraints between states. This work shows that environment effects are not trifling when computing core ionization energies, as they might be as large as 10 eV.

  4. All-atom polarizable force field for DNA based on the classical drude oscillator model

    Alexey Savelyev and Alexander D. MacKerell Jr.

    Article first published online: 18 APR 2014 | DOI: 10.1002/jcc.23611

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    The classical Drude oscillator model is used to incorporate electronic polarizability in a force field for DNA. Each polarizable (non-hydrogen) atom is supplemented with a Drude particle, which moves self consistently in the electric field, and, for hydrogen bond acceptors, lone-pair particles. Atomic polarizability is equivalent to the Drude charge, qD, divided by the force constant on the harmonic spring, kD, connecting the Drude particle and parent atom. Because of polarization effects the dipole moment of water is perturbed in the vicinity of DNA.

  5. Reactivity index based on orbital energies (pages 1093–1100)

    Takao Tsuneda and Raman K. Singh

    Article first published online: 17 APR 2014 | DOI: 10.1002/jcc.23599

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    Chemical reactivity depends on the orbital energy gap contributing to the reaction in the initial reaction process. This is because the small orbital energy gap gradient indicates the precursory charge transfer process, while the large gradient implies the initial structural transformation. Analyses using a normalized reaction diagram show that large orbital energy gap gradients are given for specific reactions, including several SN2 reactions, which are experimentally established to get around the optimum reaction pathways.