Journal of Computational Chemistry

Cover image for Vol. 36 Issue 9

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. Fep1d: A script for the analysis of reaction coordinates

    Polina V. Banushkina and Sergei V. Krivov

    Article first published online: 25 FEB 2015 | DOI: 10.1002/jcc.23868

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    Multidimensional dynamical processes can be analyzed by projecting them onto one or few coordinates (collective variables). The dynamics is often described then as diffusion on a free energy landscape associated with the coordinates. Fep1d is a script which can be used to answer questions appearing during such an analysis. In particular, the determination of the associated free energy profile and the diffusion coefficient and establishing whether the used coordinate is optimal.

  2. Toward the complete range separation of non-hybrid exchange–correlation functional

    Bun Chan, Jong-Won Song, Yukio Kawashima and Kimihiko Hirao

    Article first published online: 25 FEB 2015 | DOI: 10.1002/jcc.23867

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    Range separation for the exchanged functional has contributed significantly to the advancement of DFT. A simple “Range-separated eXchange–Correlation” (RXC) scheme is used to divide a total exchange–correlation functional. For properties that are short-range in nature, the performance of the RXC-DFT protocol resembles that of the short-range component, and vice versa. The general RXC scheme can be easily implemented in computational chemistry software packages.

  3. An ab initio study of nuclear volume effects for isotope fractionations using two-component relativistic methods

    Keisuke Nemoto, Minori Abe, Junji Seino and Masahiko Hada

    Article first published online: 25 FEB 2015 | DOI: 10.1002/jcc.23858

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    Nuclear volume term is a main term in the chemical equilibrium constants of isotope fractionations with heavy-element isotopes. The nuclear volume term can be calculated by the four-component Dirac-Hartree-Fock method. In this work, various types of two-component quasi-relativistic methods are performed in an attempt to find alternatives to the time-consuming four-component method. One of the infinite-order Douglass-Kroll-Hess methods is found to be accurate, but 30 times faster than the four-component method.

  4. Estimating π binding energy of N-Heterocyclic carbenes: The role of polarization (pages 564–572)

    Elixabete Rezabal and Gilles Frison

    Article first published online: 24 FEB 2015 | DOI: 10.1002/jcc.23852

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    The π donor and acceptor properties of a wide set of N-heterocyclic carbenes are analysed using energy decomposition analysis tools. Different contributions to the π interactions, including intrafragment π polarization, could be identified and isolated, making it possible to correlate π donor and acceptor properties of NHCs to some of their electronic parameters.

  5. How does a hydrocarbon staple affect peptide hydrophobicity?

    Adelene Y. L. Sim and Chandra Verma

    Article first published online: 23 FEB 2015 | DOI: 10.1002/jcc.23859

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    Protein–peptide interfaces have nonuniform chemical properties and geometry, posing challenges to understanding the driving forces of hydrophobicity, particularly at atomic-level detail. The dynamics of water between an E3 ubiquitin ligase (MDM2) and peptides derived from the tumor suppressor protein p53 (including a hydrocarbon “stapled” one) are studied using molecular dynamics. The interdomain densities show two-state behavior, and the relative fraction of wet and dry states is used to compare the extent of hydrophobicity.