Journal of Computational Chemistry

Cover image for Vol. 36 Issue 17

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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  1. Polarizable coarse-grained models for molecular dynamics simulation of liquid cyclohexane (pages 1311–1321)

    Oliwia M. Szklarczyk, Eirini Arvaniti and Wilfred F. van Gunsteren

    Article first published online: 27 MAY 2015 | DOI: 10.1002/jcc.23929

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    In this work, a polarizable coarse-grained (CG) force field for molecular dynamics simulations of liquid cyclohexane is reported. The polarizability of the compounds is introduced through the charge-on-spring or Drude's oscillator model. The model parameters were tested for structural, thermodynamic, dielectric, and dynamic properties. A good agreement with the experimental data for a large set of properties was obtained for two different CG models of cyclohexane.

  2. The origins of the directionality of noncovalent intermolecular interactions#

    Changwei Wang, Liangyu Guan, David Danovich, Sason Shaik and Yirong Mo

    Article first published online: 25 MAY 2015 | DOI: 10.1002/jcc.23946

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    The block-localized wavefunction method, which can derive hypothetical structures without the charge transfer effect and conduct intermolecular energy decomposition analysis, is used to probe the origins of the directionality of weak noncovalent bonds. While the overall steric energy exhibits certain angular dependency, in all cases the charge transfer exhibits the strongest directionality, suggesting that the linearity or near linearity of noncovalent bonds is largely governed by the charge-transfer interaction whose magnitude determines the bond covalency.

  3. Structure and stability of supramolecular crown ether complexes

    Kim Julia Hintze, Arne Lützen and Thomas Bredow

    Article first published online: 22 MAY 2015 | DOI: 10.1002/jcc.23950

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    A protocol for the efficient calculation of supramolecular binding affinities of crown ether derivatives with ammonium cations is presented. The performance of various density functionals and the MP2 method is investigated and the influence of dispersion interaction is analyzed. CCSD(T) binding energies extrapolated to the basis set limit served as internal reference.

  4. Conformational ensembles and sampled energy landscapes: Analysis and comparison (pages 1213–1231)

    Frédéric Cazals, Tom Dreyfus, Dorian Mazauric, Christine-Andrea Roth and Charles H. Robert

    Article first published online: 21 MAY 2015 | DOI: 10.1002/jcc.23913

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    The potential energy landscape (PEL) plays a fundamental role in understanding the meta-stable states of a system as well as transitions between them. Novel methods are presented for modeling a sampled PEL and its associated transition graph (including ruggedness), and for comparing two PELs obtained, for example, from two different simulation runs. Software tools implementing these methods are made available and should prove valuable wherever conformational ensembles and energy landscapes are used.

  5. Replica state exchange metadynamics for improving the convergence of free energy estimates

    Raimondas Galvelis and Yuji Sugita

    Article first published online: 19 MAY 2015 | DOI: 10.1002/jcc.23945

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    Metadynamics (MTD) is a powerful enhanced sampling method for systems with rugged energy landscapes. It constructs a bias potential in a collective variable (CV) space to overcome barriers between metastable states. In the bias-exchange MTD (BE-MTD), multiple replicas approximate the CV space by exchanging bias potentials (replica conditions). We propose the replica state exchange metadynamics (RSE-MTD), which use a more sophisticated replica-exchange scheme to improve the convergence of free energy for a given simulation time.

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