Journal of Computational Chemistry

Cover image for Vol. 38 Issue 6

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

Impact Factor: 3.648

ISI Journal Citation Reports © Ranking: 2015: 41/163 (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. Evaluation of atomic pressure in the multiple time-step integration algorithm

    Yoshimichi Andoh, Noriyuki Yoshii, Atsushi Yamada and Susumu Okazaki

    Version of Record online: 20 JAN 2017 | DOI: 10.1002/jcc.24731

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    For molecular dynamics calculations, a series of equations to evaluate the atomic pressure in the RESPA multiple time-step (MTS) integration procedure are proposed on the basis of its equivalence to the Velocity-Verlet integration procedure with a single time step (STS). The atomic pressure calculated by our equations with the MTS integration shows excellent agreement with the reference value with the STS, whereas pressures calculated using the conventional ad hoc equations deviated from it.

  2. Global exploration of isomers and isomerization channels on the quantum chemical potential energy surface of H3CNO3

    Koichi Ohno, Naoki Kishimoto, Takeaki Iwamoto and Hiroko Satoh

    Version of Record online: 19 JAN 2017 | DOI: 10.1002/jcc.24732

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    Global exploration of isomers and isomerization channels was performed for H3CNO3 on the quantum chemical potential energy surface by means of a systematic automated method of the scaled hypersphere search-anharmonic downward distortion following technique to discover 678 equilibrium structures of various isomers with different conformations, 5181 transition structures on the elementary reaction channels, and 3619 dissociation channels indicating synthons, which demonstrates uncultivated chemical landscapes on the global reaction route map of H3CNO3.

  3. Evaluation of the hybrid resolution PACE model for the study of folding, insertion, and pore formation of membrane associated peptides

    Michael D. Ward, Shivangi Nangia and Eric R. May

    Version of Record online: 19 JAN 2017 | DOI: 10.1002/jcc.24694

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    The hybrid resolution PACE model has been applied to several well studied peptidemembrane systems. The simulations show that PACE provides a reasonably accurate model to study simple peptide topologies, such as single pass transmembrane helices. However, we find PACE does not maintain the native helical hairpin structure of the influenza hemagglutinin fusion peptide, which may be caused by an unfavorable electrostatic interaction in the model.

  4. Rigidity and flexibility in the tetrasaccharide linker of proteoglycans from atomic-resolution molecular simulation

    Cathy Ng, Padmavathy Nandha Premnath and Olgun Guvench

    Version of Record online: 19 JAN 2017 | DOI: 10.1002/jcc.24738

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    All-atom explicit-solvent molecular dynamics simulations show strong preferences for single conformations about glycosidic linkages between disaccharides in the proteoglycan linker tetrasaccharide. In contrast, the linkage between the first monosaccharide and the protein core, Xylβ1-O-Ser, shows significant flexibility with multiple likely conformations. The complete conjugate can be thought of as a mathematical vector, with the tetrasaccharide determining the length and the Xyl-Ser linkage the direction.

  5. Time-dependent density functional theory study on direction-dependent electron and hole transfer processes in molecular systems

    Pouya Partovi-Azar and Payam Kaghazchi

    Version of Record online: 19 JAN 2017 | DOI: 10.1002/jcc.24730

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    By means of real-time time-dependent density functional theory calculations, it is shown that time scale of electron transfer process in molecular crystal of α-sulfur, from a negatively charged S8 molecule to a neighboring neutral monomer is comparable to that of a strong infrared-active molecular vibrations of the dimer in transition state configuration with one negatively charged monomer. This results in a strong coupling between the electrons and the nuclei motion which eventually leads to stable open-ring structure of S8 molecule before the electron transfer process is completed. The similar infrared peak in the case of hole transfer, however, is shown to be very weak and hence no significant scattering by the nuclei is possible.

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