Journal of Computational Chemistry

Cover image for Vol. 35 Issue 31

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. A comparison between parallelization approaches in molecular dynamics simulations on GPUs

    Lorenzo Rovigatti, Petr Šulc, István Z. Reguly and Flavio Romano

    Article first published online: 30 OCT 2014 | DOI: 10.1002/jcc.23763

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    A comparison between two parallelization approaches to be used in molecular dynamics simulations on GPUs was performed. A more aggressive edge-based approach, where a thread is started per interaction, is compared to a more standard vertex-based approach where a thread is started per each particle. Three different potential interactions are tested. If the trend of increasing the number of computing units on GPUs is continued, the edge-based approach will become the best choice in an increasing number of cases.

  2. Prediction of the reduction potential of tris(2,2′-bipyridinyl)iron(III/II) derivatives

    Hyungjun Kim, Joungwon Park and Yoon Sup Lee

    Article first published online: 28 OCT 2014 | DOI: 10.1002/jcc.23766

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    The four kinds of functional groups—methoxy, methyl, chlorine atom, and cyanide—are disubstituted at the positions 3, 4, 5, and 6 of a tris(2,2-bipyridinyl)iron(III/II) redox couple in a symmetrical way. The quality of the prediction for the reduction potential are improved by optimizing the solute cavity size. High reduction potential is obtained by introducing the electron withdrawing groups at the position 3 or 6. The LUMO energy of Fe(III) complex in solution has the linear relation with the predicted reduction potential.

  3. Grid-based algorithm to search critical points, in the electron density, accelerated by graphics processing units (pages 2272–2278)

    Raymundo Hernández-Esparza, Sol-Milena Mejía-Chica, Andy D. Zapata-Escobar, Alfredo Guevara-García, Apolinar Martínez-Melchor, Julio-M. Hernández-Pérez, Rubicelia Vargas and Jorge Garza

    Article first published online: 25 OCT 2014 | DOI: 10.1002/jcc.23752

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    Grid-based methods are quite convenient to search for critical points on systems that exhibit non-nuclear attractors. However, these methods are computationally expensive. An efficient algorithm with good scaling on central processing units is proposed. The algorithm has better performance when implemented on graphics processing units (GPUs), even in GPUs not dedicated for high-performance computing.

  4. Molecular dynamics simulation of configurational ensembles compatible with experimental FRET efficiency data through a restraint on instantaneous FRET efficiencies

    Maria M. Reif and Chris Oostenbrink

    Article first published online: 22 OCT 2014 | DOI: 10.1002/jcc.23756

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    This work describes how a special restraint potential energy term can be used in molecular dynamics simulations of a system undergoing Förster resonance energy transfer (FRET) to bring the simulated FRET efficiency in agreement with the FRET efficiency measured in experiment. Thus, the methodology allows the generation of configurational ensembles that may not be accessible with unrestrained simulations, and thereby supports a meaningful interpretation of experimental FRET results in terms of the underlying molecular degrees of freedom (interchromophore distances and orientations).

  5. A comprehensive DFT investigation of bulk and low-index surfaces of ZrO2 polymorphs

    Chiara Ricca, Armelle Ringuedé, Michel Cassir, Carlo Adamo and Frederic Labat

    Article first published online: 21 OCT 2014 | DOI: 10.1002/jcc.23761

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    Zirconia is one of the most studied ceramic materials, because of the wide range of its technological applications, including Solid Oxide Fuel Cells (SOFCs). Indeed, yttria-stabilized zirconia is the most used electrolyte in high-temperature SOFC. Density functional theory (DFT) calculations are presented on the bulk structures of three ambient pressure polymorphs of zirconia. Calculations were carried out with different DFT models, from which a computational protocol is applied to selected low-index surfaces.

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