Journal of Computational Chemistry

Cover image for Vol. 36 Issue 1

January 5, 2015

Volume 36, Issue 1

Pages i–iv, 1–67

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. You have free access to this content
      Cover Image, Volume 36, Issue 1 (pages i–ii)

      Article first published online: 22 NOV 2014 | DOI: 10.1002/jcc.23794

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      Coarse-grained models with short-ranged and anisotropic interactions have recently gained significant attention from the soft matter and biophysics community. The models are being increasingly used for the investigation of biological macromolecules, self-assembly processes, and for the synthesis of new materials. On page 1 (DOI: 10.1002/jcc.23763), Lorenzo Rovigatti, Petr Šulc, István Z. Reguly, and Flavio Romano, show that molecular dynamics simulations of these systems on GPUs can greatly benefit from an unconventional edge-based algorithm. The cover represents a sketch of the method for a system of patchy particles.

    2. You have free access to this content
      Cover Image, Volume 36, Issue 1 (pages iii–iv)

      Article first published online: 22 NOV 2014 | DOI: 10.1002/jcc.23795

      Thumbnail image of graphical abstract

      On page 49 (DOI: 10.1002/jcc.23771), Chengfei Yan and Xiaoqin Zou describe a novel computational approach, ACCLUSTER, to predict peptide binding sites on protein surfaces by clustering chemical interactions. The method is assessed by diverse proteinpeptide complexes, yielding very good performance. The method does not involve any training database, and can be easily extended to other systems, such as RNA-peptide interactions, for which experimental structural data are insufficient for informatics-based modeling. The cover shows an example (pdb: 1CJF) in which ACCLUSTER correctly identifies the peptide binding site as the top prediction. The predicted sites ranked as numbers one, two, and three are colored red, green, and magenta, respectively.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. A comparison between parallelization approaches in molecular dynamics simulations on GPUs (pages 1–8)

      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. A comprehensive DFT investigation of bulk and low-index surfaces of ZrO2 polymorphs (pages 9–21)

      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, which include 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.

    3. From orientation disordered to ordered—An ab initio simulation on ammonia borane phase transition within van der Waals corrections (pages 22–32)

      Qi Song, Zhenyi Jiang, Zhiyong Zhang, Yuqing Hou and Xiaodong Zhang

      Article first published online: 18 OCT 2014 | DOI: 10.1002/jcc.23762

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      The phase transition of ammonia borane (NH3BH3), from a tetragonal I4mm ( inline image) phase with disordered orientation of hydrogen to an orthorhombic phase with Pmn21 ( inline image) symmetry, is investigated as a function of temperature, based on density functional theory calculations with semi-empirical dispersion potential correction. A series of substructures are defined and the partially occupied high temperature state can be described as a continuous transformation between these substructures. The total energies with phonon spectrum of each substructure allow the minimal free energy structure at each temperature to be determined explicitly.

    4. Prediction of the reduction potential of tris(2,2′-bipyridinyl)iron(III/II) derivatives (pages 33–41)

      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 position 3 or 6. The LUMO energy of the Fe(III) complex in solution has a linear relation with the predicted reduction potential.

    5. 1,2-migration in N-phosphano functionalized N-heterocyclic carbenes (pages 42–48)

      Andrey A. Kirilchuk, Aleksandr A. Yurchenko, Aleksandr N. Kostyuk and Alexander B. Rozhenko

      Article first published online: 3 NOV 2014 | DOI: 10.1002/jcc.23767

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      1,2-Phosphorus migration reaction in N-phosphano functionalized N-heterocyclic carbenes is investigated. The results show that the most appropriate mechanism is the three-center intramolecular pathway.

    6. Predicting peptide binding sites on protein surfaces by clustering chemical interactions (pages 49–61)

      Chengfei Yan and Xiaoqin Zou

      Article first published online: 3 NOV 2014 | DOI: 10.1002/jcc.23771

      Thumbnail image of graphical abstract

      A new computational method is developed to predict peptide binding sites on protein surfaces by clustering chemical interactions. The method has been assessed by diverse protein–peptide complexes and achieved encouraging performance in the identification of peptide binding sites. The method can also be used as an alternative for prediction of ligand binding pockets. The algorithm can be easily generalized to predict peptide-RNA binding sites.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Development and implementation of (Q)SAR modeling within the CHARMMing web-user interface (pages 62–67)

      Iwona E. Weidlich, Yuri Pevzner, Benjamin T. Miller, Igor V. Filippov, H. Lee Woodcock and Bernard R. Brooks

      Article first published online: 3 NOV 2014 | DOI: 10.1002/jcc.23765

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      An easy-to-use web tool to mine the PubChem BioAssay database and develop novel structure activity models based on modern machine learning approaches.

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