Journal of Computational Chemistry

Cover image for Vol. 34 Issue 2

15 January 2013

Volume 34, Issue 2

Pages i–iv, 77–161

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    1. You have free access to this content
      Cover Image, Volume 34, Issue 2 (pages i–ii)

      Article first published online: 4 DEC 2012 | DOI: 10.1002/jcc.23202

      Thumbnail image of graphical abstract

      The cover image shows the structure of methane hydrate, a form of water ice containing a large amount of methane within a crystal structure of water. Accurate description of hydrogen-bonding energies between water molecules and van der Waals interactions between guest molecules and host water cages is crucial for study of methane hydrates. On page 121, Yuan Liu, Jijun Zhao, Fengyu Li, and Zhongfang Chen assess the performance of a variety of exchange-correlation functionals and various basis sets in describing the non-covalent interactions in methane hydrates.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 2 (pages iii–iv)

      Article first published online: 4 DEC 2012 | DOI: 10.1002/jcc.23203

      Thumbnail image of graphical abstract

      As presented on page 149 by Kenta Yamada and Nobuaki Koga, a method to analyze intramolecular interaction energy is applied to an analysis of the P—O bonding in phosphine oxide in conjunction with a newly developed technique to interpret change in electronic structure upon the interaction. The inside cover picture demonstrates, as a result of the analysis, electron-transfer processes in sigma and pi spaces that reorganize the electronic structure with localized three lone pair orbitals on the O atom into the genuine electronic state and that play critical roles in the P—O bond formation.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    1. Very efficient search for nucleotide alignments (pages 77–82)

      Milan Randić

      Article first published online: 5 SEP 2012 | DOI: 10.1002/jcc.23105

      Thumbnail image of graphical abstract

      Nucleotide sequential labels recorded in nucleotide adjacency matrix are used to find local similarities of DNA sequences.

    2. GPGPU for orbital function evaluation with a new updating scheme (pages 83–94)

      Yutaka Uejima and Ryo Maezono

      Article first published online: 1 SEP 2012 | DOI: 10.1002/jcc.23106

      Thumbnail image of graphical abstract

      QMC electronic structure calculations are accelerated using GPGPU applied to solids [N = 216 (Si/2 × 2 × 2), 648 (TiO2/3 × 3 × 3), and 1536 (TiO2/4 × 4 × 4)]. 30.7 times faster evaluation is achieved by GPU compared with CPU, with a new quasisimultaneous scheme for Monte Carlo updating. The plot shows the computational time (ms) per a Monte Carlo step and corresponding acceleration factors depending on the system size. PbP stands for the conventional particle-by-particle updating scheme.

    3. A fast parallel clustering algorithm for molecular simulation trajectories (pages 95–104)

      Yutong Zhao, Fu Kit Sheong, Jian Sun, Pedro Sander and Xuhui Huang

      Article first published online: 20 SEP 2012 | DOI: 10.1002/jcc.23110

      Thumbnail image of graphical abstract

      A GPU-powered parallel k-centers algorithm is able to speedup the clustering of molecular dynamics simulation conformations by up to two orders of magnitude compared to the CPU implementation. For example, it is capable of grouping 250,000 conformations of the Maltose Binding Protein (∼370 residues) into 4000 clusters within 40 s. To achieve this, the code on the GPU is effectively parallelized and the triangle inequality of metric spaces is utilized.

    4. An analytical method for computing atomic contact areas in biomolecules (pages 105–120)

      Paul Mach and Patrice Koehl

      Article first published online: 10 SEP 2012 | DOI: 10.1002/jcc.23111

      Thumbnail image of graphical abstract

      The theory behind Ballcontact, a new program that measures analytically interatomic surface contacts between atoms in a biomolecule, is described. The performance of an environment free energy computed from these contact areas is assessed against a standard solvation free energy. The former outperforms the latter, thereby emphasizing the importance of taking into account the nonpolar contact areas as they complement the information represented by the accessible surface areas.

    5. Appropriate description of intermolecular interactions in the methane hydrates: An assessment of DFT methods (pages 121–131)

      Yuan Liu, Jijun Zhao, Fengyu Li and Zhongfang Chen

      Article first published online: 5 SEP 2012 | DOI: 10.1002/jcc.23112

      Thumbnail image of graphical abstract

      M06-2X and ωB97X-D combined with augcc- pVQZ basis set (either with or without BSSE correction) give rather accurate description of the EHB and EvdW in methane hydrate. However, using 6- 311++G(2d, 2p) basis set, B97-D without BSSE correction, M06-2X and ωB97X-D with or without BSSE correction are suffi- cient for describing the EHB and EvdW in methane hydrate. Considering both computational cost and accuracy, the recommendations are B97-D, M06-2X and ωB97X-D combined with 6-311++G(2d,2p) basis set without BSSE correction.

    6. A convective replica-exchange method for sampling new energy basins (pages 132–140)

      Yannick G. Spill, Guillaume Bouvier and Michael Nilges

      Article first published online: 7 SEP 2012 | DOI: 10.1002/jcc.23113

      Thumbnail image of graphical abstract

      Replica-exchange is a powerful simulation method for sampling protein energy landscapes. However, when tackling severely frustrated systems, this method might take a long time to reach equilibrium and find all free energy basins. Here, a simple modification of the exchange method is presented, in which one of the replicas steadily raises or lowers its temperature, while maintaining the correct equilibrium distributions. Results show that the proposed method is twice as fast as the standard method.

      Corrected by:

      Erratum: Erratum: A convective replica-exchange method for sampling new energy basins

      Vol. 34, Issue 18, 1609, Article first published online: 8 APR 2013

    7. An assessment of pure, hybrid, meta, and hybrid-meta GGA density functional theory methods for open-shell systems: The case of the nonheme iron enzyme 8R–LOX (pages 141–148)

      Eric A. C. Bushnell and James W. Gauld

      Article first published online: 5 SEP 2012 | DOI: 10.1002/jcc.23114

      Thumbnail image of graphical abstract

      The performance of a range of DFT functionals combined in a QM/MM approach is investigated in their ability to reliably provide geometries, electronic distributions and relative energies of a multi-centered open-shell mechanistic intermediate in the mechanism 8R–LOX. While the complex involves three open shell centers, the catalytically relevant arrangement of these electrons leads to the possibility of only having a quartet or sextet state.

    8. Variationally determined electronic states for the theoretical analysis of intramolecular interaction. II. Qualitative nature of the P[BOND]O bond in phosphine oxides (pages 149–161)

      Kenta Yamada and Nobuaki Koga

      Article first published online: 17 SEP 2012 | DOI: 10.1002/jcc.23118

      Thumbnail image of graphical abstract

      The nature of the P—O bond in phosphine oxides, which has been extensively studied, is reinvestigated with a recently developed method for analyzing various types of intramolecular interactions. This method provides a more suitable reference state with a target interaction deactivated than existing analysis methods. The results suggest two types of descriptions of the bond, depending on whether the dative P—O single bond is present or absent in the reference state.

SEARCH

SEARCH BY CITATION