Journal of Computational Chemistry

Cover image for Vol. 33 Issue 27

15 October 2012

Volume 33, Issue 27

Pages i–iv, 2131–2210

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    5. Errata
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      Cover Image, Volume 33, Issue 27 (pages i–ii)

      Version of Record online: 20 SEP 2012 | DOI: 10.1002/jcc.23132

      Thumbnail image of graphical abstract

      XO stands for the extended ONIOM method, which allows overlapping layers and can be applied to problems that require a high-level calculation not only for the active site of a partial system, but also for the entire system. A metric called “force-error test” was introduced to guide the design of the appropriate XO model by Wenping Guo, Anan Wu, Igor Ying Zhang, and Xin Xu on page 2142. As shown on the cover, force errors (dark blue) are mainly distributed along the alpha-1,4 linkages if this cooperativity of hydrogen-bonds is broken during the fragmentation. Adding a “Hat” patch can greatly reduce the force errors, which guarantees a good description of the fully optimized geometry, total energy, and vibrational spectra of the whole system.

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      Inside Cover, Volume 33, Issue 27 (pages iii–iv)

      Version of Record online: 20 SEP 2012 | DOI: 10.1002/jcc.23133

      Thumbnail image of graphical abstract

      Non-planar trigonal molecular structures, arising from deviations from sp2 hybridization, need accurate definitions of non-planarity. The work by Sergey Gavrish on page 2173 shows that the degree of pyramidalization can be estimated adequately as a square root of the excess angle of 2π over the sum of all bond angles. In this figure, the ratio of pyramid height (zero for a perfectly flat structure) to the average bond length is shown as a function of changes in two of the bond lengths. The excess angle in this case is 15°, with exact (simplified) values depicted in green (magenta).

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    5. Errata
    1. Efficient compression of molecular dynamics trajectory files (pages 2131–2141)

      Patrick Marais, Julian Kenwood, Keegan Carruthers Smith, Michelle M. Kuttel and James Gain

      Version of Record online: 25 JUN 2012 | DOI: 10.1002/jcc.23050

      Thumbnail image of graphical abstract

      Efficient compression of molecular dynamics (MD) trajectory files is mandated by the massive increase in the size of MD simulation outputs. This article presents MD compression schemes that are fast, configurable with respect to accuracy, memory efficient, and significantly outperform benchmark applications.

    2. XO: An extended ONIOM method for accurate and efficient modeling of large systems (pages 2142–2160)

      Wenping Guo, Anan Wu, Igor Ying Zhang and Xin Xu

      Version of Record online: 5 JUL 2012 | DOI: 10.1002/jcc.23051

      Thumbnail image of graphical abstract

      XO is an extended ONIOM method, which surmounts the inherited limitations of the popular ONIOM method by introducing the inclusion-exclusion principle used in the fragmentation methods for accurate yet efficient calculations of large complex systems. The present work sets up general guidelines for the construction of a good XO scheme. In particular, force-error test is proposed to quantitatively validate the usefulness of an XO scheme, taking accuracy, efficiency, and scalability all into account.

    3. DNA base stacking: The stacked uracil/uracil and thymine/thymine minima (pages 2161–2172)

      Ruairidh S. Hunter and Tanja van Mourik

      Version of Record online: 25 JUN 2012 | DOI: 10.1002/jcc.23052

      Thumbnail image of graphical abstract

      The potential energy surfaces of stacked uracil dimer (U/U) and stacked thymine dimer (T/T) have been explored at the counterpoise-corrected M06-2X/6-31+G(d) level of theory, in the gas phase and in solution (with water and, for U/U, 1,4-dioxane as the solvents). Several of the minima and transition states are reported in the literature for the first time. The M06-2X results are in excellent agreement with CCSD(T)/CBS results, where available.

    4. Approximate expressions and the relationship between pyramidalization (out-of-plane deformation) characteristics of trigonal centers (pages 2173–2179)

      Sergey P. Gavrish

      Version of Record online: 27 JUN 2012 | DOI: 10.1002/jcc.23053

      Thumbnail image of graphical abstract

      The most essential information on non-planarity is accumulated in the deviation of the sum of bond angles around a trigonal center from 360°. The main contribution is proportional to the square-root of this difference and such quantity is proposed as a simple and versatile measure of pyramidalization.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    5. Errata
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      Expedited analysis of DFT outputs: Introducing moanalyzer (pages 2180–2185)

      Mario Ulises Delgado-Jaime and Serena DeBeer

      Version of Record online: 20 JUN 2012 | DOI: 10.1002/jcc.23028

      Thumbnail image of graphical abstract

      MOAnalyzer, a Matlab-based program, has been developed to facilitate the analysis of DFT output files from ORCA. The program allows the user to define fragments within a molecule and then provides information on the contribution of each fragment to the molecular orbitals based on the Loewdin population analysis. Correlations to spectroscopy (X-ray absorption and X-ray emission) are also obtained and the resulting information can be visualized as tables or MO diagrams.

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      MOVIPAC: Vibrational spectroscopy with a robust meta-program for massively parallel standard and inverse calculations (pages 2186–2198)

      Thomas Weymuth, Moritz P. Haag, Karin Kiewisch, Sandra Luber, Stephan Schenk, Christoph R. Jacob, Carmen Herrmann, Johannes Neugebauer and Markus Reiher

      Version of Record online: 20 JUN 2012 | DOI: 10.1002/jcc.23036

      Thumbnail image of graphical abstract

      The figure shows the molecular structure of a model π-helix together with its Raman Optical Activity spectrum, which is presented and analyzed in this work. The structure consists of 20 (S)-alanine residues, resulting in a total of 203 atoms. The spectrum was calculated in a massively parallel way with MOVIPAC.

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      Parallel-ProBiS: Fast parallel algorithm for local structural comparison of protein structures and binding sites (pages 2199–2203)

      Janez Konc, Matjaž Depolli, Roman Trobec, Kati Rozman and Dušanka Janežič

      Version of Record online: 20 JUN 2012 | DOI: 10.1002/jcc.23048

      Thumbnail image of graphical abstract

      The ProBiS (protein binding sites) algorithm (http://probis.cmm.ki.si) performs a local structural comparison of the query protein surface against the nonredundant database of protein structures. It finds proteins that have binding sites in common with the query protein. Here, a new parallelized algorithm, Parallel-ProBiS, is presented for detecting similar binding sites on clusters of computers. Source code of Parallel-ProBiS is available for download free for academic users at http://probis.cmm.ki.si/download.

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      OBGMX: A web-based generator of GROMACS topologies for molecular and periodic systems using the universal force field (pages 2204–2208)

      Giovanni Garberoglio

      Version of Record online: 20 JUN 2012 | DOI: 10.1002/jcc.23049

      Thumbnail image of graphical abstract

      OBGMX is a software tool for the automatic generation of GROMACS topologies according to the Universal Force Field. OBGMX can process both molecular and periodic systems.

  4. Errata

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    5. Errata
    1. You have free access to this content
      Erratum: Symmetrization of the AMBER and CHARMM force fields [J. Comp. Chem. 31, 1402] (page 2209)

      Edyta Małolepsza, Birgit Strodel, Mey Khalili, Semen Trygubenko, Szilard Fejer, Joanne M. Carr and David J. Wales

      Version of Record online: 27 JUL 2012 | DOI: 10.1002/jcc.23064

      This article corrects:

      Symmetrization of the AMBER and CHARMM force fields

      Vol. 31, Issue 7, 1402–1409, Version of Record online: 15 JAN 2010

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      Evaluation of protein-ligand binding free energy focused on its entropic components [J. Comp. Chem. 33, 550–560] (page 2210)

      Shuntaro Chiba, Yuichi Harano, Roland Roth, Masahiro Kinoshita and Minoru Sakurai

      Version of Record online: 2 AUG 2012 | DOI: 10.1002/jcc.23084

      This article corrects:

      Evaluation of protein-ligand binding free energy focused on its entropic components

      Vol. 33, Issue 5, 550–560, Version of Record online: 8 DEC 2011

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