Journal of Computational Chemistry

Cover image for Vol. 33 Issue 19

15 July 2012

Volume 33, Issue 19

Pages 1587–1644

  1. Full Papers

    1. Top of page
    2. Full Papers
    3. Software News and Updates
    4. Software News and Updates: Commentary
    1. The electronic spectra and the H-bonding pattern of the sulfur and selenium substituted guanines (pages 1587–1593)

      Jing Wang, Jiande Gu and Jerzy Leszczynski

      Version of Record online: 19 APR 2012 | DOI: 10.1002/jcc.22991

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      The substitution of oxygen of guanine with either sulfur or selenium results in pronounced red-shifts in the UV spectra. The analysis of the electron density deformation map reveals that both sulfur and selenium atoms are less conjugated with the purine ring as compared to the conjugation of oxygen in guanine. The energy separations between the bonding and anti-bonding orbitals in the substituted guanines are thus reduced, leading to the red-shift in the corresponding UV spectra.

    2. Ab initio study of the positronation of the CaO and SrO molecules including calculation of annihilation rates (pages 1594–1602)

      Robert J. Buenker and Heinz-Peter Liebermann

      Version of Record online: 20 APR 2012 | DOI: 10.1002/jcc.22992

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      Ab initio multireference configuration interaction (MRD-CI) calculations havebeen carried out to compute potential curves for electronic states of the CaO and SrO molecules and their positronic complexes. The positron affinity (PA) of the X1Σ+ ground states of both systems are found to lie in the 0.16–0.19 eV range. The variation of annihilation rates (AR) with bond distance is generally similar to what has been found earlier for the alkali monoxide series of positronic complexes.

    3. Stereoselection in the diels–alderase ribozyme: A molecular dynamics study (pages 1603–1614)

      Tomasz Bereźniak, Andres Jäschke, Jeremy C. Smith and Petra Imhof

      Version of Record online: 2 MAY 2012 | DOI: 10.1002/jcc.22993

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      The Diels–Alderase ribozyme catalyzes a [4 + 2] cycloaddition between small organic molecules, and can be used to synthesize only one product enantiomer. We examine stereoselection and substrate recognition in the ribozyme using molecular dynamics simulations. The results are consistent with a mechanism in which the maleimide binds first followed by the anthracene. The PMFs for anthracene binding are in quantitative agreement with the enantiomeric excess of the (R,R)-product.

    4. Empirical van der Waals corrections to solid-state density functional theory: Iodine and phosphorous containing molecular crystals (pages 1615–1622)

      John Kendrick, Frank J. J. Leusen and Marcus A. Neumann

      Version of Record online: 24 APR 2012 | DOI: 10.1002/jcc.22994

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      Parameters are derived for a molecular mechanics type dispersive correction to solid-state density functional theory calculations on molecular crystals containing iodine and phosphorous. The accuracy of the parameterization is assessed by optimizing the experimental structures of several additional phosphorous and iodine containing molecular crystals and by examining the relative stabilities of the known polymorphs of phosphorous pentoxide and the stabilities of different packings of an iodine containing molecular crystal, 2,9-bis(iodo)anthanthrone.

    5. Adsorption of metadiiodobenzene on Cu(110): A theoretical study (pages 1623–1631)

      Chiara Panosetti and Werner A. Hofer

      Version of Record online: 2 MAY 2012 | DOI: 10.1002/jcc.22998

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      We have modeled the adsorption of 1,3–diiodobenzene on Cu(1 1 0) by means of density functional theory. We have compared the adsorption energies of 23 possible physisorption arrangements, and we have simulated STM images for the four most stable configurations using the Tersoff-Hamann approach. We discuss the stability and relative probabilities of experimentally observing the different structures. We find that the adsorption induces small distortions in the adsorbate and in some cases an adsorption–induced symmetry breakdown occurs. Furthermore, we find evidence that the most stable arrangement is actually a bistable system with interesting symmetry properties.

  2. Software News and Updates

    1. Top of page
    2. Full Papers
    3. Software News and Updates
    4. Software News and Updates: Commentary
    1. You have free access to this content
      Pteros: Fast and easy to use open-source C++ library for molecular analysis (pages 1632–1636)

      Semen O. Yesylevskyy

      Version of Record online: 27 APR 2012 | DOI: 10.1002/jcc.22989

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      Modern in silico studies of biomolecular systems often require complex and computationally intensive analysis of molecular dynamics trajectories. There is a lack of fast and user-friendly libraries for molecular analysis for compiled programming languages, such as C++. An open-source Pteros library is introduced for this purpose. Pteros features parallel execution of analysis routines and shows very high performance. Pteros programming interface is very simple and intuitive while the source code is easily extendible.

    2. You have free access to this content
      Symmetrizer: Algorithmic determination of point groups in nearly symmetric molecules (pages 1637–1642)

      R. Jeffrey Largent, William F. Polik and J. R. Schmidt

      Version of Record online: 2 MAY 2012 | DOI: 10.1002/jcc.22995

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      Symmetrizer is an algorithm for identifying possible symmetry elements and point groups of a nearly symmetric molecule based on a user-adjustable tolerance and then symmetrizing the structure to a selected point group. Source code and executable binary are provided.

  3. Software News and Updates: Commentary

    1. Top of page
    2. Full Papers
    3. Software News and Updates
    4. Software News and Updates: Commentary
    1. You have free access to this content
      Comment on “a minimal implementation of the AMBER–GAUSSIAN interface for Ab Initio QM/MM-MD simulation” (pages 1643–1644)

      Benjamin P. Roberts, Gustavo M. Seabra, Adrian E. Roitberg, Kenneth M. Merz, Erik Deumens, Juan Torras and Samuel B. Trickey

      Version of Record online: 8 MAY 2012 | DOI: 10.1002/jcc.23003

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      In 2010, Okamoto et al. published their implementation of an Amber-GAUSSIAN interface which they compared and contrasted with PUPIL. In this response, we address several misconceptions about PUPIL which might arise from their article, and take the opportunity to clarify PUPIL's design philosophy and feature set.

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