Journal of Computational Chemistry

Cover image for Vol. 34 Issue 25

30 September 2013

Volume 34, Issue 25

Pages i–iv, 2135–2221

  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 34, Issue 25 (pages i–ii)

      Article first published online: 19 AUG 2013 | DOI: 10.1002/jcc.23425

      Thumbnail image of graphical abstract

      GTKDynamo is an open-source graphical interface that combines the molecular modeling program (pDynamo) with the PyMOL molecular visualizer, which enables the determination of reaction pathways in biological systems using hybrid quantum chemical/molecular mechanical (QC/MM) potentials. The cover shows a chemical reaction step of the dehalogenase enzyme performed with GTKDynamo by José Fernando R. Bachega et al. on page 2190. The electron density of the quantum chemical region is shown as a blue mesh.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 25 (pages iii–iv)

      Article first published online: 19 AUG 2013 | DOI: 10.1002/jcc.23426

      Thumbnail image of graphical abstract

      The cover gives examples of several main functions of GALAMOST [graphics processing unit (GPU)-accelerated large-scale molecular simulation toolkit] by You-Liang Zhu et al. on page 2197. The bottom left illustrates a self-assembled structure of a Janus particle. The upper left describes the chain-growth polymerization model, taking the chain growth from the outer surface of a ball as an example. The lower right describes that, with a hybrid particle-field molecular dynamics technique (MD-SCF), dipalmitoylphosphatidylcholine (DPPC) molecules in water can form a micelle. The center and upper right illustrate that, using the numerical potential method, the polystyrene polymer can be described at coarse-grained level.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data (pages 2135–2145)

      Jing Huang and Alexander D. MacKerell Jr

      Article first published online: 6 JUL 2013 | DOI: 10.1002/jcc.23354

      Thumbnail image of graphical abstract

      Protein structure and dynamics can be characterized on the atomistic level with both NMR experiments and molecular dynamics (MD) simulations. The ability of the CHARMM36 (C36) force field (FF) to reproduce various NMR observables using MD simulations is quantified. The studied NMR properties include backbone scalar couplings across hydrogen bonds, residual dipolar couplings (RDCs), and relaxation order parameters, as well as scalar couplings, RDCs, and order parameters for side-chain amino- and methyl-containing groups. The C36 FF leads to better correlation with experimental data compared to the CHARMM22/CMAP FF, suggesting the use of C36 in protein simulations.

    2. Evaluation of electrostatic descriptors for predicting crystalline density (pages 2146–2151)

      Betsy M. Rice and Edward F. C. Byrd

      Article first published online: 29 JUN 2013 | DOI: 10.1002/jcc.23369

      Thumbnail image of graphical abstract

      Statistical descriptors of features of electrostatic potentials mapped onto isosurfaces of electron densities of isolated molecules are used to provide corrections to crystalline density predictions of neutral and ionic molecular energetic materials. Correlations were established using 180 and 23 for neutral and ionic CHNO molecular systems, respectively. The quality of the methods was assessed through application to 38 neutral and 48 ionic compounds not used in the parameterization.

    3. Transition polarizability model of induced resonance Raman optical activity (pages 2152–2158)

      Shigeki Yamamoto and Petr Bouř

      Article first published online: 4 JUL 2013 | DOI: 10.1002/jcc.23370

      Thumbnail image of graphical abstract

      Induced resonance Raman optical activity (IRROA) appears to be a sensitive method to detect molecular chirality. To understand the phenomenon, a transition polarizability model was developed and combined with density functional computations. The model faithfully reproduces the high ROA/Raman intensity ratio and other characteristics observed experimentally in the camphor–europium complex.

    4. Comparison of treecodes for computing electrostatic potentials in charged particle systems with disjoint targets and sources (pages 2159–2167)

      Henry A. Boateng and Robert Krasny

      Article first published online: 5 JUL 2013 | DOI: 10.1002/jcc.23371

      Thumbnail image of graphical abstract

      Two alternative fast summation treecodes are described for computing electrostatic potentials in charged particle systems with disjoint targets and sources. The treecodes are compared with direct summation. Their accuracy, CPU run time, and memory usage are documented. The particle–cluster treecode is faster when the sources outnumber the targets, and conversely, the cluster–particle treecode is faster when the targets outnumber the sources.

    5. Auxiliary basis sets for density-fitting second-order Møller–Plesset perturbation theory: Weighted core-valence correlation consistent basis sets for the 4d elements Y–Pd (pages 2168–2177)

      J. Grant Hill

      Article first published online: 5 JUL 2013 | DOI: 10.1002/jcc.23372

      Thumbnail image of graphical abstract

      New auxiliary basis sets for use in density-fitted correlated electronic structure calculations are presented for the 4d elements Y–Pd. The sets are matched to the correlation-consistent (aug-)cc-pwCVnZ-;PP orbital basis sets and are shown to produce negligible errors for small-to-medium-sized transition metal complexes. Their use in explicitly correlated calculations is also validated and benchmarked, where impressive convergence toward the basis set limit is observed.

    6. Global optimization of parameters in the reactive force field ReaxFF for SiOH (pages 2178–2189)

      Henrik R. Larsson, Adri C. T. van Duin and Bernd Hartke

      Article first published online: 15 JUL 2013 | DOI: 10.1002/jcc.23382

      Thumbnail image of graphical abstract

      Chemical reactions can be described using reactive force fields. The challenge of fitting the reactive force field parameters to reference data has been addressed with global optimization using genetic algorithms. Without expert knowledge to guide the search, this results in superior agreement with the reference data. This contribution demonstrates this approach for molecules containing silicon, oxygen, and hydrogen atoms, employing ReaxFF.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. GTKDynamo: A PyMOL plug-in for QC/MM hybrid potential simulations (pages 2190–2196)

      José Fernando R. Bachega, Luís Fernando S. M. Timmers, Lucas Assirati, Leonardo R. Bachega, Martin J. Field and Troy Wymore

      Article first published online: 19 JUN 2013 | DOI: 10.1002/jcc.23346

      Thumbnail image of graphical abstract

      This article describes the implementation and the main capabilities of GTKDynamo, a general-purpose, open-source graphical interface that combines the molecular modeling program, pDynamo, with the molecular visualizer, PyMOL. The design of the interface places particular emphasis on facilitating the determination of reaction pathways in biological systems using hybrid quantum chemical/molecular mechanical (QC/MM) potentials.

    2. GALAMOST: GPU-accelerated large-scale molecular simulation toolkit (pages 2197–2211)

      You-Liang Zhu, Hong Liu, Zhan-Wei Li, Hu-Jun Qian, Giuseppe Milano and Zhong-Yuan Lu

      Article first published online: 27 JUN 2013 | DOI: 10.1002/jcc.23365

      Thumbnail image of graphical abstract

      A new molecular simulation toolkit composed of recently developed force fields and specified models is presented to study the self-assembly, phase transition, and other properties of polymeric systems at the mesoscopic scale by using the computational power of graphics processing units. The hierarchical self-assembly of soft anisotropic particles and the problems related to polymerization can be studied by corresponding models included in this toolkit.

    3. VinaMPI: Facilitating multiple receptor high-throughput virtual docking on high-performance computers (pages 2212–2221)

      Sally R. Ellingson, Jeremy C. Smith and Jerome Baudry

      Article first published online: 29 JUN 2013 | DOI: 10.1002/jcc.23367

      Thumbnail image of graphical abstract

      VinaMPI is an efficient parallelization of the program AutodockVina on supercomputing architectures that allows for massive ensemble docking (high number of target structures, high number of chemicals).

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