Journal of Computational Chemistry

Cover image for Vol. 33 Issue 28

30 October 2012

Volume 33, Issue 28

Pages i–iv, 2211–2284

  1. Cover Image

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    4. Software News and Updates
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      Cover Image, Volume 33, Issue 28 (pages i–ii)

      Article first published online: 24 SEP 2012 | DOI: 10.1002/jcc.23140

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      The cover shows the discrepancy in the number of displacements between allatom models (top) and coarse-grained models (bottom). The work by An Ghysels, Benjamin T. Miller, Frank C. Pickard IV, and Bernard R. Brooks on page 2250 develops a methodology to derive “imploded” models from the all-atom representation, with the same amount of displacements as the coarse-grained model (middle figure).

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      Inside Cover, Volume 33, Issue 28 (pages iii–iv)

      Article first published online: 24 SEP 2012 | DOI: 10.1002/jcc.23141

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      The performance of the massive parallel version of CRYSTAL09 has been studied on different HPC architectures for mesoporous silica MCM-41, a system consisting of a large primitive cell (41 × 41 × 12 Å) with 579 atoms (H102O335Si142) and no point symmetry, as presented by Roberto Dovesi and colleagues on page 2276. MCM-41 is characterized by a long range ordered network of hexagonal pores and amorphous walls at short range. B3LYP/6-31G(d,p) full converged SCF plus gradient calculations on up to 1 × 1 × 10 MCM-41 supercells (5790 atoms) have been performed with up to 2048 cores on three different HPC architectures, showing that runs with up to 100000 AOs are now feasible.

  2. Full Papers

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    1. Transition state theory thermal rate constants and RRKM-based branching ratios for the N(2D) + CH4 reaction based on multi-sState and multi-reference Ab Initio calculations of interest for the titan's chemistry (pages 2211–2224)

      Chanda-Malis Ouk, Natalia Zvereva-Loëte, Yohann Scribano and Béatrice Bussery-Honvault

      Article first published online: 10 JUL 2012 | DOI: 10.1002/jcc.23054

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      Ab initio MRCI calculations including Davidson or Pople corrections have been conducted for the CH4 + N(2D) reaction. The influence of the electronic correlation into the energetics of the system is clearly demonstrated by the thermal rate constant evaluation and its temperature dependence by means of the transition state theory. This work applies to the nitrogen chemistry study of Titan's atmosphere.

    2. Evaluating nonpolarizable nucleic acid force fields: A systematic comparison of the nucleobases hydration free energies and chloroform-to-water partition coefficients (pages 2225–2232)

      Maarten G. Wolf and Gerrit Groenhof

      Article first published online: 10 JUL 2012 | DOI: 10.1002/jcc.23055

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      A systematic validation study of popular nucleic acid force fields used in classical molecular dynamics simulations is described. Up to now, most tests have focussed on structural properties. To extend the range of tested properties, the force fields' ability to reproduce hydration free energies and chloroform-to-water partition coefficients is analyzed. This information is important to decide what force field to use for nucleic acid/protein simulation as well as computational mutation analysis of nucleic acids.

    3. BLUF Hydrogen network dynamics and UV/Vis spectra: A combined molecular dynamics and quantum chemical study (pages 2233–2242)

      Jan P. Götze, Claudio Greco, Roland Mitrić, Vlasta Bonačić-Koutecký and Peter Saalfrank

      Article first published online: 5 JUL 2012 | DOI: 10.1002/jcc.23056

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      The signaling state structure of flavin-containing BLUF photoreceptors is still elusive due to conflicting structural data. An approach based on molecular dynamics and time-dependent density functional theory is presented, aiming at the dynamics and spectral influence of the hydrogen bonding network of different BLUF conformations. The resulting hydrogen bonding network differs from previous reports, likely due to methodological differences. The influence of the various hydrogen bonding networks on the calculated flavin spectrum remains small.

    4. Electron-pair density decomposition for core–valence separable systems (pages 2243–2249)

      Jian Wang, Yu Wang and Jesus M. Ugalde

      Article first published online: 9 JUL 2012 | DOI: 10.1002/jcc.23059

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      Analytical decomposition of the electron pair density in core-valence separable systems is derived. Both the core-core and core-valence pair densities can be expressed as functionals of 1-matrix in closed form, which leaves only the valence-valence part to be determined from the frozen-core type wave function. The decomposition allows analysis of the electron correlation in molecules, which is essentially that of the valence electrons.

    5. Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining (pages 2250–2275)

      An Ghysels, Benjamin T. Miller, Frank C. Pickard IV and Bernard R. Brooks

      Article first published online: 3 SEP 2012 | DOI: 10.1002/jcc.23076

      Thumbnail image of graphical abstract

      As a consequence of dimension reduction, the simplified models may yield normal mode vectors of different length, making a comparison by calculating their dot product impossible. This article first investigates a horizontal mapping procedure for the reduced Hessian techniques, which project out degrees of freedom. A vertical mapping procedure is then designed for the “implosion” of the all-atom Hessian to a coarse-grained scale. Finally, metrics that can distinguish between good and bad coarse-graining models are provided.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
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      A new massively parallel version of CRYSTAL for large systems on high performance computing architectures (pages 2276–2284)

      Roberto Orlando, Massimo Delle Piane, Ian J. Bush, Piero Ugliengo, Matteo Ferrabone and Roberto Dovesi

      Article first published online: 19 JUL 2012 | DOI: 10.1002/jcc.23072

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      Recent improvements in CRYSTAL, a periodic ab initio code that uses a Gaussian basis set, allow high parallel efficiency in terms of CPU time and memory requirements on high performance computing (HPC) architectures. Performance analysis shows that calculations based on B3LYP functional of systems with no symmetry containing up to 100,000 atomic orbitals and 8000 atoms are feasible on the most advanced HPC architectures using thousands of processors.

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