Journal of Computational Chemistry

Cover image for Vol. 38 Issue 13

Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner

Impact Factor: 3.648

ISI Journal Citation Reports © Ranking: 2015: 41/163 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

Associated Title(s): International Journal of Quantum Chemistry, Wiley Interdisciplinary Reviews: Computational Molecular Science

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  1. Regularized regression analysis of digitized molecular structures in organic reactions for quantification of steric effects

    Shigeru Yamaguchi, Takahiro Nishimura, Yuta Hibe, Masaki Nagai, Hirofumi Sato and Ian Johnston

    Version of Record online: 27 MAR 2017 | DOI: 10.1002/jcc.24791

    Thumbnail image of graphical abstract

    The performance of a regularized regression method, LASSO/Elastic Net, in obtaining information about the steric effects in organic reactions is examined. Important partial structures for the reactions are extracted and visualized from high-dimensional digitized molecular structures (the indicator field) using regularized regression. We compare the performance of the regularized regression analyses with those of classical PLS regression. Regularized regressions provide highly interpretable models that include less noise than those from PLS regression.

  2. Phage-like packing structures with mean field sequence dependence

    Christopher G. Myers and B. Montgomery Pettitt

    Version of Record online: 27 MAR 2017 | DOI: 10.1002/jcc.24727

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    DNA sequence determines the response to packing stress in some phages. Left is a purely elastic model and right is a mean field sequence model with structural defects determined by the nonlinear elastic response to sequence thermodynamics.

  3. Evaluation of the restricted virtual space approximation in the algebraic-diagrammatic construction scheme for the polarization propagator to speed-up excited-state calculations

    Chong Yang and Andreas Dreuw

    Version of Record online: 27 MAR 2017 | DOI: 10.1002/jcc.24794

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    Within the reduced virtual space (RVS) approximation a significant amount of energetically high-lying virtual orbitals are discarded speeding up excited-state calculations substantially. The applicability and limitations of the RVS approximation within the algebraic-diagrammatic construction (ADC) for the polarization propagator at second and third order are discussed. While RVS-ADC(2) turns out to be useful for ππ* excited states only, RVS-ADC(3) is more robust and applicable also for nπ* excited states.

  4. Photo absorption of p-coumaric acid in aqueous solution: RISM-SCF-SEDD theory approach

    Kenji Hirano, Hiroshi Nakano, Yoshihide Nakao, Hirofumi Sato and Shigeyoshi Sakaki

    Version of Record online: 27 MAR 2017 | DOI: 10.1002/jcc.24784

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    Photo absorption properties of p-coumaric acid, the chromophore of photoactive yellow protein, in aqueous solution were investigated based on a hybrid method of quantum chemistry and statistical mechanics for molecular liquids. The electronic structure and excited energy of the solvated chromophore are significantly changed from the isolated one.

  5. GPU accelerated implementation of NCI calculations using promolecular density

    Gaëtan Rubez, Jean-Matthieu Etancelin, Xavier Vigouroux, Michael Krajecki, Jean-Charles Boisson and Eric Hénon

    Version of Record online: 25 MAR 2017 | DOI: 10.1002/jcc.24786

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    Molecular interactions (noncovalent interactions [NCI]) are forces, either attractive or repulsive, between molecules. They are involved in important processes like boiling or crystallization or drug action. The NCI methodology provides a visual picture of these interactions from grid-based calculations relying on the electron density knowledge. A graphics processing unit (GPU) accelerated NCI algorithm is described that leads to a 39-fold speedup compared to an OpenMP parallel run with 16 CPU cores. The NCI GPU implementation is attractive in terms of runtime and energy efficiency.

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