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. 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.

  2. “Solvent hydrogen-bond occlusion”: A new model of polar desolvation for biomolecular energetics

    Andrea Bazzoli and John Karanicolas

    Version of Record online: 20 MAR 2017 | DOI: 10.1002/jcc.24740

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    The “Solvent Hydrogen bond Occlusion” approach assigns desolvation free energies for individual polar groups, by evaluating the extent to which neighboring atoms prevent the polar group from engaging in hydrogen bonds with solvent. A single probe water molecule is considered, which can occupy grid points around the polar group of interest; the energetics on the grid reflect the preferred hydrogen bonding geometry for the polar atom of interest (color gradient). Neighboring atoms (shown in gray) sterically occlude the probe water from certain locations on the grid: by writing a partition function that sums over these grid points, we can explicitly evaluate the desolvation free energy due to these occluding atoms.

  3. Study of the cold charge transfer state separation at the TQ1/PC71BM interface

    Riccardo Volpi and Mathieu Linares

    Version of Record online: 20 MAR 2017 | DOI: 10.1002/jcc.24776

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    We study the charge transfer (CT) state separation at the interface between TQ1 polymer and PC71BM, two materials used in organic solar cells. With the CT state splitting diagram, we can determine the distribution of rates in function of the electric field for the separation of hole and electron at the interface and for their conduction in the bulk. Kinetic Monte Carlo simulations performed at interesting electric fields allow us to establish relationship between morphology and efficiency of the CT state splitting.

  4. Numerical interpretation of molecular surface field in dielectric modeling of solvation

    Changhao Wang, Li Xiao and Ray Luo

    Version of Record online: 20 MAR 2017 | DOI: 10.1002/jcc.24782

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    A semi-log plot of mean absolute errors of atomic dielectric boundary forces (kcal/mol-e-Å) versus grid spacing (tested from 1/16 Å to 1/2 Å) for a nucleic acid base pair with multiple surface field fitting methods: one-sided first-order (black circle), one-sided second-order (black square), two-sided first-order (red circle), two-sided second-order (red square), and finally, the approximated one-dimensional method (blue star). Our analysis shows that the efficient one-dimensional method achieves similar accuracy as the more expensive second-order method but with a fraction of the computational cost.

  5. Computational study of the reactivity of cytosine derivatives

    Jihène Jerbi and Michael Springborg

    Version of Record online: 20 MAR 2017 | DOI: 10.1002/jcc.24781

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    DNA demethylation can be both passive and active. The passive process is related to a dilution of the 5hmC during cell divisions, whereas the active process involves successive TET-mediated conversions of 5-hmC to 5-formyl-cytosine (5fC) and 5-carboxyl-cytosine (5caC), both of which can be transformed back to the unmodified cytosine through the base excision repair (BER) mechanism. The role of DNA demethylation in the development of cancer has been studied only little in the past. Therefore, a computational study is useful to identify relationships between reactivity and stability for the modified compounds to understand their biological functionalities

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