Journal of Computational Chemistry

Cover image for Vol. 38 Issue 14

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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Recently Published Articles

  1. On the formation of smaller p-block endohedral fullerenes: Bonding analysis in the E@C20 (E = Si, Ge, Sn, Pb) series from relativistic DFT calculations

    Alvaro Muñoz-Castro and R. Bruce King

    Version of Record online: 20 APR 2017 | DOI: 10.1002/jcc.24809

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    The plausible encapsulation of main-group element in the smaller fullerene is evaluated, discussing electronic, bonding, and spectroscopic characteristics.

  2. Are induced fit protein conformational changes caused by ligand-binding predictable? A molecular dynamics investigation

    Cen Gao, Jeremy Desaphy and Michal Vieth

    Version of Record online: 16 APR 2017 | DOI: 10.1002/jcc.24714

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    Conventional MD was run on 39 apo structures (no ligand), and the resulting trajectories were compared to a set of 147 holo X-ray structures (ligand-bound). The simulation results did not perform better than using the normalized crystallographic structural factors as predictors of active-site rigid residues (87% predictive power) and mobile residues (47% predictive power). These results suggest potential issues in the use of unligated simulation frames directly for drug design applications such as ligand docking.

  3. A rapid solvent accessible surface area estimator for coarse grained molecular simulations

    Shuai Wei, Charles L. Brooks III and Aaron T. Frank

    Version of Record online: 16 APR 2017 | DOI: 10.1002/jcc.24709

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    A fast and straightforward method is developed that predicts residue-wise solvent accessible surface areas (SASAs) from inline image coordinates of protein structures. The method, Protein-Cinline imageSolvent Accessibilities or PCASA, should find utility as a tool for energetic and structural analysis of coarse-grained protein models. To ensure that the method was not biased toward native-like (folded) structures, PCASA is trained on a large dataset containing both folded and unfolded protein conformations. The resulting model is found to accurately recapitulate all-atom reference SASAs.

  4. Comparing the performance of TD-DFT and SAC-CI methods in the description of excited states potential energy surfaces: An excited state proton transfer reaction as case study (pages 1084–1092)

    Marika Savarese, Umberto Raucci, Ryoichi Fukuda, Carlo Adamo, Masahiro Ehara, Nadia Rega and Ilaria Ciofini

    Version of Record online: 13 APR 2017 | DOI: 10.1002/jcc.24780

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    The performances, in the description of excited state potential energy surfaces, of several density functional approximations representative of the currently most applied exchange correlation functionals’ families have been tested with respect to post Symmetry Adapted Cluster-Configuration Interaction results. An experimentally well-characterized intermolecular excited state proton transfer reaction has been considered as test case showing the delicate balance between solvent effects and electronic structure description needed for the correct recovering of excited states ordering.

  5. Density functional theory study of mechanism of epoxy-carboxylic acid curing reaction (pages 1093–1102)

    Uyen Q. Ly, My-Phuong Pham, Maurice J. Marks and Thanh N. Truong

    Version of Record online: 13 APR 2017 | DOI: 10.1002/jcc.24779

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    Epoxy-based polymers with an imperative set of physical properties has established billion-USD business whereas curing by carboxylic acid forms an important class of these materials. Despite its importance, fundamental understanding of its mechanism at the molecular level is rather limited. This study provides for the first time a full underlying atomistic detailed picture of epoxy-carboxylic acid curing reactions from first principles.

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