Journal of Computational Chemistry

Cover image for Vol. 36 Issue 15

June 5, 2015

Volume 36, Issue 15

Pages i–ii, 1103–1186

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      Cover Image, Volume 36, Issue 15 (pages i–ii)

      Article first published online: 27 APR 2015 | DOI: 10.1002/jcc.23940

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      The inaugural molecular docking program DOCK has a long history of new advances and accomplishments in the field of structure-based design. On page 1132 (DOI: 10.1002/jcc.23905), William Allen, Trent Balius, Sudipto Mukherjee, Scott Brozell, Demetri Moustakas, Therese Lang, David Case, Irwin Kuntz, and Robert Rizzo report and evaluate the latest algorithmic and methodological developments for the program using experiments that include pose reproduction, cross-docking, and database enrichment. The cover art shows family-based receptor alignments, heatmaps for cross-docking outcomes, and examples of docked results which account for symmetry-corrected RMSD.

  2. Full Papers

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    2. Cover Image
    3. Full Papers
    1. An anisotropic coarse-grained model based on Gay–Berne and electric multipole potentials and its application to simulate a DMPC bilayer in an implicit solvent model (pages 1103–1113)

      Hujun Shen, Yan Li, Peijun Xu, Xiaofang Li, Huiying Chu, Dinglin Zhang and Guohui Li

      Article first published online: 18 MAR 2015 | DOI: 10.1002/jcc.23895

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      The promising performance of an anisotropic coarse-grained model (so-called GBEMP) has been demonstrated in modeling a DMPC lipid bilayer. A 72-DMPC bilayer system was used for testing the performance of the GBEMP model, and it has shown a few important structural properties. In addition, the atomistic and experimental results for electron density profiles and order parameters can be reproduced reasonably well by this GBEMP model.

    2. Solvents effects on the mechanism of cellulose hydrolysis: A QM/MM study (pages 1114–1123)

      Claudia Loerbroks, Andreas Heimermann and Walter Thiel

      Article first published online: 21 MAR 2015 | DOI: 10.1002/jcc.23898

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      Acid hydrolysis of cellulose yields glucose. This process is investigated computationally in water using two cellulose models (cellobiose and a 40-unit glucose chain) and explicit solvation. Hydrogen bonding is found to have a large impact on the reaction mechanism and on the barriers to hydrolysis. The results are compared to those from to a previous study with implicit solvation.

    3. Toward assessment of density functionals for vibronic coupling in two-photon absorption: A case study of 4-nitroaniline (pages 1124–1131)

      Robert Zaleśny, Guangjun Tian, Christof Hättig, Wojciech Bartkowiak and Hans Ågren

      Article first published online: 31 MAR 2015 | DOI: 10.1002/jcc.23903

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      CC2 method and several exchange-correlation functionals are used to predict vibronic two-photon absorption spectra of 4-nitroaniline.

    4. DOCK 6: Impact of new features and current docking performance (pages 1132–1156)

      William J. Allen, Trent E. Balius, Sudipto Mukherjee, Scott R. Brozell, Demetri T. Moustakas, P. Therese Lang, David A. Case, Irwin D. Kuntz and Robert C. Rizzo

      Article first published online: 27 APR 2015 | DOI: 10.1002/jcc.23905

      Thumbnail image of graphical abstract

      DOCK is a structure-based design program developed over the past 30+ years. The current performance of DOCK version 6.7, made possible by new advances to the codebase, algorithmic updates, and optimized input parameters, is presented. The effectiveness of DOCK is demonstrated in pose reproduction, cross-docking (pictured), and enrichment experiments to systems that are of interest as drug targets. The current release is available for download at:

    5. Using bonding to guide transition state optimization (pages 1157–1166)

      Adam B. Birkholz and H. Bernhard Schlegel

      Article first published online: 2 APR 2015 | DOI: 10.1002/jcc.23910

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      Bonding information from the reactants and products is used to obtain a better initial guess of the transition state and to improve the efficiency of the transition state optimization.

    6. Bridging organometallics and quantum chemical topology: Understanding electronic relocalisation during palladium-catalyzed reductive elimination (pages 1167–1175)

      Benoit de Courcy, Etienne Derat and Jean-Philip Piquemal

      Article first published online: 21 APR 2015 | DOI: 10.1002/jcc.23911

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      The proposed computational strategy based on quantum topological analyses allows a deeper understanding of the interactions between the constitutive elements of a reactive organometallic complex. The coupled QTAIM/ELF partitioning used here is able to dissect the electronic rearrangement along a chemical pathway. This methodology was applied here to reinvestigate a classical process in organometallic chemistry, namely the reductive elimination and more specifically the one induced by palladium.

    7. Interaction potential models for bulk Zns, Zns nanoparticle, and Zns nanoparticle-PMMA from first-principles (pages 1176–1186)

      Sadanandam Namsani, Nisanth N. Nair and Jayant K. Singh

      Article first published online: 21 APR 2015 | DOI: 10.1002/jcc.23912

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      Interaction models for bulk ZnS, ZnS nanoparticles, and ZnS–PMMA systems have been developed using ab initio calculations. Molecular dynamics simulations using the derived empirical force-field show that PMMA and ZnS interact through Zn[BOND]O bond formation. The obtained radial distribution function for Zn[BOND]O is in good agreement with the density functional theory calculations.