Journal of Computational Chemistry

Cover image for Vol. 36 Issue 25

September 30, 2015

Volume 36, Issue 25

Pages i–ii, 1859–1927

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      Cover Image, Volume 36, Issue 25 (pages i–ii)

      Article first published online: 27 AUG 2015 | DOI: 10.1002/jcc.24056

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      HIV-1 protease (PR) is a promising drug target for anti-HIV therapy. However, the susceptibility of PR to mutation has reduced the efficacy of protease inhibitors (PIs), such as indinavir, as a viable anti-HIV drug. On page 1885 (DOI: 10.1002/jcc.24020), Dawei Zhang and coworkers use molecular dynamics (MD) simulation with the inclusion of a polarization effect using a polarized protein-specific charge scheme to examine the effect of the I50V mutation on the binding affinity of PIs to HIV-1 PR. The mutation-induced affinity variations were calculated and significant agreement between the experiments and MD simulations was observed.

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    1. Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (FabI) (pages 1859–1873)

      Pin-Chih Su, Cheng-Chieh Tsai, Shahila Mehboob, Kirk E. Hevener and Michael E. Johnson

      Article first published online: 27 JUL 2015 | DOI: 10.1002/jcc.24011

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      Computation prediction on ligand-protein binding activities (Molecular Mechanics Poisson-Boltzmann surface area (MM-PBSA), and Quantum Mechanics/MM-Generalized Born surface area (QM/MM-GBSA)), has gained attention in the pharmaceutical community due to its efficiency and accuracy. However, the effect of radii sets, GB methods, QM Hamiltonians, sampling protocols, and simulation length on the MM-PBSA and QM/MM-GBSA performance has not been extensively studied. The article highlights the importance of these factors in the MM-PBSA and QM/MM-GBSA performance using the bacterial enoyl-ACP reductase and benzimidazole inhibitors as a test case.

    2. Transferability and additivity of dihedral parameters in polarizable and nonpolarizable empirical force fields (pages 1874–1884)

      Marie Zgarbová, Andreana M. Rosnik, F. Javier Luque, Carles Curutchet and Petr Jurečka

      Article first published online: 30 JUL 2015 | DOI: 10.1002/jcc.24012

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      Explicit inclusion of polarization in empirical force fields may improve transferability of dihedral angle parameters between molecules and different environments and also additivity of the dihedral terms in larger molecules. However, treatment of the short range polarization interactions between close neighbors, e.g. 1–2 and 1–3 interactions, seems to be crucial in achieving the desired effects.

    3. Understanding the basis of I50V-induced affinity decrease in HIV-1 protease via molecular dynamics simulations using polarized force field (pages 1885–1892)

      Rui Duan, Raudah Lazim and Dawei Zhang

      Article first published online: 22 JUL 2015 | DOI: 10.1002/jcc.24020

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      Polarization effects play a crucial role in the precise depiction of proteins in molecular dynamics (MD) simulations. In this study, MD simulations using a polarized force field were used to examine the effect of I50V mutation on the binding affinities of inhibitors to HIV-1 protease. The polarization effect was introduced using a polarized protein-specific charge scheme. The charges of complexes were derived using a newly proposed delta-RESP method to overcome the poorly determined charges of buried atoms. The calculated variations in mutation-induced affinities agreed well with the experiment.

    4. A new QM/MM method oriented to the study of ionic liquids (pages 1893–1901)

      M. Luz Sánchez, José C. Corchado, M. Elena Martín, Ignacio Fdez. Galván, Rute Barata-Morgado and Manuel A. Aguilar

      Article first published online: 24 JUL 2015 | DOI: 10.1002/jcc.24023

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      A new quantum mechanic/molecular mechanic method, related to the average solvent electrostatic potential/molecular dynamics methodology, is presented to the study of pure ionic liquids. The method permits, through an iterative procedure, the full coupling between the polarized charge distribution of the ions and the liquid structure around them. The procedure has been tested with 1-ethyl-3-methylimidazolium tetrafluoroborate.

    5. An enhanced Monte Carlo outlier detection method (pages 1902–1906)

      Liangxiao Zhang, Peiwu Li, Jin Mao, Fei Ma, Xiaoxia Ding and Qi Zhang

      Article first published online: 31 JUL 2015 | DOI: 10.1002/jcc.24026

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      An enhanced Monte Carlo outlier detection method is introduced by establishing cross-prediction models using determinate normal samples and analyzing the distribution of prediction errors individually for dubious samples.

    6. A topological assessment of the electronic structure of mesoionic compounds (pages 1907–1918)

      Italo Curvelo Anjos and Gerd Bruno Rocha

      Article first published online: 31 JUL 2015 | DOI: 10.1002/jcc.24027

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      Mesoionic compounds have been described as heterocyclic molecules with delocalized π-bonds and strong charge separation. Classical representations of these compounds place the positive and negative charges at well-defined regions. Topological calculations, however, show that neither the charge nor the π-delocalization are restricted to these specific regions. They both depend on the nature of the ring atoms and the substituent groups attached to them.

    7. Van der Waals Effects on semiconductor clusters (pages 1919–1927)

      Haisheng Li, Weiguang Chen, Xiaoyu Han, Liben Li, Qiang Sun, Zhengxiao Guo and Yu Jia

      Article first published online: 12 AUG 2015 | DOI: 10.1002/jcc.24028

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      The charge density of two Ge20 clusters along the bonds in normalized scale (with the bond center at zero), as well as the bond lengths, are shown. Different symbols and colors represent different bonds and methods, respectively. The vdW effects strengthen the covalent bond from different units more strikingly than that in a single unit. PBE-TS+SCS method may properly describe the vdW effects on semiconductor clusters.

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