Journal of Computational Chemistry

Cover image for Vol. 34 Issue 4

5 February 2013

Volume 34, Issue 4

Pages i–iv, 259–336

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. You have free access to this content
      Cover Image, Volume 34, Issue 4 (pages i–ii)

      Version of Record online: 15 JAN 2013 | DOI: 10.1002/jcc.23232

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      On page 311, Sheng-You Huang and Xiaoqin Zou present the development of a novel non-redundant, diverse benchmark dataset for protein–RNA docking and scoring, which is expected to benefit the development and improvement of docking and scoring algorithms for the docking community. The dataset is classified into three categories according to the interface RMSD and the percentage of native contacts in the unbound structures: 49 easy, 16 medium, and 7 difficult targets. The front cover shows the comparison of the bound and unbound structures of a target (PDB entry: 2FMT) in the benchmark, in which the bound/unbound conformations of the protein are colored in magenta/cyan and the bound/unbound conformations of the RNA are colored in red/yellow.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 4 (pages iii–iv)

      Version of Record online: 15 JAN 2013 | DOI: 10.1002/jcc.23233

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      In the study by Łukasz Piȩkoś and Mariusz PawelPaweł Mitoraj on page 294, ab initio Car-Parrinello molecular dynamics simulations and static DFT calculations are performed to characterize ansa-bridged molybdocene complexes [(C5H4)2XMe2MoH3]+ for X = C, Si, Ge, Sn, and Pb. The bottom part of the cover presents the crucial role of the size of the ansa-bridge, XMe2, on the equilibrium of dihydrogen/hydride (H2/H) [LEFT RIGHT ARROW] trihydride (H3) for molybdocene complexes. The mechanism of breaking of dihydrogen is elucidated by deformation density channels (Δρi) originating from natural orbitals for chemical valence (NOCV) combined with an energy decomposition method (ETS). In the upper part of the image, subsequent dihydrogen bond activation is presented based on NOCVdeformation density channels.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Relations frequency hypermatrices in mutual, conditional, and joint entropy-based information indices (pages 259–274)

      Stephen J. Barigye, Yovani Marrero-Ponce, Yoan Martínez-López, Francisco Torrens, Luis Manuel Artiles-Martínez, Ricardo W. Pino-Urias and Oscar Martínez-Santiago

      Version of Record online: 26 SEP 2012 | DOI: 10.1002/jcc.23123

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      An extension of the duplex relations frequency matrix is presented, introducing for the first time the concept of a hypermatrix in mathematical chemistry. The hypermatrix representation explores the n-tuple participation frequencies of vertices in a set of connected subgraphs. Specifically, triple and quadruple participation frequencies are focused upon, generating triple and quadruple relations frequency matrices. These allow the mutual, conditional, and joint entropy- based information indices to be rede- fined in a generalized way.

    2. New basis sets for the evaluation of interaction-induced electric properties in hydrogen-bonded complexes (pages 275–283)

      Angelika Baranowska-Łączkowska, Berta Fernández and Robert Zaleśny

      Version of Record online: 20 SEP 2012 | DOI: 10.1002/jcc.23124

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      Interaction-induced electric properties, that is, dipole moment, polarizability, and first hyperpolarizability, are calculated within the CCSD(T) approximation using the recently developed LPol-ds basis set for linear CO—(HF)n and N2—(HF)n hydrogenbonded complexes containing up to eight hydrogen bonded units. The Møller-Plesset second-order perturbation theory and density functional theory results are compared with the CCSD(T) reference values.

    3. Comparison of two simulation methods to compute solvation free energies and partition coefficients (pages 284–293)

      Li Yang, Alauddin Ahmed and Stanley I. Sandler

      Version of Record online: 29 OCT 2012 | DOI: 10.1002/jcc.23127

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      Gibbs free energy calculations are computationally demanding. Many of the available molecular dynamics-based algorithms use multiple equilibrated configurations and production runs to calculate solvation free energy in a solvent. In contrast, expanded ensemble (EE) algorithm uses a single simulation assisted by automatically generated biasing factors. The efficiency of the conventional thermodynamic integration method is compared with the EE method.

    4. Theoretical description of dihydrogen/hydride and trihydride molybdocene complexes: An insight from static and molecular dynamics simulations (pages 294–304)

      Łukasz Piękoś and Mariusz Paweł Mitoraj

      Version of Record online: 26 SEP 2012 | DOI: 10.1002/jcc.23129

      Thumbnail image of graphical abstract

      Molybdenocene (d2) complexes containing bridged (XMe2) cyclopentadienyl ligands, [(C5H4)2XMe2MoH3]+ can exist in two conformations, dihydrogen/hydride (H2/H) and trihydride (H3). Based on the Car–Parinello molecular dynamics simulations, the size of bridging substituent (XMe2, X = C, Si, Ge, Sn, Pb) plays a crucial role in determining dihydrogen/hydride [RIGHTWARDS ARROW] trihydride equilibrium. In addition, ETS-NOCV and QTAIM bonding analyses are performed to understand the origin of dynamic behavior of these complexes.

    5. Electric field assisted oxygen removal from the basal plane of the graphitic material (pages 305–310)

      Hongguang Liu and Jin Yong Lee

      Version of Record online: 26 SEP 2012 | DOI: 10.1002/jcc.23131

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      The epoxy group on the graphene oxide plane is regarded as one of the most widely existing oxygen species. Other than the hydroxyl group, the epoxide is much more stable but chemically reactive in the nucleophilic reaction with the reducing agent, such as CO. Based on systematical simulations, it is found that the electric field can be utilized to perturb the stability of the epoxide and facilitate the CO-assisted oxygen removal from the carbon basal plane.

    6. A nonredundant structure dataset for benchmarking protein-RNA computational docking (pages 311–318)

      Sheng-You Huang and Xiaoqin Zou

      Version of Record online: 10 OCT 2012 | DOI: 10.1002/jcc.23149

      Thumbnail image of graphical abstract

      A novel non-redundant, diverse benchmark dataset is developed for protein-RNA docking and scoring. The dataset is classi- fied into three categories according to the interface RMSD and the percentage of native contacts in the unbound structures: 49 easy, 16 medium, and 7 difficult targets. The bound and unbound cases of the benchmark dataset are expected to bene- fit the development and improvement of docking and scoring algorithms for the docking community.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. You have free access to this content
      MDTRA: A molecular dynamics trajectory analyzer with a graphical user interface (pages 319–325)

      Alexander V. Popov, Yury N. Vorobjev and Dmitry O. Zharkov

      Version of Record online: 10 OCT 2012 | DOI: 10.1002/jcc.23135

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      Trajectory post-processing and analysis are vital parts of any molecular dynamics computational experiment. MDTRA, the new graphical, portable, open-source software, has been developed to facilitate these tasks. This article describes the main features of the program, provides an example of its use in a study of E. coli DNA repair enzyme Fpg, and discusses how MDTRA can be used in the analysis of other molecular dynamics simulations.

    2. CovalentDock: Automated covalent docking with parameterized covalent linkage energy estimation and molecular geometry constraints (pages 326–336)

      Xuchang Ouyang, Shuo Zhou, Chinh Tran To Su, Zemei Ge, Runtao Li and Chee Keong Kwoh

      Version of Record online: 4 OCT 2012 | DOI: 10.1002/jcc.23136

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      Covalent linkage formation is a very important mechanism for many covalent drugs to work. However, the existing computational tools do not account for this kind of important chemical event very well. In this article, a new covalent docking package, the CovalentDock, is presented with parameterized covalent linkage energy estimation and molecular geometry constraints for accurate and automated covalent docking.

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