Journal of Computational Chemistry

Cover image for Vol. 34 Issue 26

5 October 2013

Volume 34, Issue 26

Pages 2223–2312

  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 26 (pages i–ii)

      Version of Record online: 12 SEP 2013 | DOI: 10.1002/jcc.23431

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      The cover shows an artistic rendering of some of the results obtained through the application of the program grcarma by Panagiotis Koukos and Nicholas Glykos on page 2310. The background surface is a color representation of the variance–covariance matrix of LmbE, a homohexameric protein. The molecular model in the foreground shows a dimer of the same protein colored according to its atomic root mean squared fluctuations.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 26 (pages iii–iv)

      Version of Record online: 12 SEP 2013 | DOI: 10.1002/jcc.23432

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      The cover depicts a Stone–Wales (SW) defective single-walled carbon nanotube (SWNT) surrounded with several 1,3- dipoles such as azomethine ylide and nitrone. Using a two-layered ONIOM method by Tao Yang, Xiang Zhao, and Shigeru Nagase on page 2223, 1,3–dipolar cycloadditions of several 1,3-dipoles upon SW defective and defect-free SWNTs are systematically studied. Compared with defect-free SWNTs, the SW defective SWNTs exhibit the higher chemical reactivity. The larger the diameter of the SWNT, the lower chemical reactivity the SW defective SWNT shows.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. 1,3-Dipolar cycloadditions of Stone–Wales defective single-walled carbon nanotubes: A theoretical study (pages 2223–2232)

      Tao Yang, Xiang Zhao and Shigeru Nagase

      Version of Record online: 6 JUL 2013 | DOI: 10.1002/jcc.23368

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      In contrast to previous theoretical results, density functional theory calculations reveal that the Stone–Wales defect in armchair single-walled carbon nanotubes (SWNTs) displays higher thermodynamic and kinetic reactivity than the perfect bond in 1,3-dipolar cycloadditions. Small-diameter defective SWNTs are found to react more easily than large ones.

    2. A protocol to evaluate one electron redox potential for iron complexes (pages 2233–2241)

      Hyungjun Kim, Joungwon Park and Yoon Sup Lee

      Version of Record online: 19 JUL 2013 | DOI: 10.1002/jcc.23380

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      A new protocol to calculate the reduction potential of iron complexes is proposed. The correct ground spin state can be predicted by using spin state corrected basis sets for the metal atom and including the cavity creation energy. The spin state corrected basis sets also improve the calculated reduction potential. More refined results can be obtained by considering the charge of atoms on the molecular surface.

    3. Bonding analysis of planar hypercoordinate atoms via the generalized BLW-LOL (pages 2242–2248)

      Laetitia Bomble, Stephan N. Steinmann, Nancy Perez-Peralta, Gabriel Merino and Clemence Corminboeuf

      Version of Record online: 29 JUL 2013 | DOI: 10.1002/jcc.23383

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      The multicenter bonding pattern of hypercoordinate boron wheels series is revisited using the block-localized variant of the localized orbital locator function (BLW-LOL). The novel implementation of the BLW method combined with the LOL scalar field is not restricted to the analysis of the out-of-plane π-system, but can also provide a picture of the σ-radial delocalization. The analysis of the σ-framework in these boron wheels is in line with a cyclic rather than disk-type delocalization.

    4. GPU-accelerated molecular mechanics computations (pages 2249–2260)

      Athanasios Anthopoulos, Ian Grimstead and Andrea Brancale

      Version of Record online: 17 JUL 2013 | DOI: 10.1002/jcc.23384

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      The 2D scheme shows a load-balanced, cell-list-based decomposition aimed for the Cuda architecture. Supercells in the green borders consist of 256 atoms. Base dimensions are greater than rc (the cut-off), and r2b (where rc > rc) is the initial base dimension of each cell. Supercells are partitioned in eight 32-atom warp-groups, so cell-pair interactions become 8 × 8 warp-group pair interactions. Warp-group pairs whose bounding boxes are farther than the cut-off are eliminated, and warp-group intrinsic functions can be fully exploited.

    5. Bond detectors for molecular dynamics simulations, Part I: Hydrogen bonds (pages 2261–2269)

      Anna Stachowicz and Jacek Korchowiec

      Version of Record online: 23 JUL 2013 | DOI: 10.1002/jcc.23385

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      The influence of hydrogen bond formation on different charge sensitivities is investigated. The process of hydrogen bond formation is analyzed on ab initio classical trajectories (B3LYP/6-31G*) of different nucleobase pairs. Fukui function indices and polarization matrix elements are demonstrated to be good detectors of hydrogen bond formation.

    6. Ligand release mechanisms and channels in histone deacetylases (pages 2270–2283)

      Subha Kalyaanamoorthy and Yi-Ping Phoebe Chen

      Version of Record online: 27 JUL 2013 | DOI: 10.1002/jcc.23390

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      The investigation of molecular channels in histone deacetylase (HDAC) enzymes is important in the understanding of the structures and functionalities of these cancer targets. Molecular channels of HDAC3 and HDAC8 enzymes are reported using ligand unbinding simulations. This reveals the role of amino acid substitutions in governing the ligand access to these enzymes, which in turn aids the design of isoform-selective HDAC inhibitors.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. LIBEFP: A new parallel implementation of the effective fragment potential method as a portable software library (pages 2284–2292)

      Ilya A. Kaliman and Lyudmila V. Slipchenko

      Version of Record online: 15 JUL 2013 | DOI: 10.1002/jcc.23375

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      The effective fragment potential (EFP) method is a promising technique for performing simulations on extended molecular systems. A new, high-performance parallel implementation of the general EFP method in a form of a portable software library called LIBEFP is presented. The library can be integrated into various quantum chemistry packages, allowing a straightforward extension of unique electronic structure methodologies designed for accurate simulations in the gas phase to condensed phases via quantum mechanics/EFP.

    2. New implementation of high-level correlated methods using a general block tensor library for high-performance electronic structure calculations (pages 2293–2309)

      Evgeny Epifanovsky, Michael Wormit, Tomasz Kuś, Arie Landau, Dmitry Zuev, Kirill Khistyaev, Prashant Manohar, Ilya Kaliman, Andreas Dreuw and Anna I. Krylov

      Version of Record online: 10 JUL 2013 | DOI: 10.1002/jcc.23377

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      The software library provides a programming interface and efficient parallel computational kernels to perform general block tensor algebra. The primary application is many-body electronic structure methods, such as coupled-cluster and equation-of-motion theories. The library specializes in computing very large tensors using divide-and-conquer algorithms, while utilizing the resources of just one compute node.

    3. Grcarma: A fully automated task-oriented interface for the analysis of molecular dynamics trajectories (pages 2310–2312)

      Panagiotis I. Koukos and Nicholas M. Glykos

      Version of Record online: 15 JUL 2013 | DOI: 10.1002/jcc.23381

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      Grcarma is a computer program that fully automates an extensive set of tasks, simplifying the analysis of molecular dynamics trajectories of biological macromolecules, with an emphasis on dihedral and Cartesian principal component analyses.