Journal of Computational Chemistry

Cover image for Vol. 35 Issue 8

30 March 2014

Volume 35, Issue 8

Pages i–vi, 595–681

  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 35, Issue 8 (pages i–ii)

      Version of Record online: 18 FEB 2014 | DOI: 10.1002/jcc.23566

      Thumbnail image of graphical abstract

      The cover illustrates the explicit proton transfer in classical molecular dynamics simulations. To simulate the proton transfer, Maarten Wolf and Gerrit Groenhof on page 657 introduce a newly developed hydrogen dynamics protocol, which combines λ dynamics with Monte Carlo. At regular time steps, Monte Carlo sampling is used to select a unique donor–acceptor pair. In the intervals between these selection steps, λ dynamics is used to model the dynamics of the proton transfer between the donor and the acceptor.

    2. You have free access to this content
      Cover Image, Volume 35, Issue 8 (pages iii–iv)

      Version of Record online: 18 FEB 2014 | DOI: 10.1002/jcc.23567

      Thumbnail image of graphical abstract

      Tryptophan, an essential amino acid, exists in a number of conformations and adopts cationic, anionic, and zwitterionic forms at various pH values. On page 595, Uppula Purushotham and G. Narahari Sastry report a comprehensive computational analysis using DFT, dispersion-corrected DFT, and MP2 methods, quantifying the role played by various noncovalent interactions that impart stability to tryptophan dimers. They also analyze dimers of tryptophan residues in Protein Data Bank (PDB) structures. The cover depicts the various ionic forms of tryptophan and selected orientations of tryptophan dimers obtained from the PDB.

    3. You have free access to this content
      Cover Image, Volume 35, Issue 8 (pages v–vi)

      Version of Record online: 18 FEB 2014 | DOI: 10.1002/jcc.23568

      Thumbnail image of graphical abstract

      On page 611, Elda Rossi et al. show the benefit of common data standards in view of the interoperability of quantum chemical and quantum dynamics codes. The cover represents the program interoperability across domains; the Q5cost and D5cost library system renders the data format and the tools to interconnect different resources, including electronic structure and molecular dynamics codes. The lower image is produced by the Avogadro program from a cube file obtained from a Q5cost file, and illustrates one of the two edge orbital isodensity surfaces of a linear beryllium chain.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. A comprehensive conformational analysis of tryptophan, its ionic and dimeric forms (pages 595–610)

      Uppula Purushotham and G. Narahari Sastry

      Version of Record online: 1 NOV 2013 | DOI: 10.1002/jcc.23482

      Thumbnail image of graphical abstract

      An exhaustive quantum mechanical analysis of tryptophan dimers and monomers is carried out. Protein Data Bank analysis of dimers reveals that stacked orientations are preferred at shorter centroid-to-centroid distances, while T-shaped orientations are preferred at longer distances.

    2. Code interoperability and standard data formats in quantum chemistry and quantum dynamics: The Q5/D5Cost data model (pages 611–621)

      Elda Rossi, Stefano Evangelisti, Antonio Laganà, Antonio Monari, Sergio Rampino, Marco Verdicchio, Kim K. Baldridge, Gian Luigi Bendazzoli, Stefano Borini, Renzo Cimiraglia, Celestino Angeli, Peter Kallay, Hans P. Lüthi, Kenneth Ruud, José Sanchez-Marin, Anthony Scemama, Peter G. Szalay and Attila Tajti

      Version of Record online: 28 NOV 2013 | DOI: 10.1002/jcc.23492

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      Given today's computing infrastructure, which includes distributed services and cloud computing, the ability of application programs to communicate (interoperate) with each other is increasingly important in quantum chemical modeling and simulations. However, a strong de facto standard for (exchange-)data formats is still missing. This article presents one possible solution (Q5/D5Cost) that allows the integration of programs representing a wide spectrum of applications (electronic structure calculation, molecular dynamics, and post processing/visualization) into one workflow.

    3. A general, recursive, and open-ended response code (pages 622–633)

      Magnus Ringholm, Dan Jonsson and Kenneth Ruud

      Version of Record online: 5 FEB 2014 | DOI: 10.1002/jcc.23533

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      Recursive routines are used to calculate molecular properties analytically in an open-ended fashion. Calculations of the third geometrical derivatives of the second hyperpolarizability for the HSOH molecule are presented.

    4. New accurate benchmark energies for large water clusters: DFT is better than expected (pages 634–643)

      Tony Anacker and Joachim Friedrich

      Version of Record online: 30 JAN 2014 | DOI: 10.1002/jcc.23539

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      An incremental scheme is used to compute benchmark energies at the CCSD(T) (coupled-cluster with single, double, and perturbative triple excitations) level of theory. The four structures—dodecahedron, edge-sharing, face-sharing, and fused cubes—are part of the WATER27 test set and require highly accurate interaction energies. All methods applied in this work lead to new benchmark energies for these four systems. These new benchmarks are used for different density functionals.

    5. SSThread: Template-free protein structure prediction by threading pairs of contacting secondary structures followed by assembly of overlapping pairs (pages 644–656)

      Kevin J. Maurice

      Version of Record online: 12 FEB 2014 | DOI: 10.1002/jcc.23543

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      SSThread, a new template-free protein structure prediction algorithm, is developed. This algorithm predicts contacting pairs of α-helices and β-strands derived from a database of experimental structures by using a knowledge-based potential, secondary structure prediction, and contact map prediction, followed by the assembly of overlapping pair predictions in order to create an ensemble of core structure predictions. SSThread compares well to the best template-free methods, especially for cases with β-strand content and a high relative contact order.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Explicit proton transfer in classical molecular dynamics simulations (pages 657–671)

      Maarten G. Wolf and Gerrit Groenhof

      Version of Record online: 5 FEB 2014 | DOI: 10.1002/jcc.23536

      Thumbnail image of graphical abstract

      Hydrogen dynamics (HYDYN) is a method that allows explicit proton transfer in classical force field molecular dynamics simulations at thermodynamic equilibrium. HYDYN reproduces the characteristic properties of the excess proton in water, including the special pair dance, the continuous fluctuation between the limiting Eigen and Zundel complexes, and the water reorientation beyond the first solvation layer. Advantages of HYDYN with respect to existing methods are computational efficiency, microscopic reversibility, and easy parameterization for any force field.

    2. Voronota: A fast and reliable tool for computing the vertices of the Voronoi diagram of atomic balls (pages 672–681)

      Kliment Olechnovič and Česlovas Venclovas

      Version of Record online: 12 FEB 2014 | DOI: 10.1002/jcc.23538

      Thumbnail image of graphical abstract

      The Voronoi diagram of balls is a powerful tool for the analysis of macromolecular structures. Given a set of balls, where each ball stands for an atom, the presented software application, Voronota, finds quadruples of balls that have empty tangent spheres. The centers of these spheres correspond to the vertices of Voronoi cells of the set of balls. Voronota is especially suitable for processing three-dimensional structures of biological macromolecules, such as proteins and RNA.

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