Journal of Computational Chemistry

Cover image for Vol. 34 Issue 6

5 March 2013

Volume 34, Issue 6

Pages i–iv, 429–522

  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 6 (pages i–ii)

      Article first published online: 6 FEB 2013 | DOI: 10.1002/jcc.23252

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      Natural bond orbital lone pairs and antibonds participating in hydrogen bonds between biotin (magenta sticks) and the avidin binding pocket within the entire 8006-atom protein structure are treated quantum mechanically using linear-scaling density functional theory, as presented by Louis P. Lee, Daniel J. Cole, Mike C. Payne, and Chris-Kriton Skylaris on page 429. Natural bond orbital analysis can enhance information obtainable from simulations of such large systems by providing a decomposition of the electronic structure into chemical bonds and interactions between functional groups.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 6 (pages iii–iv)

      Article first published online: 6 FEB 2013 | DOI: 10.1002/jcc.23253

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      The cover shows how the segregation of atoms to the surface of the binary rare-gas cluster varies with both the atomic size ratio (vertical arrow, σBBAA) and the relative strength of the pair interactions (horizontal arrow, ϵBBAA); σBBAA = 1.0, 1.02, 1.04, 1.06, and 1.08, and ϵBBAA = 1.0, 1.15, 1.25, 1.35, and 1.45. The work by Jorge M. C. Marques and Francisco B. Pereira on page 505 employs an evolutionary algorithm to search for the global minimum structure of mixed Ar-Kr, Ar-Xe, and Kr-Xe clusters modeled with different potential functions. The influence of key features of the potential (e.g., σBBAA or ϵBBAA) on both structural and energetic properties of the clusters are assessed.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Natural bond orbital analysis in the ONETEP code: Applications to large protein systems (pages 429–444)

      Louis P. Lee, Daniel J. Cole, Mike C. Payne and Chris-Kriton Skylaris

      Article first published online: 15 OCT 2012 | DOI: 10.1002/jcc.23150

      Thumbnail image of graphical abstract

      Natural bond orbital lone pairs and antibonds participating in hydrogen bonds between biotin (magenta sticks) and the avidin binding pocket within the entire 8006-atom protein structure are treated quantum-mechanically using linear-scaling density functional theory. Natural bond orbital analysis can enhance information obtainable from simulations of such large systems by providing a decomposition of the electronic structure into chemical bonds and interactions between functional groups.

    2. GRID: A high-resolution protein structure refinement algorithm (pages 445–450)

      Mohsen Chitsaz and Stephen L. Mayo

      Article first published online: 14 OCT 2012 | DOI: 10.1002/jcc.23151

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      The energy-based refinement of protein structures to atomic-level accuracy remains a major challenge in structural biology. A new high-resolution refinement algorithm called GRID is developed that seeks to improve the energy of a structure using a move set that allows for backbone flexibility by sequentially perturbing φ and ψ angles and side-chain conformations of each of the residues. GRID achieves significantly better refinement with the same computational resources as a wellknown stochastic-based algorithm.

    3. Consistent Gaussian basis sets of triple-zeta valence with polarization quality for solid-state calculations (pages 451–459)

      Michael F. Peintinger, Daniel Vilela Oliveira and Thomas Bredow

      Article first published online: 31 OCT 2012 | DOI: 10.1002/jcc.23153

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      For molecular calculations, there is a vast variety of standard Gaussian basis sets of different quality levels available. This is not the case for solid-state calculations. Gaussian basis sets are optimized for the currently investigated system. In this article, a generally applicable, consistent triple-zeta valence with polarization quality basis set is presented for periodic quantum-chemical solid-state calculations.

    4. An economic prediction of refinement coefficients in wavelet-based adaptive methods for electron structure calculations (pages 460–465)

      János Pipek and Szilvia Nagy

      Article first published online: 31 OCT 2012 | DOI: 10.1002/jcc.23154

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      Wavelet expansion of the electronic wave functions offers a convenient method for starting with a coarse description of the system and including necessary details in a later phase of the calculations. The article describes an effective prediction algorithm for the next resolution level wavelet coefficients. The prediction results in a reasonable approximation of the wave function, and allows to sort out the unnecessary wavelets with a great reliability.

    5. Revealing noncovalent interactions in quantum crystallography: Taurine revisited (pages 466–470)

      Jack Yang and Mark P. Waller

      Article first published online: 29 OCT 2012 | DOI: 10.1002/jcc.23155

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      Noncovalent interactions (NCIs) in a molecular crystal of taurine are analyzed using the NCI theory. This leads to an intuitive visualization of NCIs in experimentally refined densities.

    6. Structure and spectroscopic aspects of water-halide ion clusters: A study based on a conjunction of stochastic and quantum chemical methods (pages 471–491)

      Soumya Ganguly Neogi and Pinaki Chaudhury

      Article first published online: 15 OCT 2012 | DOI: 10.1002/jcc.23156

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      The structures of (H2O)nX (X=Cl, Br, I) can show numerous local structures other than the global minimum. Stochastic optimization (genetic algorithm)-based study in conjunction with quantum chemical methods can reveal the correct structures (especially the preference for surface capped geometries as opposed to encapsulated geometry preferred by the smaller F ion) and hence the spectroscopic properties of these systems.

    7. Block-adaptive quantum mechanics: An adaptive divide-and-conquer approach to interactive quantum chemistry (pages 492–504)

      Maël Bosson, Sergei Grudinin and Stephane Redon

      Article first published online: 29 OCT 2012 | DOI: 10.1002/jcc.23157

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      Block-adaptive quantum mechanics (BAQM) is a new approach to interactive quantum chemistry. BAQM is based on a divide-and-conquer technique and constrains some nucleus positions and some electronic degrees of freedom on the fly to simplify the simulation. By applying this approach to the nonself-consistent atom superposition and electron delocalization molecular orbital theory, interactive rates and efficient virtual prototyping are demonstrated for systems containing more than a thousand atoms on a standard desktop computer.

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      Errata: Characterization of PDZ domain-peptide interaction interface based on energetic patterns

      Vol. 81, Issue 9, 1676, Article first published online: 23 AUG 2013

    8. A detailed investigation on the global minimum structures of mixed rare-gas clusters: Geometry, energetics, and site occupancy (pages 505–517)

      Jorge M. C. Marques and Francisco B. Pereira

      Article first published online: 29 OCT 2012 | DOI: 10.1002/jcc.23161

      Thumbnail image of graphical abstract

      Global minimum structures of mixed raregas clusters were discovered using an evolutionary algorithm. Core–shell structures are mostly observed for binary rare-gas clusters, but the long-range tail of the potential may have influence on the type of atoms that segregate on the surface. This study also reveals that the preferential site occupancy is mainly determined by the combination of the size ratio between unlike atoms and the minimum-energy ratio corresponding to the pairinteractions.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. STAAR: Statistical analysis of aromatic rings (pages 518–522)

      David D. Jenkins, Jason B. Harris, Elizabeth E. Howell, Robert J. Hinde and Jerome Baudry

      Article first published online: 31 OCT 2012 | DOI: 10.1002/jcc.23164

      Thumbnail image of graphical abstract

      Anion-π interactions are nonbonded interactions between negatively charged species and resonant functional groups. Such interactions are investigated between PHE and GLU or ASP side chains in proteins using the new program STAAR. These interactions are found to be common and of potentially strong energies in protein structures. This article describes the STAAR program and its web implementation and summarizes the results obtained in applying it to the protein data bank.

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