Journal of Computational Chemistry

Cover image for Vol. 34 Issue 21

5 August 2013

Volume 34, Issue 21

Pages i–iv, 1797–1879

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      Cover Image, Volume 34, Issue 21 (pages i–ii)

      Article first published online: 27 JUN 2013 | DOI: 10.1002/jcc.23378

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      The structural characterization of protein α-helices is an important topic in structural bioinformatics. Hischenhuber et al. on page 1862 present a new methodology, based on differential geometric parameters, that compares helices to each other and determines the relative spatial orientation between two helices. The whole methodology is implemented in an easy-to-use, opensource Matlab package. The cover illustrates the ruled surface between the two α-helices of the homodimeric X-ray structure of the proto-oncoprotein MafA in complex with DNA (Protein Data Bank accession code 4eot).

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      Inside Cover, Volume 34, Issue 21 (pages iii–iv)

      Article first published online: 27 JUN 2013 | DOI: 10.1002/jcc.23379

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      Knowledge about all possible transition and reaction pathways is important for the description of many processes, such as protein-folding and complex enzymatic reactions. A new algorithm is proposed by Christoph Grebner et al. on page 1810 to determine such transition routes. The energy minima in the perpendicular (n–1) dimensional hyperplane located between reactant and product states, as illustrated in the cover image, represent traces of possible reaction paths. These are ideal starting points for the identification of several transition routes and intermediate minima. The strength of the new approach is shown in the investigation of transition pathways for Ar12 and Ar13 clusters.

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    1. Low cost prediction of relative stabilities of hydrogen bonded complexes from atomic multipole moments for overly short intermolecular distances (pages 1797–1799)

      Wiktor Beker, Karol M. Langner, Edyta Dyguda-Kazimierowicz, Mikołaj Feliks and W. Andrzej Sokalski

      Article first published online: 21 MAY 2013 | DOI: 10.1002/jcc.23326

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      The relative stability of biologically relevant hydrogen bonded complexes with shortened distances can be better assessed by electrostatic multipole interactions than by ab initio methods.

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    1. Improved partition–expansion of two-center distributions involving slater functions (pages 1800–1809)

      Rafael López, Guillermo Ramírez, Ignacio Ema and Jaime Fernández Rico

      Article first published online: 24 MAY 2013 | DOI: 10.1002/jcc.23306

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      The calculation of the electronic structure of large systems is facilitated by expanding the two-center distributions in terms of one-center functions. The partition–expansion method is an alternative to the standard projection methods which yields a systematic procedure for improving the fit of two-center distributions in pairs of one-center expansions. The method does not require auxiliary basis sets for projection and it allows to attain accurate expansions at a reduced cost.

    2. PathOpt—A global transition state search approach: Outline of algorithm (pages 1810–1818)

      Christoph Grebner, Lukas P. Pason and Bernd Engels

      Article first published online: 4 MAY 2013 | DOI: 10.1002/jcc.23307

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      Knowledge about possible transition and reaction pathways is of utmost importance for the description of many processes like protein folding or complex enzymatic reactions. We propose a new algorithm based on a global optimization in a reduced phase space to locate possible transition states between reactants and products. Investigations for Ar12 and Ar13 underline the capability of the algorithm to find several reaction pathways in one shot.

    3. The Becke Fuzzy Cells Integration Scheme in the Amsterdam Density Functional Program Suite (pages 1819–1827)

      Mirko Franchini, Pierre Herman Theodoor Philipsen and Lucas Visscher

      Article first published online: 29 MAY 2013 | DOI: 10.1002/jcc.23323

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      Efficient numerical integration techniques are of key importance for Density Functional Theory (DFT) calculations. In this paper the performance of two popular integration schemes is compared for prototypical DFT applications. The concept of a locally dense grid is introduced as a simple way to improve the efficiency in applications to local molecular properties.

    4. XPS of oxygen atoms on Ag(111) and Ag(110) surfaces: Accurate study with SAC/SAC-CI combined with dipped adcluster model (pages 1828–1834)

      Atsushi Ishikawa and Hiroshi Nakatsuji

      Article first published online: 16 MAY 2013 | DOI: 10.1002/jcc.23324

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      O1s core-electron binding energies of electrophilic and nucleophilic oxygens important for olefin epoxidation on silver surface were investigated by the symmetry-adapted-cluster configuration-interaction (SAC-CI) method combined with the dipped adcluster model (DAM). The experimental information and our theoretical results indicate that Oelec is the atomic oxygen adsorbed on the fcc site of Ag(111) and that Onuc is the one on the reconstructed added-row site of Ag(110).

    5. Heuristic control of kinetic energy in dynamic reaction coordinate calculations (pages 1835–1841)

      Arnim Hellweg

      Article first published online: 23 MAY 2013 | DOI: 10.1002/jcc.23332

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      A heuristic control methodology of atomic kinetic energies in dynamic reaction coordinate calculations using fuzzy logic is proposed. Hereby, the minimum energy path between reactants and transition state can be studied in a computationally efficient way. A diversified test set of reactions has been collected to examine the performance of this approach.

    6. Internal-to-Cartesian back transformation of molecular geometry steps using high-order geometric derivatives (pages 1842–1849)

      Vladimir V. Rybkin, Ulf Ekström and Trygve Helgaker

      Article first published online: 23 MAY 2013 | DOI: 10.1002/jcc.23327

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      In chemical simulations and geometry optimization, it is often necessary to transform back and forth between Cartesian and internal atomic coordinates (bond lengths and angles). The internal to Cartesian transformation has typically been performed by successive linear approximations. This article presents a very high-order perturbative method that generates a continuous polynomial path, connecting initial and final molecular geometries. Implementation is made possible by the use of automatic differentiation techniques.

    7. Accuracy and tractability of a kriging model of intramolecular polarizable multipolar electrostatics and its application to histidine (pages 1850–1861)

      Shaun M. Kandathil, Timothy L. Fletcher, Yongna Yuan, Joshua Knowles and Paul L. A. Popelier

      Article first published online: 29 MAY 2013 | DOI: 10.1002/jcc.23333

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      Biomolecular modeling urgently needs a more accurate force field. Contemporary computing power enables the overhaul of standard architectures of polarisible electrostatics. We propose a novel method that captures, directly and accurately, how the multipole moments of an atom change with the positions of the atoms that surround it. Proof of concept is illustrated on an important amino acid: histidine.

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    1. You have full text access to this OnlineOpen article
      Differential geometric analysis of alterations in MH α-helices (pages 1862–1879)

      Birgit Hischenhuber, Hans Havlicek, Jelena Todoric, Sonja Höllrigl-Binder, Wolfgang Schreiner and Bernhard Knapp

      Article first published online: 24 MAY 2013 | DOI: 10.1002/jcc.23328

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      The structural characterization of the major histocompatibility complex α-helices in reaction to different loaded peptides and liganded T cell receptors is an essential step in understanding how very early T cell activation takes place. For this purpose, we introduce a new differential geometric methodology to characterize these helices in a structured and comparable way.

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