Journal of Computational Chemistry

Cover image for Vol. 35 Issue 4

5 February 2014

Volume 35, Issue 4

Pages i–iv, 271–341

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Rapid Communication
    4. Full Papers
    1. You have free access to this content
      Cover Image, Volume 35, Issue 4 (pages i–ii)

      Article first published online: 9 JAN 2014 | DOI: 10.1002/jcc.23527

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      The cover features a snapshot from a molecular dynamics simulation of an ionic fluid mixture. The four spherical particle species, shown here, exhibit strong asymmetry in their hard-core diameters and electric charges. The diameters of the small red and blue particles are exaggerated by a factor of 15 in the figures. The obtained results can be used to extract colloidal effective interaction potentials, including nonsaturated effective charge numbers, at a high-numerical efficiency. The method described by Marco Heinen, Elshad Allahyarov, and Hartmut Löwen on page 275 could be augmented to include colloidal surface chemistry in future projects.

    2. You have free access to this content
      Cover Image, Volume 35, Issue 4 (pages iii–iv)

      Article first published online: 9 JAN 2014 | DOI: 10.1002/jcc.23528

      Thumbnail image of graphical abstract

      On page 271, Taro Udagawa and Masanori Tachikawa perform the MP2 level of multicomponent molecular orbital (MCMO-MP2) calculations, which can take account of nuclear quantum nature, in order to analyze the H/D/T geometrical isotope effect (GIE) on NH3X+···YBeH (X,Y 5 H/D/T) dihydrogen-bonded systems. The cover shows a schematic illustration of the GIE of NH3H+···DBeH (HD) and NH3D+···HBeH (DH) dihydrogen-bonded systems. Although a proton is replaced with a deuteron in both systems, the dihydrogen-bond distance becomes shorter and longer in HD- and DH-species, respectively. These interesting geometrical changes are induced by the difference of the quantum nature between the proton and the deuteron.

  2. Rapid Communication

    1. Top of page
    2. Cover Image
    3. Rapid Communication
    4. Full Papers
    1. Why is N···Be distance of NH3H+···DBeH shorter than that of NH3D+···HBeH? paradoxical geometrical isotope effects for partially isotope-substituted dihydrogen-bonded isotopomers (pages 271–274)

      Taro Udagawa and Masanori Tachikawa

      Article first published online: 9 DEC 2013 | DOI: 10.1002/jcc.23505

      Thumbnail image of graphical abstract

      The geometrical isotope effect (GIE), which is induced by the isotope-substitution of hydrogen in dihydrogen-bonded NH3X+···YBeH (X, Y  =  H, D, and T) systems, is systematically analyzed using the ab initio multi-component molecular orbital method. Isotope effects of interaction energies and magnetic shieldings are also analyzed. The GIE of RN···Be can be explained by the cooperative effect of primary and secondary GIEs. The dihydrogen-bonded distance becomes shorter by heavier Y and lighter X isotope-substitution.

  3. Full Papers

    1. Top of page
    2. Cover Image
    3. Rapid Communication
    4. Full Papers
    1. Highly asymmetric electrolytes in the primitive model: Hypernetted chain solution in arbitrary spatial dimensions (pages 275–289)

      Marco Heinen, Elshad Allahyarov and Hartmut Löwen

      Article first published online: 9 OCT 2013 | DOI: 10.1002/jcc.23446

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      A numerically robust and efficient Fourier–Bessel transform technique is applied to solve liquid integral equations for ion pair correlations in electrolytes, in an arbitrary number of spatial dimensions. The method is applicable in very large ranges of ion size and charge asymmetries, including values that correspond to micrometer-sized charged colloidal particles in electrolytes of sub-nanometer-sized, monovalent microions. The accuracy of the approximate liquid integral equation predictions is investigated in comparison with numerically expensive molecular dynamics simulations.

    2. Algorithms for computer detection of symmetry elements in molecular systems (pages 290–299)

      Otávio Beruski and Luciano N. Vidal

      Article first published online: 25 NOV 2013 | DOI: 10.1002/jcc.23493

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      Knowledge of molecular symmetry is helpful in many areas of physics and chemistry, such as spectroscopy and computational chemistry, where symmetry exploitation has qualitative (e.g., selection rules) and quantitative (reduction of the active space) advantages. This article introduces a novel and intuitive approach to identifing symmetry elements in molecular systems based on the analysis of the inertia tensors of atoms that are interchanged by a symmetry operation.

    3. Multidimensional umbrella sampling and replica-exchange molecular dynamics simulations for structure prediction of transmembrane helix dimers (pages 300–308)

      Pai-Chi Li, Naoyuki Miyashita, Wonpil Im, Satoshi Ishido and Yuji Sugita

      Article first published online: 21 NOV 2013 | DOI: 10.1002/jcc.23494

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      To predict structures of transmembrane (TM) helix dimers, multidimensional umbrella sampling simulations are performed using the interhelical crossing angle and the TM–TM relative rotational angle as reaction coordinates. The results of the umbrella sampling as reference data are used to establish a reliable protocol of temperature replica-exchange molecular dynamics simulations for TM helix dimers.

    4. Are accurate computations of the 13C′ shielding feasible at the DFT level of theory? (pages 309–312)

      Jorge A. Vila, Yelena A. Arnautova, Osvaldo A. Martin and Harold A. Scheraga

      Article first published online: 3 DEC 2013 | DOI: 10.1002/jcc.23499

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      Accurate calculations of the 13C′ shielding are two orders of magnitude more demanding of CPU time than the computation of the 13Cα shielding and, hence, difficult to achieve in a reasonable amount of time. Recent progress in the development of a powerful new type of quantum computers opens a new venue to solve scientific problems. Consequently, the development of new and more accurate validation methods for protein structures may be possible in the near future.

    5. Multireference space without first solving the configuration interaction problem (pages 313–323)

      Vitaly N. Glushkov and Xavier Assfeld

      Article first published online: 3 DEC 2013 | DOI: 10.1002/jcc.23502

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      A method is presented for generating a compact multireference space for the ground and excited states without first solving the configuration interaction problem. The proposed scheme is applied to small molecules to illustrate and calibrate calculations. The expressions for the second-order corrections of many-body perturbation theory based on this multireference space keep the computational advantages of the genuine Møller–Plesset scheme.

    6. A combined semiempirical and DFT computational protocol for studying bioorganometallic complexes: Application to molybdocene–cysteine complexes (pages 324–334)

      Dimas Suárez, Natalia Díaz and Ramón López

      Article first published online: 2 DEC 2013 | DOI: 10.1002/jcc.23503

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      The presence of multi-hapto or σ/π metal–ligand bonding still precludes the direct application of either pure MM or hybrid QM-MM methods to study the flexibility of bioorganometallic compounds. As an alternative, the conformational space of molybdocene–cysteine complexes is explored by performing molecular dynamics simulations using the PM6 method coupled with the COSMO solvation model. The structure and energy of the most stable conformers are refined by DFT calculations, including the DFT-D3 dispersion energy correction.

    7. LEAP: Highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains (pages 335–341)

      Shide Liang, Chi Zhang and Yaoqi Zhou

      Article first published online: 10 DEC 2013 | DOI: 10.1002/jcc.23509

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      Loop prediction is an integral part of homolog modeling and protein structure prediction. The loop prediction by the energy-assisted protocol technique combines coarse-grained scoring, backbone refinement, and all-atom minimization for improved loop prediction.

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