Journal of Computational Chemistry

Cover image for Vol. 36 Issue 5

February 15, 2015

Volume 36, Issue 5

Pages i–vi, 273–354

  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 36, Issue 5 (pages i–ii)

      Article first published online: 23 JAN 2015 | DOI: 10.1002/jcc.23847

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      On page 273 (DOI: 10.1002/jcc.23800), Dmitry Zuev, Eugene Vecharynski, Chao Yang, Natalie Orms, and Anna I. Krylov report on new iterative diagonalization algorithms targeting interior eigenstates of large matrices, which enable calculations of highly excited states within equation-of-motion coupled-cluster framework.

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      Cover Image, Volume 36, Issue 5 (pages iii–iv)

      Article first published online: 23 JAN 2015 | DOI: 10.1002/jcc.23848

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      A graphical user interface (VMS-Draw) for a virtualmultifrequency spectrometer provides user-friendly access to the latest developments of computational spectroscopy. Also appropriate for nonspecialists, Daniele Licari, Alberto Baiardi, Malgorzata Biczysko, Franco Egidi, Camille Latouche, and Vincenzo Barone report on page 321 (DOI: 10.1002/jcc.23785) that VMS-Draw produces various graphical representations, offering invaluable aid in organizing and clearly presenting the information produced by computations. Special attention is paid to ease of use, generality, and robustness for a panel of spectroscopic techniques and quantum mechanical approaches. Among other integrated features, one may quote the visualization and analysis of vibrationally resolved electronic or anharmonic vibrational spectra, including convolution of stick spectra, to obtain realistic line-shapes.

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      Cover Image, Volume 36, Issue 5 (pages v–vi)

      Article first published online: 23 JAN 2015 | DOI: 10.1002/jcc.23849

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      Todor Dudev,Mike Devereux, Markus Meuwly, Carmay Lim, Jean-Philip Piquemal and Nohad Gresh present on page 285 (DOI: 10.1002/jcc.23801) a new parametrization of thewell-established, polarizable SIBFA force field for the series of Li+—Cs+ alkali cations, which are of outstanding importance in a diversity of biochemical and bioinorganic processes. With direct application to the study of cation selectivity, illustrated here by Na+ at the mouth of a sodium ion channel, the delicate balance between different competing structures waswell accounted for using polarizablemolecular mechanics for the series of test complexes included in the study.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. New algorithms for iterative matrix-free eigensolvers in quantum chemistry (pages 273–284)

      Dmitry Zuev, Eugene Vecharynski, Chao Yang, Natalie Orms and Anna I. Krylov

      Article first published online: 2 DEC 2014 | DOI: 10.1002/jcc.23800

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      Finding a few eigenpairs of large matrices is a common task in science and engineering. In the present work, new algorithms are introduced for iterative diagonalization that solve for a small set of eigenstates of a large matrix. A modified version of Davidson's algorithm enabling a user to solve for interior eigenpairs at low computational cost is presented. A new solver is also introduced, and its performance is compared against the canonical Davidson procedure.

    2. Quantum-chemistry based calibration of the alkali metal cation series (Li+[BOND]Cs+) for large-scale polarizable molecular mechanics/dynamics simulations (pages 285–302)

      Todor Dudev, Mike Devereux, Markus Meuwly, Carmay Lim, Jean-Philip Piquemal and Nohad Gresh

      Article first published online: 24 DEC 2014 | DOI: 10.1002/jcc.23801

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      In the context of the SIBFA polarizable molecular mechanics procedure, the alkali cations in the series Li+[BOND]Cs+ are calibrated and validated. This is done upon referring to ab initio quantum-chemical calculations at the aug-cc-pVTZ(-f) level, with representative O-, N-, S-, and Se-based ligands. The validations are done on several polycoordinated complexes of these cations, and a close reproduction of the quantum chemical results can be obtained.

    3. Local response dispersion method in periodic systems: Implementation and assessment (pages 303–311)

      Yasuhiro Ikabata, Yusuke Tsukamoto, Yutaka Imamura and Hiromi Nakai

      Article first published online: 8 DEC 2014 | DOI: 10.1002/jcc.23807

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      The local response dispersion (LRD) method, which has been developed as a dispersion correction method for isolated molecules, is implemented in the package based on periodic boundary condition and plane-wave basis set. After atomic polarizabilities are calculated using the real-space grid, the dispersion energy is obtained as the sum of atomic pair contributions. The availability of LRD with PBE and revPBE functionals is assessed for simple substances, molecular crystals, and physical adsorption.

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      A surface hopping algorithm for nonadiabatic minimum energy path calculations (pages 312–320)

      Igor Schapiro, Daniel Roca-Sanjuán, Roland Lindh and Massimo Olivucci

      Article first published online: 6 JAN 2015 | DOI: 10.1002/jcc.23805

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      A new computational scheme that combines a simulation technique to find a minimum energy path and an algorithm to switch between different electronic states is presented. It is applied to study the photochemical reaction path of four different molecules.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Implementation of a graphical user interface for the virtual multifrequency spectrometer: The VMS-Draw tool (pages 321–334)

      Daniele Licari, Alberto Baiardi, Malgorzata Biczysko, Franco Egidi, Camille Latouche and Vincenzo Barone

      Article first published online: 18 NOV 2014 | DOI: 10.1002/jcc.23785

      Thumbnail image of graphical abstract

      This article presents the setup and implementation of a new graphical user interface (VMS-Draw) for a multifrequency spectrometer. Among other integrated features, one may quote the convolution of stick spectra to obtain realistic line-shapes. It is also possible to analyze and visualize, together with the structure, the molecular orbitals and/or the vibrational motions of molecular systems thanks to 3D interactive tools.

    2. Automatic algorithms for completeness-optimization of Gaussian basis sets (pages 335–347)

      Susi Lehtola

      Article first published online: 8 DEC 2014 | DOI: 10.1002/jcc.23802

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      The completeness-optimization procedure is based on a sequence of consecutive additions of functions into the basis set, illustrated here for augmentation with tight and diffuse functions, until the studied property attains convergence to the complete basis set limit. Once the limit has been achieved, the procedure is run in reverse to form computationally efficient basis sets for production-level calculations.

    3. You have full text access to this OnlineOpen article
      pmx: Automated protein structure and topology generation for alchemical perturbations (pages 348–354)

      Vytautas Gapsys, Servaas Michielssens, Daniel Seeliger and Bert L. de Groot

      Article first published online: 8 DEC 2014 | DOI: 10.1002/jcc.23804

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      Molecular dynamics-based alchemical free energy calculations present a powerful method to evaluate protein thermostability and changes in the interaction affinities upon an amino acid mutation. The approach requires a description of the mutatable amino acids as a two state system connected via an alchemical pathway. In the current work, we present a framework and its implementation to generate hybrid amino acid structures and topologies for a number of commonly used biomolecular force fields.

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