Journal of Computational Chemistry

Cover image for Vol. 35 Issue 20

July 30, 2014

Volume 35, Issue 20

Pages i–iv, 1473–1531

  1. Cover Image

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    4. Software News and Updates
    1. You have free access to this content
      Cover Image, Volume 35, Issue 20 (pages i–ii)

      Version of Record online: 24 JUN 2014 | DOI: 10.1002/jcc.23667

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      Frank A. Weinhold et al. report on page 1499 (DOI: 10.1002/jcc.23654) that quantitative NBO-based evaluations of steric (left) and hyperconjugative (right) interactions in the illustrative model cis-2-butene demonstrate the dominance of steric repulsions over attractive ′H-H bonding′ in biphenyl and related species, contrary to inferences based on QTAIM analysis.

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      Cover Image, Volume 35, Issue 20 (pages iii–iv)

      Version of Record online: 24 JUN 2014 | DOI: 10.1002/jcc.23668

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      Ab initio molecular dynamics (AIMD) simulation with multi-configurational wave function theories is a powerful tool to demonstrate chemical reaction dynamics, particularly for photochemical reactions with non-radiative transitions. However, the highly computational costs of ab initio calculations are one of the bottlenecks of AIMD simulations. Hiromi Nakai et al. on page 1473 (DOI: 10.1002/jcc.23617), extend the Lagrange interpolation of molecular orbital (LIMO) technique, which provides an efficient MO initial guess by MO propagations along the time axis, into multi-configurational self-consistent field (MCSCF) theories. The extended LIMO method accelerated SCF convergences in AIMD simulations, involving chemical reactions in the excited state.

  2. Full Papers

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    1. Acceleration of self-consistent field convergence in ab initio molecular dynamics simulation with multiconfigurational wave function (pages 1473–1480)

      Masaki Okoshi and Hiromi Nakai

      Version of Record online: 24 APR 2014 | DOI: 10.1002/jcc.23617

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      The Lagrange interpolation of molecular orbital (LIMO) method, which accelerates the self-consistent field (SCF) convergence in ab initio molecular dynamics simulations, is extended to the multiconfigurational (MC) wave function theories, including the complete active space SCF and restricted active space SCF methods. The reduction in the number of SCF iterations of 20–70% is achieved by the MC-type LIMO method.

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      Visualizing energy landscapes with metric disconnectivity graphs (pages 1481–1490)

      Lewis C. Smeeton, Mark T. Oakley and Roy L. Johnston

      Version of Record online: 28 MAY 2014 | DOI: 10.1002/jcc.23643

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      The visualization of multidimensional energy landscapes provides insight into the kinetics and thermodynamics of a system, and the range of structures a system can adopt. Metric disconnectivity graphs provide a possible solution, incorporating landscape connectivity information with structural information. An analysis of the 69-bead BLN coarse-grained model protein is presented as a test case.

    3. In silico concurrent multisite pH titration in proteins (pages 1491–1498)

      Hao Hu and Lin Shen

      Version of Record online: 2 JUN 2014 | DOI: 10.1002/jcc.23645

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      An effective energy function is constructed to combine the contribution of all protonation states of multiple sites in macromolecules. Molecular dynamics simulations with the effective energy function allow for an efficient sampling of all protonation states in one simulation to determine relative free energies and recover the grand canonical partition function. The latter determines the population of all protonation states at any given pH, as well as the pKa of all sites.

    4. Bay-type H···H “bonding” in cis-2-butene and related species: QTAIM versus NBO description (pages 1499–1508)

      Frank Weinhold, Paul von Ragué Schleyer and William Chadwick McKee

      Version of Record online: 12 JUN 2014 | DOI: 10.1002/jcc.23654

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      NBO assessment of donor–donor (steric) versus donor–acceptor (resonance-type) contributions confirms the predominantly repulsive nature of bay-type σCH-σCH interactions in cis-2-butene and related species, contrary to QTAIM-based claims of net “H···H bonding” attraction.

    5. Implementation of nuclear gradients of range-separated hybrid density functionals and benchmarking on rotational constants for organic molecules (pages 1509–1516)

      Tobias Risthaus, Marc Steinmetz and Stefan Grimme

      Version of Record online: 13 JUN 2014 | DOI: 10.1002/jcc.23649

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      Benchmarking of dispersion-corrected range-separated hybrid density functionals on geometries by means of rotational constants yields surprisingly good performances. Options to save computational time are discussed and a new MP2 variant for this special field of application is presented.

    6. Extension of accompanying coordinate expansion and recurrence relation method for general-contraction basis sets (pages 1517–1527)

      Masao Hayami, Junji Seino and Hiromi Nakai

      Version of Record online: 3 JUN 2014 | DOI: 10.1002/jcc.23646

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      The rapid evaluations of electron repulsion integrals (ERIs) have been a challenging problem in quantum chemistry, especially for molecules containing heavy elements for which general-contraction (GC) basis functions with high angular momentum are used. Accompanying coordinate expansion and recurrence relation method is extended to the GC scheme. This article shows the procedure of the ERI evaluations and the efficiency of this method in comparison with other methods.

  3. Software News and Updates

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    4. Software News and Updates
    1. Gro2mat: A package to efficiently read gromacs output in MATLAB (pages 1528–1531)

      Hung Dien, Charlotte M. Deane and Bernhard Knapp

      Version of Record online: 12 JUN 2014 | DOI: 10.1002/jcc.23650

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      Molecular Dynamics simulations are computational methods used to investigate molecular interactions at atomic scale. Interaction processes out of experimental reach can be monitored using Molecular Dynamics software such as Gromacs. In this article, the gro2mat package is presented. It allows fast and easy access to Gromacs output files from Matlab. This package is especially useful for scientists with an interest in quick prototyping of new mathematical and statistical approaches for Gromacs trajectory analyses.

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