Journal of Computational Chemistry

Cover image for Vol. 34 Issue 32

15 December 2013

Volume 34, Issue 32

Pages i–iv, 2757–2834

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    5. Corrigendum
    1. You have free access to this content
      Cover Image, Volume 34, Issue 32 (pages i–ii)

      Version of Record online: 4 NOV 2013 | DOI: 10.1002/jcc.23488

      Thumbnail image of graphical abstract

      The Force Field Toolkit (ffTK), a new plugin for visual molecular dynamics by Christopher G. Mayne et al. on page 2757, aids users in the development of CHARMM/CGenFF-compatible force field parameters for small molecules. The primary function of ffTK is to generate quantum mechanical target data and optimize molecular mechanics force field parameters. The cover shows water interation profiles (center left), which are computed at each iteration of the partial atomic charge optimization, and torsion scans (left to right), which are used to compute potential energy surfaces during dihedral parameter optimization. ffTK also provides a suite of analytical tools to assess optimization metrics and parameter performance using embedded plotting utilities (background).

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      Inside Cover, Volume 34, Issue 32 (pages iii–iv)

      Version of Record online: 4 NOV 2013 | DOI: 10.1002/jcc.23489

      Thumbnail image of graphical abstract

      The surface-enhanced Raman scattering spectrum (SERS) of pyridine adsorbed on Ag20 clusters at room temperature is calculated by Jen-Ping Su, Yung-Ting Lee, Shao-Yu Lu, and Jyh Shing Lin on page 2806. They perform ab initio molecular dynamics simulations in connection with a Fourier transform of the polarizability autocorrelation function to investigate the static chemical enhancement behind the SERS spectrum. At a finite temperature, the enhanced vibrational modes of pyridine can be assigned through visual identification by using a new analytical scheme, that is, the single-frequency-pass filter (SFPF).

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    5. Corrigendum
    1. Rapid parameterization of small molecules using the force field toolkit (pages 2757–2770)

      Christopher G. Mayne, Jan Saam, Klaus Schulten, Emad Tajkhorshid and James C. Gumbart

      Version of Record online: 2 SEP 2013 | DOI: 10.1002/jcc.23422

      Thumbnail image of graphical abstract

      The generation of novel force-field parameters for small molecules is a major obstacle in the simulation of many biological systems. While adopting parameters by analogy is a common approach, when the molecule of interest is not sufficiently similar to those in the force field already, parameters must be developed from first principles. The force field toolkit presented in this article significantly streamlines the development process, effectively reducing the time spent from weeks to less than a day.

    2. A new set of bending Td symmetry coordinates for MX4 molecules (pages 2771–2773)

      David Schmidling

      Version of Record online: 2 OCT 2013 | DOI: 10.1002/jcc.23447

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      The conventional set of Td symmetry coordinates for the bending modes of MX4 molecules can lead to ambiguous geometries when displacements from equilibrium are large. It is proposed here to use internal coordinates that are haversines of the bending angles divided by their sum. The A1 representation becomes a constant, enabling recovery of the bending angles unambiguously, analytically, and without approximation.

    3. Elucidating protein secondary structure with circular dichroism and a neural network (pages 2774–2786)

      Vincent Hall, Anthony Nash, Evor Hines and Alison Rodger

      Version of Record online: 5 OCT 2013 | DOI: 10.1002/jcc.23456

      Thumbnail image of graphical abstract

      Secondary Structure Neural Network (SSNN) is a 3-module self-organizing map neural network approach for predicting protein structure from circular dichroism (CD) spectra. SSNN1 takes spectra for known proteins, clusters them into a map, and SSNN2 creates a matching structure map. SSNN3 places unknown spectra on the map and gives them structure vectors. SSNN3 output illustrates the process and results obtained.

    4. Kinetic energy decomposition scheme based on information theory (pages 2787–2795)

      Yutaka Imamura, Jun Suzuki and Hiromi Nakai

      Version of Record online: 16 OCT 2013 | DOI: 10.1002/jcc.23457

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      A novel kinetic energy decomposition analysis based on information theory is proposed. The numerical assessments confirm that the current kinetic energy decomposition scheme provides reasonable chemical pictures for ionic and covalent molecules. It can also estimate atomic energies using a correction with viral ratios.

    5. Refinement of the application of the GROMOS 54A7 force field to β-peptides (pages 2796–2805)

      Zhixiong Lin and Wilfred F. van Gunsteren

      Version of Record online: 7 OCT 2013 | DOI: 10.1002/jcc.23459

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      The assignment of the 54A7 torsional-angle terms and parameters for β-peptides is reversed to the 53A6 ones, and denoted as 54A7_β. The parameter set 54A7_β corrects the wrong description of the conformational ensemble of a hexa-β-peptide obtained using 54A7, and yields in good agreement with NMR data for other β-peptides that adopt a single helical or a hairpin fold.

    6. Chemical mechanism of surface-enhanced raman scattering spectrum of pyridine adsorbed on Ag cluster: Ab initio molecular dynamics approach (pages 2806–2815)

      Jen-Ping Su, Yung-Ting Lee, Shao-Yu Lu and Jyh Shing Lin

      Version of Record online: 24 OCT 2013 | DOI: 10.1002/jcc.23464

      Thumbnail image of graphical abstract

      Using density functional theory (DFT)-based molecular dynamics simulations in connection with a Fourier transformation of the polarizability autocorrelation function, the normal Raman and surface-enhanced Raman scattering (SERS) spectra of pyridine are calculated. The Raman peaks are assigned by the visual identification of certain molecular vibrational modes at a given vibrational frequency. The structural change, vibrational coupling, and charge transfer within pyridine-Ag20 are analyzed to rationalize the static chemical enhancement behind the SERS spectrum.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    5. Corrigendum
    1. QuanPol: A full spectrum and seamless QM/MM program (pages 2816–2833)

      Nandun M. Thellamurege, Dejun Si, Fengchao Cui, Hongbo Zhu, Rui Lai and Hui Li

      Version of Record online: 30 SEP 2013 | DOI: 10.1002/jcc.23435

      Thumbnail image of graphical abstract

      QuanPol can perform combined quantum mechanical and molecular mechanical (QM/MM) calculations with induced dipole polarizable force fields and induced surface charge continuum solvation models. Various ground state and excited state QM electronic structure methods such as density functional theory (DFT), time-dependent DFT, MP2, and the multiconfiguration self-consistent-field method can be used together with standard MM force fields such as MMFF94, CHARMM, and AMBER to perform molecular dynamics free energy simulations.

  4. Corrigendum

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    5. Corrigendum
    1. You have free access to this content
      Corrigendum: Differential geometric analysis of alterations in MH α-helices (page 2834)

      B. Hischenhuber, H. Havlicek, J. Todoric, S. Höllrigl-Binder, W. Schreiner and B. Knapp

      Version of Record online: 12 OCT 2013 | DOI: 10.1002/jcc.23453

      This article corrects:

      Differential geometric analysis of alterations in MH α-helices

      Vol. 34, Issue 21, 1862–1879, Version of Record online: 24 MAY 2013

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