Journal of Computational Chemistry

Cover image for Vol. 36 Issue 2

January 15, 2015

Volume 36, Issue 2

Pages i–vi, 69–136

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    5. Erratum
    1. You have free access to this content
      Cover Image, Volume 36, Issue 2 (pages i–ii)

      Article first published online: 13 DEC 2014 | DOI: 10.1002/jcc.23809

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      Aqueous pKA values for hexa-aqua complexes of first and second row transition metals are computed using a combination of quantum chemical and electrostatic methods. On page 69 (DOI: 10.1002/jcc.23764), Gegham Galstyan and Ernst-Walter Knapp report the computed pKA values show very good agreement with measured pKA values with a root mean square deviation of 1 pH unit. Compared to previous approaches, the precision of the method is systematically improved.

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      Cover Image, Volume 36, Issue 2 (pages iii–iv)

      Article first published online: 13 DEC 2014 | DOI: 10.1002/jcc.23810

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      On page 79 (DOI: 10.1002/jcc.23775), Robin M. Betz and Ross C. Walker report on Paramfit, a new program that generates force field parameters for molecular dynamics simulation by minimizing the difference between ab-initio quantum and classical energies of a set of input molecular conformations. The program incorporates a novel minimization algorithm capable of reliably locating global minima, shown by testing on various surfaces like the three-dimensional Rastrigin function illustrated here, which features numerous attractive local minima. Several molecular conformations of a small peptide used for demonstrating the program's efficacy on biological systems are also shown at the border. Structures like these are input into Paramfit, along with associated quantum energies, and are used to generate parameters of interest.

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      Cover Image, Volume 36, Issue 2 (pages v–vi)

      Article first published online: 16 DEC 2014 | DOI: 10.1002/jcc.23815

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      Encapsulating rare-gas atoms into fullerenes smaller than C60 quickly becomes repulsive and follows an exponential law with decreasing number of carbon atoms. The reason comes from a rather rigid cage structure that determines the space available inside the fullerene. On page 88 (DOI: 10.1002/jcc.23787), Rebecca Sure, Ralf Tonner, and Peter Schwerdtfeger provide detailed insight into rare-gas fullerene interactions ranging from C20 to C60 and from He to Ar using Grimme's dispersion corrected density functional theory. The maximum inscribing inner sphere inside a fullerene cage gives a good qualitative picture for the space available.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    5. Erratum
    1. Computing pKA values of hexa-aqua transition metal complexes (pages 69–78)

      Gegham Galstyan and Ernst-Walter Knapp

      Article first published online: 19 OCT 2014 | DOI: 10.1002/jcc.23764

      Thumbnail image of graphical abstract

      Aqueous pKA values for hexa-aqua complexes of first and second row transition metals were computed using a combination of quantum chemical and electrostatic methods. Computed pKA values show very good agreement with measured pKA values with a root mean square deviation of 1 pH unit. Compared to previous approaches from the same lab, the precision of the method was systematically improved.

    2. Paramfit: Automated optimization of force field parameters for molecular dynamics simulations (pages 79–87)

      Robin M. Betz and Ross C. Walker

      Article first published online: 21 NOV 2014 | DOI: 10.1002/jcc.23775

      Thumbnail image of graphical abstract

      Classical molecular dynamics parameters are obtained by fitting so that the energy of a set of structures calculated with the parameters matches a set of input energies calculated at a quantum level of theory. The Paramfit program automates this fitting process using a novel hybrid of genetic and simplex algorithms to fit multiple parameters simultaneously to any set of input molecule conformations that can include different molecules, enabling rapid, accurate force field development.

    3. A systematic study of rare gas atoms encapsulated in small fullerenes using dispersion corrected density functional theory (pages 88–96)

      Rebecca Sure, Ralf Tonner and Peter Schwerdtfeger

      Article first published online: 13 DEC 2014 | DOI: 10.1002/jcc.23787

      Thumbnail image of graphical abstract

      Dispersion interactions are essential for a density functional treatment of rare gas encapsulation into fullerene cages. A systematic DFT study using Grimme's dispersion correction for fullerenes from C20 to C60 shows that rare gas element enclosure becomes energetically favorable only at He@C48, Ne@C52, and Ar@C58.

    4. Protein folding pathways extracted by OFLOOD: Outlier FLOODing method (pages 97–102)

      Ryuhei Harada, Tomotake Nakamura, Yu Takano and Yasuteru Shigeta

      Article first published online: 3 NOV 2014 | DOI: 10.1002/jcc.23773

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      The Outlier FLOODing method (OFLOOD) is proposed as an efficient conformational sampling method to extract biologically rare events such as protein folding. OFLOOD consists of (i) detections of outliers from conformational distributions and (ii) conformational resampling from the outliers by MD simulations. As demonstrations, OFLOOD was applied to folding of Chignolin and HP35. In both cases, OFLOOD automatically extracted folding pathways from unfolded structures with ns-order computational costs, although µs-order canonical MD failed to extract them.

    5. Expected degree for RNA secondary structure networks (pages 103–117)

      Peter Clote

      Article first published online: 7 NOV 2014 | DOI: 10.1002/jcc.23776

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      The first efficient dynamic programming algorithm is presented to compute the expected network degree, for the exponentially large network of all secondary structures of a given RNA sequence. The program RNAexpNumNbors is written in C, runs in cubic time and quadratic space, can compute the expected number of neighbors, or expected network degree, of an input sequence, and is publicly available.

    6. How does hybrid bridging core modification enhance the nonlinear optical properties in donor-π-acceptor configuration? A case study of dinitrophenol derivatives (pages 118–128)

      Shabbir Muhammad, Ahmad Irfan, Mohd Shkir, Aijaz R. Chaudhry, Abul Kalam, Salem AlFaify, Abdullah G. Al-Sehemi, A. E. Al-Salami, I. S. Yahia, Hong-Liang Xu and Zhong-Min Su

      Article first published online: 10 NOV 2014 | DOI: 10.1002/jcc.23777

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      A fundamental quantum chemical structure–property relationship spotlights the surprising effect of bridging core modification to robust nonlinear optical properties of dinitrophenol derivatives.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    5. Erratum
    1. Hybrid MPI/OpenMP parallelization of the effective fragment potential method in the libefp software library (pages 129–135)

      Ilya A. Kaliman and Lyudmila V. Slipchenko

      Article first published online: 13 NOV 2014 | DOI: 10.1002/jcc.23772

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      A new hybrid MPI/OpenMP parallelization scheme is introduced for the Effective Fragment Potential (EFP) method implemented in the libefp software library. The new implementation employs dynamic load balancing that uses a master/slave model. This new parallel EFP implementation greatly expands the applicability of the EFP and QM/EFP methods by extending attainable time- and length-scales.

  4. Erratum

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    5. Erratum
    1. You have free access to this content

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