Journal of Computational Chemistry

Cover image for Vol. 33 Issue 24

15 September 2012

Volume 33, Issue 24

Pages i–iv, 1907–1968

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    5. Letters to the Editor
    1. You have free access to this content
      Cover Image, Volume 33, Issue 24 (pages i–ii)

      Version of Record online: 2 AUG 2012 | DOI: 10.1002/jcc.22079

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      A theoretical study of the hydrolysis of a b-lactam antibiotic, cefotaxime (CEF), in gas phase with semi-empirical and density functional theory (DFT) methods, and in aqueous solution by means of hybrid quantum mechanics/molecular mechanics (QM/MM) potentials, is presented on page 1948 by Conchín Meliá, Silvia Ferrer, Vicent Moliner, Iñaki Tuñón, and Juan Bertrán. The inclusion of the full molecule of the CEF in the gas phase molecular model has been demonstrated to be crucial since its carboxylate group can activate the nucleophilic water molecule. In aqueous solution, the free energy profiles show a step-wise mechanism that is kinetically determined by the nucleophilic attack of a water molecule which, in turn, can be activated by a proton transfer from the carboxylate group of the substrate (the first step). The image represents the molecule of CEF and the water molecule that hydrolizes the b-lactam ring.

    2. You have free access to this content
      Inside Cover, Volume 33, Issue 24 (pages iii–iv)

      Version of Record online: 2 AUG 2012 | DOI: 10.1002/jcc.22080

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      As presented by Chuan Li, Lin Li, Jie Zhang, and Emil Alexov on page 1960, the image shows the distribution of electrostatic field mapped onto the surface of the adeno-associated virus, PDB ID 3KIC. The structural file, after a standard protonation, contains approximately 484,500 atoms. The corresponding potential map is obtained by numerically solving the Poisson-Boltzmann equation in a box domain of size 407Å × 407Å × 407Å and 815 × 815 × 815 mesh points in total via the MPI-parallelized DelPhi program utilizing 100 CPUs. The iteration algorithm converged within less than three minutes at 100 CPUs without reaching the saturation point, indicating that employing more CPUs will further reduce the computational time.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    5. Letters to the Editor
    1. Reoptimized interaction parameters for the peptide-backbone model compound N-methylacetamide in the GROMOS force field: Influence on the folding properties of two beta-peptides in methanol (pages 1907–1917)

      Bruno A. C. Horta, Zhixiong Lin, Wei Huang, Sereina Riniker, Wilfred F. van Gunsteren and Philippe H. Hünenberger

      Version of Record online: 30 MAY 2012 | DOI: 10.1002/jcc.23021

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      New interaction-function parameters are developed for the amide function in the GROMOS force field, which are compatible with the recently derived 53A6OXY parameter set for oxygen-containing chemical functions. The resulting set, referred to as 53A6OXY+A, represents an improvement over earlier GROMOS force-field versions in the context of the pure-liquid properties of NMA, including the density, heat of vaporization, dielectric permittivity, self-diffusion constant, and viscosity, as well as in terms of the Gibbs hydration free energy of this molecule.

    2. Gas-phase reactions of SiHn+ (n = 1,2) with NF3: A computational investigation on the detailed mechanistic aspects (pages 1918–1926)

      Paola Antoniotti, Elena Bottizzo, Stefano Borocci, Maria Giordani and Felice Grandinetti

      Version of Record online: 28 MAY 2012 | DOI: 10.1002/jcc.23023

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      The mechanism of the gas-phase reactions of SiHn+ (n = 1,2) with NF3 were investigated by ab initio calculations at the MP2 and CAS-MCSCF level of theory. In the reaction of SiH+ the kinetically relevant intermediates are the two isomeric forms of fluorine-coordinated intermediate HSi-F-NF2. The reaction of SiH2+ with NF3 involves instead the concomitant formation of the nitrogen-coordinated complex H2Si-NF3+ and of the fluorine-coordinated complex H2Si-F-NF2+.

    3. A simplified homology-model builder toward highly protein-like structures: An inspection of restraining potentials (pages 1927–1935)

      Tae-Rae Kim, Sangho Oh, Joshua SungWoo Yang, Sanghyuk Lee, Seokmin Shin and Jinhyuk Lee

      Version of Record online: 30 MAY 2012 | DOI: 10.1002/jcc.23024

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      A homology model builder using simple restraining potentials based on spline-interpolated quadratic functions is developed and interfaced with the CHARMM package. Our approach yields model structures with balanced protein-likeliness and backbone accuracy. As our model builder is interfaced with CHARMM, it is advantageous to directly use other CHARMM functionality and energy functions for further computational studies.

    4. A quantum chemical calculation on Fe(CO)5 revealing the operation of the Dewar–Chatt–Duncanson model (pages 1936–1947)

      Vinzenz Bachler

      Version of Record online: 6 JUN 2012 | DOI: 10.1002/jcc.23029

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      The classic Dewar-–Chatt-–Duncanson (DCD) model is a qualitative theoretical device for rationalizing the bond nature in compounds where a central transition metal is surrounded by ligands. The model assumes that ligand electrons get donated to the transition metal atom. The resulting electron excess at the metal induces an electron back- donation from the metal to the ligands. The article shows how the DCDDewar-Chatt-Duncanson model is substantiated by emerging from a non-standard ab initio calculation on Fe(CO)5.

    5. Computational study on hydrolysis of cefotaxime in gas phase and in aqueous solution (pages 1948–1959)

      Conchín Meliá, Silvia Ferrer, Vicent Moliner, Iñaki Tuñón and Juan Bertrán

      Version of Record online: 7 JUN 2012 | DOI: 10.1002/jcc.23030

      Thumbnail image of graphical abstract

      We are presenting in this article a theoretical study of the hydrolysis of a β-lactam antibiotic, Cefotaxime, in gas phase with semiempirical and density functional theory level methods, and in aqueous solution by means of hybrid quantum mechanics/molecular mechanics potentials. After exploring the potential energy surfaces, potentials of mean force have been computed for the reaction in solution with hybrid PM3/TIP3P calculations and corrections with the B3LYP and M06-2X functionals.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    5. Letters to the Editor
    1. Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi (pages 1960–1966)

      Chuan Li, Lin Li, Jie Zhang and Emil Alexov

      Version of Record online: 4 JUN 2012 | DOI: 10.1002/jcc.23033

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      Accurately solving the PoissonBoltzmann equation and calculating electrostatic potential and energies of biological macromolecules are highly desired for modeling biological molecules and nano-objects immersed in water. Existing methods implemented in serial solvers are restricted to relatively small biomolecular systems due to high computational cost. In this article, we introduce a newly developed efficient parallelization algorithm, implemented in DelPhi, which uses cutting-edge high performance computing techniques to accelerate calculations on large supramolecular structures without compromising accuracy.

  4. Letters to the Editor

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    5. Letters to the Editor
    1. Comment on the paper “Extensive Theoretical Studies of a New Energetic Material: Tetrazino-Tetrazine-Tetraoxide (TTTO)” by Xinli Song, Jicun Li, Hua Hou, and Baoshan Wang (pages 1967–1968)

      Kameron R. Jorgensen and Angela K. Wilson

      Version of Record online: 28 MAY 2012 | DOI: 10.1002/jcc.23015

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      Discrepancies are noted in the implementation and presentation of the ccCA methodology in a previous publication, ‘Extensive Theoretical Studies of a New Energetic Material: Tetrazino-tetrazine-tetraoxide (TTTO)’ by Xinli Song, Jicun Li, Hua Hou, and Baoshan Wang. The enthalpy of formation for TTTO has been re-evaluated using the correct implementation of the ccCA methodology, demonstrating the results to be comparable to those of other ab initio composite methods.

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