Journal of Computational Chemistry

Cover image for Vol. 36 Issue 9

Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner

Impact Factor: 3.601

ISI Journal Citation Reports © Ranking: 2013: 36/148 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

Associated Title(s): International Journal of Quantum Chemistry, Wiley Interdisciplinary Reviews: Computational Molecular Science

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Recently Published Articles

  1. Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg2+ ion models commonly used in biomolecular simulations

    Maria T. Panteva, George M. Giambaşu and Darrin M. York

    Article first published online: 4 MAR 2015 | DOI: 10.1002/jcc.23881

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    Mg2+ ions are essential for nucleic acid structure and function and this has motivated the development of several Mg2+ models for use in molecular simulations. As a first step in developing improved Mg2+ models for biomolecular simulations, we focus on the ability to which 17 different pairwise potential Mg2+ models, which belong to the most mature force fields for modeling nucleic acid dynamics, can simultaneously reproduce structural, thermodynamic, kinetic and mass transport properties in aqueous solution. These represent a balanced set of solution properties that serve as a useful departure point from which robust models for molecular dynamics simulations of biological processes can be developed by tuning pairwise interaction parameters.

  2. Are the reduction and oxidation properties of nitrocompounds dissolved in water different from those produced when adsorbed on a silica surface? A DFT M05-2X computational study

    Liudmyla K. Sviatenko, Olexandr Isayev, Leonid Gorb, Frances C. Hill, Danuta Leszczynska and Jerzy Leszczynski

    Article first published online: 3 MAR 2015 | DOI: 10.1002/jcc.23878

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    Reduction and oxidation properties of trinitrotoluene (TNT), 2,4-dinitrotoluene (DNT), 2,4-dinitroanisole (DNAN), and 5-nitro-2,4-dihydro-3H-1,2,4-triazol-3-one (NTO) were studied in gas phase, in water, and adsorbed on a silica surface state. It was found that adsorption and solvation promote redox transformation of nitrocompounds. Nitrocompounds dissolved in water are easier to transform than adsorbed ones. Reactivity in an electron attachment and electron detachment processes increases in the rows: DNT < DNAN ≈ NTO < TNT and TNT < DNT < DNAN < NTO, respectively.

  3. Symmetry classification of electron and phonon states in TiO2-based nanowires and nanotubes

    Robert A. Evarestov and Andrej I. Panin

    Article first published online: 3 MAR 2015 | DOI: 10.1002/jcc.23875

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    General approach to the phonon symmetry analysis for nanowires and nanotubes is outlined. It is illustrated on the example of TiO2 rutile-based nanorods and TiO2 anatase-based nanotubes with the hexagonal and rectangular morphology, respectively. The number and symmetry of Infrared active, Raman active, and silent modes is found, which is important for the vibrational spectra interpretations of the systems in consideration. There are four acoustic modes with zero frequencies for k = 0: three longitudinal acoustic and one twisting.

  4. Theoretical investigation of the halogen bonded complexes between carbonyl bases and molecular chlorine

    Wiktor Zierkiewicz, Dariusz C. Bieńko, Danuta Michalska and Thérèse Zeegers-Huyskens

    Article first published online: 27 FEB 2015 | DOI: 10.1002/jcc.23860

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    The halogen-bonded complexes between six carbonyl bases and molecular chlorine are investigated theoretically. The study includes the optimized geometries and the interaction energies along with an extended natural bond orbital analysis. The interaction energies calculated at the CCSD(T)/aug-cc-pVTZ level range between −1.61 and −3.50 kcal mol−1. These energies are related to the ionization potential and the proton affinity of the carbonyl bases.

  5. Fep1d: A script for the analysis of reaction coordinates

    Polina V. Banushkina and Sergei V. Krivov

    Article first published online: 25 FEB 2015 | DOI: 10.1002/jcc.23868

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    Multidimensional dynamical processes can be analyzed by projecting them onto one or few coordinates (collective variables). The dynamics is often described then as diffusion on a free energy landscape associated with the coordinates. Fep1d is a script which can be used to answer questions appearing during such an analysis. In particular, the determination of the associated free energy profile and the diffusion coefficient and establishing whether the used coordinate is optimal.