Journal of Computational Chemistry

Cover image for Vol. 34 Issue 9

5 April 2013

Volume 34, Issue 9

Pages i–iv, 707–801

  1. Cover Image

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      Cover Image, Volume 34, Issue 9 (pages i–ii)

      Article first published online: 27 FEB 2013 | DOI: 10.1002/jcc.23268

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      The rapid development of drug resistance in microbes, the toxicity, and side effects of existing anti-infectious drugs are factors stimulating the effort directed toward a new generation of antibiotics. On page 790, Nikola Minovski, Andrej Perdih, Marjana Novic, and Tom Solmajer demonstrate how carefully validated in silico models using the recently determined structures of M. tuberculosis- DNA gyrase apoprotein and topoisomerase II-DNA-6-fluoroquinolones complexes are proficiently used for defining the drugs' binding pockets and the subsequent design of a series of novel inhibitors of DNA gyrase from the class of substituted 6-fluoroquinolones (shown on the cover).

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      Inside Cover, Volume 34, Issue 9 (pages iii–iv)

      Article first published online: 27 FEB 2013 | DOI: 10.1002/jcc.23269

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      The image shows a snapshot taken from an AMOEBA molecular dynamics trajectory of a Cu(II) ion in water. The work by Jin Yu Xiang and Jay W. Ponder on page 739 describes a general molecular mechanics (MM) model for treating aqueous Cu(II) and Zn(II) ions based on valence bond (VB) theory and incorporated into the AMOEBA polarizable force field. Gas phase calculations of ion-aqua complexes show that the proposed AMOEBA-VB model improves the accuracy of MM model energetics for a number of ligation geometries when compared to results obtained by ab initio methods. Analyses of the molecular dynamics trajectories revealed a 6-coordination first solvation shell for both Cu(II) and Zn(II) ions in aqueous solution, with ligation geometries falling in the range reported by previous studies.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    1. Further insights in the ability of classical nonadditive potentials to model actinide ion–water interactions (pages 707–719)

      Florent Réal, Michael Trumm, Bernd Schimmelpfennig, Michel Masella and Valérie Vallet

      Article first published online: 12 DEC 2012 | DOI: 10.1002/jcc.23184

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      The scheme summarizes an approach to define the parameters of polarizable force- field models that also account for noncooperative covalent effects. All model parameters are adjusted to quantum chemical data for dimers and representative hydrated clusters. A key issue to validating the polarizable force-field models is to explore the sensitivity of the computed structural, dynamical, and temporal properties to the model's uncertainties. This is illustrated by the radial distribution functions displayed for two-test ions, curium(III) and thorium(IV).

    2. Efficient implementation of restricted active space configuration interaction with the hole and particle approximation (pages 720–730)

      David Casanova

      Article first published online: 7 DEC 2012 | DOI: 10.1002/jcc.23188

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      An integral-driven approach-based algorithm is presented for the implementation of the restricted active space configuration interaction method within the hole and particle truncation of the wavefunction expansion, restricted active space configuration interaction (h,p). The performance of the new code and its flexibility in the choice of the single configuration reference and the excitation operator form are tested in the computation of electronic ground and excited states.

    3. Membrane protein native state discrimination by implicit membrane models (pages 731–738)

      Olga Yuzlenko and Themis Lazaridis

      Article first published online: 7 DEC 2012 | DOI: 10.1002/jcc.23189

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      Four implicit membrane models were tested for their ability to discriminate native from non-native conformations of membrane proteins. The ranking based on Z-score is: IMM1 all-atom > GBSW > HDGB > IMM1 extended-atom > GBSAIM.

    4. A valence bond model for aqueous Cu(II) and Zn(II) ions in the AMOEBA polarizable force field (pages 739–749)

      Jin Yu Xiang and Jay W. Ponder

      Article first published online: 5 DEC 2012 | DOI: 10.1002/jcc.23190

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      The accurate description of d-orbital electronic effects is important for reliable molecular mechanics simulation of third-row transition metal ions. An efficient polarizable force field parameterization is proposed for aqueous Cu(II) and Zn(II) ions that utilizes a valence bond model to treat d-shell energetics.

    5. The MM2QM tool for combining docking, molecular dynamics, molecular mechanics, and quantum mechanics (pages 750–756)

      Marcin Nowosielski, Marcin Hoffmann, Aneta Kuron, Malgorzata Korycka-Machala and Jaroslaw Dziadek

      Article first published online: 12 DEC 2012 | DOI: 10.1002/jcc.23192

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      The ideal procedure for protein-ligand binding affinity prediction should be accurate, easily affordable in terms of computational time, and fully automated. Unfortunately, no method exists now that can satisfy all three requirements at the same time. A modified combined docking + molecular mechanics + quantum mechanical method is presented for accurate protein-ligand binding affinity prediction, together with the MM2QM tool for procedure automation. The procedure may be useful for finding analog inhibitors or improving drug candidates.

    6. An analytical approach for computing Franck-Condon integrals of harmonic oscillators with arbitrary dimensions (pages 757–765)

      Jia-Lin Chang, Cyong-Huei Huang, Sue-Chang Chen, Tsung-Hao Yin and Yi-Tsung Chen

      Article first published online: 5 DEC 2012 | DOI: 10.1002/jcc.23194

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      An analytical approach was developed for computing Franck-Condon integrals of harmonic oscillators with arbitrary dimensions, in which the mode-mixing Duschinsky effect was taken into account. A general formula of FCIs of harmonic oscillators was obtained and applied to study the photoelectron spectroscopy of vinyl alcohol and ovalene (C32H14). For the first time, the analytical approach of computing FCIs was shown to be efficient and promising for the studies of vibronic spectra of macrosystems.

    7. Notes on quantitative structure–property relationships (QSPR), part 3: Density functions origin shift as a source of quantum QSPR algorithms in molecular spaces (pages 766–779)

      Ramon Carbó-Dorca

      Article first published online: 12 DEC 2012 | DOI: 10.1002/jcc.23198

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      Cramer steroid set experimental CBG biological activity versus estimated values of this molecular parameter are presented. Activities are computed by a quantum QSPR algorithm via molecular space (MS) definition. Every molecule is a MS point associated with a quantum mechanical (QM) density function (DF). The resultant DF set of MS points is origin-shifted. Using shifted DF, a QQSPR operator is built up, and activities are easily computed with QM expectation values.

    8. New insight into the electronic structure of iron(IV)-oxo porphyrin compound I. A quantum chemical topological analysis (pages 780–789)

      Ignacio Viciano, Slawomir Berski, Sergio Martí and Juan Andrés

      Article first published online: 12 DEC 2012 | DOI: 10.1002/jcc.23201

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      The electronic structure of an iron-oxo porphyrin p-cation radical complex was studied for doublet and quartet electronic states by two methods of quantum chemical topology analysis: electron localization function h(r) and electron density r(r). The formation of this complex led to essential perturbation of the topological structure of the carbon-carbon bonds in the porphyrin moiety.

    9. Cluster-based molecular docking study for in silico identification of novel 6-fluoroquinolones as potential inhibitors against Mycobacterium tuberculosis (pages 790–801)

      Nikola Minovski, Andrej Perdih, Marjana Novic and Tom Solmajer

      Article first published online: 19 DEC 2012 | DOI: 10.1002/jcc.23205

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      A novel, rational “bottleneck” VS methodology for in silico identification of new 6- fluoroquinolone (6-FQ) hits as potential DNA gyrase inhibitors against Myobacterium tuberculosis. For the first time, recent experimental data on 6-FQs in clinical use in complex with the DNA gyrase enzyme enable the use of structure-based methods to analyze the structure-activity relationship of the compounds with known bioactivity. The data also enable the design and bioactivity prediction of novel compounds not yet synthesized.

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