Journal of Computational Chemistry

Cover image for Vol. 35 Issue 13

15 May 2014

Volume 35, Issue 13

Pages i–iv, 965–1044

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. You have free access to this content
      Cover Image, Volume 35, Issue 13 (pages i–ii)

      Article first published online: 10 APR 2014 | DOI: 10.1002/jcc.23605

      Thumbnail image of graphical abstract

      Ligand-protected metal clusters are difficult to describe within density functional theory due to the need to treat the electronic structure of the cluster, possible charge-transfer between the ligands and the cluster, and weak ligand–ligand interactions. On page 986 (DOI: 10.1002/jcc.23578), Doreen Mollenhauer and Nicola Gaston demonstrate the use of an appropriate, stepwise benchmarking process that accounts for the non-additivity of these different contributions to stability and catalytic activity. The performance of density functional theory is thereby tested for gold phosphine clusters and their different components, with increasing system size, open and closed shell systems, and for different charged states.

    2. You have free access to this content
      Cover Image, Volume 35, Issue 13 (pages iii–iv)

      Article first published online: 10 APR 2014 | DOI: 10.1002/jcc.23606

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      The cover illustrates how atomic basins allow splitting of the bond electronic distribution (BED) between attached atoms. On page 978 (DOI: 10.1002/jcc.23574), David Ferro-Costas, Ignacio Pérez-Juste, and Ricardo A. Mosquera introduce a novel electronegativity estimator, the gAH index, based on dividing (by means of quantum theory of atoms in molecules [QTAIM] basins) the BED of hydrogen-containing compounds described by natural localized molecular orbitals or electron localization function disynaptic basins. The periodic trends exhibited by this new estimator are shown for second and third periods. Its values are compared with the most popular electronegativity scales.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Investigation of the distinction between van der Waals interaction and chemical bonding based on the PAEM-MO diagram (pages 965–977)

      Dong-Xia Zhao and Zhong-Zhi Yang

      Article first published online: 24 FEB 2014 | DOI: 10.1002/jcc.23570

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      The potential acting on one electron in a molecule-molecular orbital (PAEM-MO) diagram is proposed. The PAEM-MO diagram can show clear distinctions of chemical bonding from nonbonded and/or van der Waals interactions. The existence of chemical bonding between two atoms in a molecule or a complex needs to satisfy two conditions: a critical point of PAEM exists; and the major valence-shell bonding MO is higher in energy than the PAEM barrier.

    2. Electronegativity estimator built on QTAIM-based domains of the bond electron density (pages 978–985)

      David Ferro-Costas, Ignacio Pérez-Juste and Ricardo A. Mosquera

      Article first published online: 9 MAR 2014 | DOI: 10.1002/jcc.23574

      Thumbnail image of graphical abstract

      Entities related to bonds, such as natural localized molecular orbitals, are susceptible to being partitioned into atomic contributions. This partition, which can be carried out by using the quantum theory of atoms in molecules basin limits, provides a procedure for analyzing how the bond electron density is distributed between the corresponding bonded atoms. Magnitudes arising from such an analysis can be related to the electronegativity difference between the atoms of the bond.

    3. A balanced procedure for the treatment of cluster–ligand interactions on gold phosphine systems in catalysis (pages 986–997)

      Doreen Mollenhauer and Nicola Gaston

      Article first published online: 20 MAR 2014 | DOI: 10.1002/jcc.23578

      Thumbnail image of graphical abstract

      Ligand-protected metal clusters are difficult to describe within density functional theory due to the need to treat the electronic structure of the cluster, possible charge-transfer between the ligands and the cluster, and weak ligand–ligand interactions. This study demonstrates the use of an appropriate, stepwise benchmarking process that accounts for the nonadditivity of these different contributions to stability and catalytic activity.

    4. The reactions of Cr(CO)6, Fe(CO)5, and Ni(CO)4 with O2 yield viable oxo-metal carbonyls (pages 998–1009)

      Zhi Sun, Henry F. Schaefer III, Yaoming Xie, Yongdong Liu and Rugang Zhong

      Article first published online: 13 MAR 2014 | DOI: 10.1002/jcc.23585

      Thumbnail image of graphical abstract

      The classic parent compounds Cr(CO)6, Fe(CO)5, and Ni(CO)4 all exhibit thermodynamic instability in the presence of O2, driving the displacement of CO to form CO2 and viable oxo-metal carbonyls.

    5. Extraction of site–site bridge functions and effective pair potentials from simulations of polar molecular liquids (pages 1010–1023)

      Gennady N. Chuev, Ivan Vyalov and Nikolaj Georgi

      Article first published online: 23 MAR 2014 | DOI: 10.1002/jcc.23586

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      A method is developed to extract site–site bridge functions from molecular simulations, based on the inverse solution of the reference site interaction model. Site–site bridge functions and effective pair potentials are calculated for ambient water, methanol, and ethanol.

    6. Free energy calculations, enhanced by a gaussian ansatz, for the “chemical work” distribution (pages 1024–1035)

      Georgios C. Boulougouris

      Article first published online: 24 MAR 2014 | DOI: 10.1002/jcc.23590

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      The link between free energy perturbation schemes and modern nonequilibrium theories is investigated. It is possible to evaluate free energy in molecular simulations by accounting for the chemical work of transforming each interacting molecule into an ideal gas, over a liquid–vapor phase transition. A Gaussian model is proposed for the chemical work distribution, which dramatically reduces the computational cost by avoiding the necessity of sampling the tails of the distribution.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. QSARINS-chem: Insubria datasets and new QSAR/QSPR models for environmental pollutants in QSARINS (pages 1036–1044)

      Paola Gramatica, Stefano Cassani and Nicola Chirico

      Article first published online: 5 MAR 2014 | DOI: 10.1002/jcc.23576

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      QSARINS-Chem is a module implemented in the new version of QSARINS, the software for OLS-GA QSAR models that includes a database of various environmental pollutants and new validated PaDEL-Descriptor models on several end points. The chemicals can be accessed by CAS, SMILES, and name, obtaining the structure and available end points. The new PaDEL-Descriptor models, accompanied by the QSAR model reporting format for REACH, can be applied for the prediction of unavailable data, verifying the applicability domain to new chemicals.

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