Journal of Computational Chemistry

Cover image for Vol. 35 Issue 3

30 January 2014

Volume 35, Issue 3

Pages i–iv, 181–269

  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 3 (pages i–ii)

      Article first published online: 25 DEC 2013 | DOI: 10.1002/jcc.23520

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      When capturing molecules, the catcher needs to fit like a glove around its target. The weak interactions between a buckyball and a series of corannulene-derived buckybowls are analyzed for possible substitution patterns that improve the bonding between the two. More important than a description of the interaction is a reliable way to experimentally establish a binding constant for the molecular capture. To this end, Ivan Welsh and Matthias Lein on page 181 analyze and predict the NMR chemical shifts of selected protons that can be used when new catch-and-release compounds are designed.

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      Cover Image, Volume 35, Issue 3 (pages iii–iv)

      Article first published online: 25 DEC 2013 | DOI: 10.1002/jcc.23521

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      Transition metal complexes are used in drug design projects because of their geometrical patterns. The study by Elisabeth Ortega-Carrasco, Agusti Lledós, and Jean-Didier Maréchal on page 192 shows that state-of-the-art protein–ligand docking can reliably predict binding modes of metalodrugs. Excellent results are obtained for a series of wellcharacterized systems for which the first coordination sphere of the metal is not altered during the binding process. The general trends obtained in this work can further the use of protein–ligand docking in medicinal bioinorganics.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Accurate density functional theory description of binding constants and NMR chemical shifts of weakly interacting complexes of C60 with corannulene-based molecular bowls (pages 181–191)

      Ivan Welsh and Matthias Lein

      Article first published online: 9 OCT 2013 | DOI: 10.1002/jcc.23455

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      Density functional calculations on “catch and release” complexes of C60 with corannulene derived molecular bowls show that computationally obtained 1H NMR chemical shifts can be used as a reliable predictor of binding constants. A wide range of functionals are benchmarked against accurate ab initio calculations to ensure a credible representation of the weak forces that dominate the interactions in these systems. The most reliable DFT results are then calibrated using experimentally observed NMR data.

    2. Assessing protein–ligand docking for the binding of organometallic compounds to proteins (pages 192–198)

      Elisabeth Ortega-Carrasco, Agusti Lledós and Jean-Didier Maréchal

      Article first published online: 28 OCT 2013 | DOI: 10.1002/jcc.23472

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      Organometallic compounds are increasingly used as molecular scaffolds in drug development projects. In this study, the predictiveness of protein–ligand docking programs for the binding of inert organometallic scaffolds with protein receptors is investigated. Using the software GOLD as an illustrative case, scoring functions, preprocessing calculations, and flexibility schemes are tested. The work shows that actual methodologies are efficient for such systems without requiring major improvements.

    3. Basis sets for the evaluation of van der Waals complex interaction energies: Ne–N2 intermolecular potential and microwave spectrum (pages 199–203)

      Angelika Baranowska-Łączkowska and Berta Fernández

      Article first published online: 31 OCT 2013 | DOI: 10.1002/jcc.23483

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      To obtain efficient basis sets for the evaluation of the Ne–N2 complex intermolecular potential, a systematic basis set study is carried out using the CCSD(T) method and the LPol-n and the aug-pc-2 basis sets augmented with midbond functions. For this, 30 intermolecular geometries are selected. The new potentials provide accurate values for microwave transitions.

    4. Adsorption of multivalent alkylthiols on Au(111) surface: Insights from DFT (pages 204–213)

      Edoardo Fertitta, Elena Voloshina and Beate Paulus

      Article first published online: 18 NOV 2013 | DOI: 10.1002/jcc.23484

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      The adsorption of multivalent thiols on gold(111) is investigated through DFT. The analysis of charge density differences allows a better understanding of factors affecting the structure of the adsorption system.

    5. Quantitative structure–property relationship modeling of Grätzel solar cell dyes (pages 214–226)

      Vishwesh Venkatraman, Per-Olof Åstrand and Bjørn Kåre Alsberg

      Article first published online: 12 NOV 2013 | DOI: 10.1002/jcc.23485

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      With fossil fuel reserves on the decline, much research has focused on environmentally friendly, renewable energy resources. Dye-sensitized solar cells are particularly popular because of their flexibility and low cost of fabrication. Central to improving the performance of these devices is the design of better dye molecules. To this purpose, a statistical structure–photovoltaic performance relationship model is presented for a set of coumarin-based dyes.

    6. You have full text access to this OnlineOpen article
      Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation (pages 227–243)

      Maria M. Reif and Chris Oostenbrink

      Article first published online: 19 NOV 2013 | DOI: 10.1002/jcc.23490

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      This work describes free energy calculations involving the binding of small charged molecules to a model host system. The charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology. The thermodynamic interpretation of guest–host interactions is impaired by the neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function.

    7. Atomistic kinetic Monte Carlo study of atomic layer deposition derived from density functional theory (pages 244–259)

      Mahdi Shirazi and Simon D. Elliott

      Article first published online: 19 NOV 2013 | DOI: 10.1002/jcc.23491

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      A three-dimensional, on-lattice kinetic Monte Carlo (KMC) approach is developed to describe the reaction kinetics of atomic layer deposition (ALD). The challenge of implementing the ALD chemistry is addressed using a neighbor list and a coordination number. All DFT-derived reaction pathways are implemented into the KMC approach without any fitting parameters, including molecular adsorption, steric effect, adsorbate–adsorbate interaction, densification, and migration of the remaining fragments. The resulting surface intermediates, growth behavior, and the level of agreement are examined with experimental data.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. An efficient and extensible format, library, and API for binary trajectory data from molecular simulations (pages 260–269)

      Magnus Lundborg, Rossen Apostolov, Daniel Spångberg, Anders Gärdenäs, David van der Spoel and Erik Lindahl

      Article first published online: 20 NOV 2013 | DOI: 10.1002/jcc.23495

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      Trajectory Next Generation is a new binary file format for storing trajectory data from molecular dynamics simulations. It is architecture-independent, features state-of-the-art compression algorithms for storing large data sets, and is highly extensible. A high-level API is available, and the library allows for liberal usage in both academic and commercial codes.

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