Journal of Computational Chemistry

Cover image for Vol. 33 Issue 25

30 September 2012

Volume 33, Issue 25

Pages i–iv, 1969–2048

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      Cover Image, Volume 33, Issue 25 (pages i–ii)

      Version of Record online: 22 AUG 2012 | DOI: 10.1002/jcc.23097

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      The cover image shows the crystal structure of V2O5 (grey: V, red: O). The bonding between the layers is dominated by weak interactions of van der Waals type. Conventional density functional theory (DFT) methods do not describe the structure and energetics correctly. This is a general problem for all systems where nonlocal dispersion effects play a role. On page 2023, Werner Reckien, Florian Janetzko, Michael F. Peintinger, and Thomas Bredow describe the implementation of an empirical dispersion correction (Grimme's DFT-D3 scheme) into a plane wave code that enables a correct description of weak noncovalent interactions in solids. Benchmark tests on selected solids, surfaces, and adsorbate systems demonstrate a significant improvement over standard DFT.

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      Inside Cover, Volume 33, Issue 25 (pages iii–iv)

      Version of Record online: 22 AUG 2012 | DOI: 10.1002/jcc.23098

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      Debye summation arises in computation of small and wide-angle scattering of X-rays or neutrons by molecules in solution and in powder diffraction. Its direct evaluation has quadratic cost, resulting in a computational bottleneck where such evaluation is iteratively used to predict scattering data from a structure model under refinement. On page 1981, Nail A. Gumerov, Konstantin Berlin, David Fushman, and Ramani Duraiswami present a computationally efficient summation algorithm with linear cost that avoids large global expansions, instead using a hierarchical algorithm to quickly aggregate small local expansions into a globally valid expansion, while ensuring that a user-prescribed error bound is satisfied. This significantly improves both computational complexity and accuracy over existing methods.

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    1. Force field development for cofactors in the photosystem II (pages 1969–1980)

      Lu Zhang, Daniel-Adriano Silva, YiJing Yan and Xuhui Huang

      Version of Record online: 8 JUN 2012 | DOI: 10.1002/jcc.23016

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      We present a set of force field parameters compatible with the AMBER03 force field to describe five cofactors in the photosystem II (PSII) of oxygenic photosynthetic organisms: plastoquinone-9, chlorophyll-a, pheophytin-a, heme-b, and β-carotene. The development of a reliable force field for these cofactors is an essential step for performing molecular dynamics simulations of the PSII to study the system at atomic resolution. Our force field parameters are derived from a systematic comparison with quantum mechanical calculations and have also been further validated by available structural experimental data in small molecule crystals as well as protein complexes.

    2. A hierarchical algorithm for fast debye summation with applications to small angle scattering (pages 1981–1996)

      Nail A. Gumerov, Konstantin Berlin, David Fushman and Ramani Duraiswami

      Version of Record online: 18 JUN 2012 | DOI: 10.1002/jcc.23025

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      Debye summation arises in crystallography, SAXS/WAXS and SANS, and has quadratic complexity. A fast algorithm, based on the fast multipole method that computes the summation to any prescribed accuracy ϵ in linear time is presented. We show that existing approximate methods for profile computation may result in inaccurate profile computations, unless an error-bound derived in this article is used. Our results show orders of magnitude improvement in computation complexity over existing methods.

    3. Dendrimer building toolkit: Model building and characterization of various dendrimer architectures (pages 1997–2011)

      Vishal Maingi, Vaibhav Jain, Prasad V. Bharatam and Prabal K. Maiti

      Version of Record online: 14 JUN 2012 | DOI: 10.1002/jcc.23031

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      Dendrimer builder toolkit (DBT), an open source GUI, integrated with AMBER software to build molecular model of dendrimers. DBT is validated by building molecular model of PAMAM and PPI dendrimers and comparing the structural properties with the reported experimental and theoretical studies. We also report structural properties of a new class of nitrogen core PETIM dendrimer. DBT will help to study dendrimer interactions with proteins, nucleic acids, and membrane.

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    1. On the importance of excited state dynamic response electron correlation in polarizable embedding methods (pages 2012–2022)

      Janus J. Eriksen, Stephan P. A. Sauer, Kurt V. Mikkelsen, Hans J. Aa. Jensen and Jacob Kongsted

      Version of Record online: 8 JUN 2012 | DOI: 10.1002/jcc.23032

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      The effect of electron correlation in the description of excited state dynamic response in polarizable embedding (PE) methods may be investigated by constructing a hierarchy of models within the PE-random phase approximation and the PE-second-order polarization propagator approximation. The scheme illustrates how the hierarchy is constructed through the build of electronic Hessians with and without dynamic response PE terms.

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    1. Implementation of empirical dispersion corrections to density functional theory for periodic systems (pages 2023–2031)

      Werner Reckien, Florian Janetzko, Michael F. Peintinger and Thomas Bredow

      Version of Record online: 8 JUN 2012 | DOI: 10.1002/jcc.23037

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      Plane wave DFT calculations in combination with the empirical D3 correction enable a correct description of dispersion interaction within solids.

    2. Prediction of hydrocarbon enthalpies of formation by various thermochemical schemes (pages 2032–2042)

      Brent R. Wilson, Nathan J. DeYonker and Angela K. Wilson

      Version of Record online: 13 JUN 2012 | DOI: 10.1002/jcc.23038

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      Prediction of the thermodynamic properties of molecules of increasing size is one of the central challenges of computational chemistry. The correlation consistent composite approach and the G4, G3, and G3(MP2) methods have been used to compute the enthalpies of formation (ΔHf′s) for 60 closed-shell, neutral hydrocarbon molecules. The accuracies of these composite approaches are compared in terms of their accuracy using atomization, isodesmic, and hypohomodesmotic reactions.

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      nMoldyn 3: Using task farming for a parallel spectroscopy-oriented analysis of molecular dynamics simulations (pages 2043–2048)

      Konrad Hinsen, Eric Pellegrini, Sławomir Stachura and Gerald R. Kneller

      Version of Record online: 8 JUN 2012 | DOI: 10.1002/jcc.23035

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      The validation of molecular simulations requires the calculation of experimentally observable quantities. The program nMOLDYN calculates various quantities accessible by spectroscopic techniques from molecular dynamics trajectories. These calculations can take as much CPU time as the simulations themselves, and therefore benefit equally from parallelization. We present a fully parallelized version of nMOLDYN and evaluate its scaling behavior for a large molecular system.

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