Journal of Computational Chemistry

Cover image for Journal of Computational Chemistry

30 June 2012

Volume 33, Issue 17

Pages 1467–1524

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    1. Calculation of the relative free energy of oxidation of azurin at pH 5 and pH 9 (pages 1467–1477)

      Denise Steiner, Chris Oostenbrink and Wilfred F. van Gunsteren

      Version of Record online: 24 APR 2012 | DOI: 10.1002/jcc.22972

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      Free energy calculations are described for the small copper-containing redox protein Azurin from Pseudomonas aeruginosa. A thermodynamic cycle connecting the reduced and oxidized states at pH 5 and pH 9 is considered. Previously published thermodynamic integration (TI) data is compared to Hamiltonian replica exchange TI (RE-TI) simulations using different simulation setups. It is found that RE-TI simulations do stimulate the distribution of conformational changes over the relevant values of the TI coupling parameter λ. This results in significantly improved values for hysteresis and cycle closure when compared to regular TI.

    2. Efficient treatment of solvation shells in 3D molecular theory of solvation (pages 1478–1494)

      Sergey Gusarov, Bhalchandra S. Pujari and Andriy Kovalenko

      Version of Record online: 20 APR 2012 | DOI: 10.1002/jcc.22974

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    3. Localization of molecular orbitals on fragments (pages 1495–1510)

      Alexander F. Sax

      Version of Record online: 20 APR 2012 | DOI: 10.1002/jcc.22980

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      The reliability of localized fragment orbitals depends on the quality of the molecular orbitals used in the localization process; it is important that orbitals that describe different bonding situations, such as CH-bonding and CC-bonding, are not mixed. Also mixing of occupied and virtual orbitals deteriorates the reliability of the localized fragment orbitals and should be avoided. CAS-SCF orbitals fulfill these requirements much better than HF orbitals.

    4. Interaction between alkyl radicals and single wall carbon nanotubes (pages 1511–1516)

      Pablo A. Denis

      Version of Record online: 23 APR 2012 | DOI: 10.1002/jcc.22981

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      Bulky alkyl radicals can be chemisorbed or physisorbed onto single wall carbon nanotubes depending on the tube's diameter. For isopropyl and tert-butyl, radicals physisorption can be stronger than chemisorption. Dispersion interactions are essential to estimate bond dissociation energies.

    5. The effect of conjugated spacer on novel carbazole derivatives for dye-sensitized solar cells: Density functional theory/time-dependent density functional theory study (pages 1517–1523)

      Siriporn Jungsuttiwong, Thanisorn Yakhanthip, Yaowarat Surakhot, Janeeya Khunchalee, Taweesak Sudyoadsuk, Vinich Promarak, Nawee Kungwan and Supawadee Namuangruk

      Version of Record online: 16 APR 2012 | DOI: 10.1002/jcc.22983

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      Introducing of thiophene-thiophene unit (T-T) as conjugated spacer in D-π-A dye (CFT2A) could significantly affects the performance of intramolecular charge transfer which leads to a high-efficiency photocurrent generation.

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