Journal of Computational Chemistry

Cover image for Journal of Computational Chemistry

5 June 2012

Volume 33, Issue 15

Pages 1347–1405

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    1. Assessment of ab initio MP2 and density functionals for characterizing the potential energy profiles of the SN2 reactions at N center (pages 1347–1352)

      Feng Yu

      Version of Record online: 20 MAR 2012 | DOI: 10.1002/jcc.22963

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      Taking the relative energies at the CCSD(T)/CBS level of theory as benchmarks, we suggest utilizing the MP2, B97-K, B2K-PLYP, BMK, ωB97X-D, M06-2X, M05-2X, CAM-B3LYP, M08-SO, and ωB97X methods to explore the potential energy profiles of the SN2 reactions at N center.

    2. Design of donors with broad absorption regions and suitable frontier molecular orbitals to match typical acceptors via substitution on oligo(thienylenevinylene) toward solar cells (pages 1353–1363)

      Shanshan Tang and Jingping Zhang

      Version of Record online: 4 APR 2012 | DOI: 10.1002/jcc.22966

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      Novel donors of solar cells were designed possessing suitable FMO energies to match those of PCBM and its derivatives, broad absorption region, high and balance charge transfer properties, and high ambient stability.

    3. Molecular dynamics extended for fluctuating networks: Application to water (pages 1364–1373)

      Jennifer M. Kashmirian, Alfred Uhlherr, Alan Dorin and David G. Green

      Version of Record online: 27 MAR 2012 | DOI: 10.1002/jcc.22967

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      This paper proposes a new Fluctuating Network algorithm as an extension of the standard molecular dynamics algorithm which allows for the simulation of a molecular system based upon an underlying network. We model liquid water with this new technique using a single-site, isotropic, short range potential. We successfully reproduce liquid water's signature molecular spacing (as represented by the radial distribution function) and characterize its dynamic properties including the exponential hydrogen bond lifetime distribution, diffusion rate and average hydrogen bonds per molecule.

    4. Electrostatic polarization is critical for the strong binding in streptavidin-biotin system (pages 1374–1382)

      Ye Mei, Yong L. Li, Juan Zeng and John Z. H. Zhang

      Version of Record online: 30 MAR 2012 | DOI: 10.1002/jcc.22970

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      Three atomic charge schemes are applied to the thermodynamic integration study of the relative binding free energy between biotin and iminobiotin. Polarization effect is included by employing the recently proposed polarized protein-specific charge. When nonpolarized AMBER force field is applied, the result deviates from the experimental measurement. When electronic polarization is gradually included, the calculated binding affinity increases along with it. And we employ the linear-response approximation to eliminate the errors in self-charging process, the calculated binding affinity agrees well with the experimental observation.

    5. Benchmarking the thermodynamic analysis of water molecules around a model beta sheet (pages 1383–1392)

      David J. Huggins

      Version of Record online: 27 MAR 2012 | DOI: 10.1002/jcc.22971

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      In this study, simulations of water molecules around a model beta sheet are used to investigate the orientational correlations and predicted thermodynamic properties of water molecules at a protein surface. The protein surface is calculated to affect the free energy contribution of water molecules to a distance of 4.0 Å and a new technique for calculating the water-water entropy term is introduced. Its use is predicted to be very important in accurately calculating solvent thermodynamics. 529 × 447m (96 × 96 DPI)

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      HolT Hunter: Software for identifying and characterizing low-strain DNA holliday triangles (pages 1393–1405)

      William B. Sherman

      Version of Record online: 4 APR 2012 | DOI: 10.1002/jcc.22975

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      A two-stage, rods-then-helices, geometrical-modeling method has been developed for identifying low-strain configurations of DNA nanostructures held together via Holliday junctions. A program, Holliday Triangle Hunter, implements this algorithm and successfully identifies over 95% of the low-strain triangular configurations sought, including triangles with a wide variety of possible angles that may be convenient for molecular architects - such as those shown. Routine techniques of DNA self-assembly should enable the formation of many of the structures identified.

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