Journal of Computational Chemistry

Cover image for Vol. 34 Issue 12

5 May 2013

Volume 34, Issue 12

Pages i–iv, 987–1082

  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 34, Issue 12 (pages i–ii)

      Version of Record online: 3 APR 2013 | DOI: 10.1002/jcc.23294

      Thumbnail image of graphical abstract

      A parallel differential evolution algorithm for the optimization of atomic clusters is presented by Zhanghui Chen, Xiangwei Jiang, Jingbo Li, Shushen Li, and Linwang Wang on page 1046. It combines a modified differential evolution algorithm with improved genetic operators and a parallel strategy with a migration operator to address the problems of numerous local optima and large computational demands. Results of Lennard-Jones clusters, Co clusters, and Pt clusters demonstrate its superior performance. The figure shows the lowest unoccupied molecular orbital (LUMO) of Pt75 clusters, which are only located in several small regions. Only the central passage and five thin arms can accept electrons. The whole surface has almost no acceptor sites, indicating low activity in reaction.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 12 (pages iii–iv)

      Version of Record online: 3 APR 2013 | DOI: 10.1002/jcc.23295

      Thumbnail image of graphical abstract

      The energy transfer pathways in trimeric and hexameric aggregation states of cyanobacteria C-phycocyanin (C-PC) are investigated in the framework of the Förster model at TDDFT/B3LYP/6-311G* level by Yanliang Ren, Bo Chi, Osama Melhem, Ke Wei, Lingling Feng, Yongjian Li, Xinya Han, Ding Li, Ying Zhang, Jian Wan, Xin Xu, and Minghui Yang on page 1005. When the protonation of phycocyanobilins and their long- and short-range interactions are considered, the calculated energy transfer rates are in good agreement with the experimental results of the C-PC monomer and trimer. In the C-PC hexamer, an additional energy flow is predicted from β-155 in the top trimer to adjacent β-155 in the bottom trimer.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Electronic structure of the S1 state in methylcobalamin: Insight from CASSCF/MC-XQDPT2, EOM-CCSD, and TD-DFT calculations (pages 987–1004)

      Karina Kornobis, Neeraj Kumar, Piotr Lodowski, Maria Jaworska, Piotr Piecuch, Jesse J. Lutz, Bryan M. Wong and Pawel M. Kozlowski

      Version of Record online: 19 JAN 2013 | DOI: 10.1002/jcc.23204

      Thumbnail image of graphical abstract

      The existing controversy regarding the π [RIGHTWARDS ARROW] π* versus metal-to-ligand charge transfer (MLCT) interpretation of the lowestenergy part of the photoabsorbtion spectrum (α/β band) of methylcobalamin (MeCbl) is explored theoretically. Time-dependent density functional theory calculations are benchmarked against two ab initio wavefunction-based methodologies: the second-order multireference perturbation theory and the equation-of-motion coupled-cluster singles and doubles approach. The advantage of generalizedgradient- approximation-type over hybrid functionals is demonstrated, indicating the MLCT nature of the S0 [RIGHTWARDS ARROW] S1 transition.

    2. Understanding the electronic energy transfer pathways in the trimeric and hexameric aggregation state of cyanobacteria phycocyanin within the framework of Förster theory (pages 1005–1012)

      Yanliang Ren, Bo Chi, Osama Melhem, Ke Wei, Lingling Feng, Yongjian Li, Xinya Han, Ding Li, Ying Zhang, Jian Wan, Xin Xu and Minghui Yang

      Version of Record online: 8 JAN 2013 | DOI: 10.1002/jcc.23221

      Thumbnail image of graphical abstract

      The electronic energy transfer pathways in trimeric and hexameric aggregation state of cyanobacteria C-phycocyanin are theoretically investigated in terms of the Förster theory.

    3. NMR shielding constants of CuX, AgX, and AuX (X = F, Cl, Br, and I) investigated by density functional theory based on the Douglas–Kroll–Hess Hamiltonian (pages 1013–1023)

      Terutaka Yoshizawa and Shigeyoshi Sakaki

      Version of Record online: 19 JAN 2013 | DOI: 10.1002/jcc.23224

      Thumbnail image of graphical abstract

      AuF exhibits an extremely large Au shielding constant, which is the largest in AuX (X = halogen). The Fermi contact (FC) term in the sdσ + pσ [RIGHTWARDS ARROW] sdσpσ transition is responsible for the large FC term of AuF. One reason is the small orbital energy separation between the sdσ + pσ and sdσpσ MOs in AuF. The large paramagnetic term of AuF arises from the large metal d-orbital components in the dπpπ and sdσpσ MOs.

    4. Comparison of thermodynamic integration and Bennett acceptance ratio for calculating relative protein-ligand binding free energies (pages 1024–1034)

      Anita de Ruiter, Stefan Boresch and Chris Oostenbrink

      Version of Record online: 19 JAN 2013 | DOI: 10.1002/jcc.23229

      Thumbnail image of graphical abstract

      The influence of the number and definition of intermediate states on the precision, accuracy, and efficiency of relative binding free energy calculations using the Bennett acceptance ratio and thermodynamic integration with various integration schemes is studied.

    5. Bis-μ-oxo and μ-η22-peroxo dicopper complexes studied within (time-dependent) density-functional and many-body perturbation theory (pages 1035–1045)

      M. Rohrmüller, S. Herres-Pawlis, M. Witte and W. G. Schmidt

      Version of Record online: 8 JAN 2013 | DOI: 10.1002/jcc.23230

      Thumbnail image of graphical abstract

      The electron transfer and oxidation processes in bis-μ-oxo and μ-η22-peroxo dicopper complexes are challenging for theory. Ground-state structure, electronic properties, and optical-response calculations of two prototypical Cu2O2 complexes, [Cu2(en)2 O2]2+ and [Cu2(dbdmed)2 O2]2+, are presented. The amount of exact exchange in the XC functional considerably affects the respective stability of the complexes. TDDFT and manybody perturbation theory results (GWA1BSE) of these binuclear copper complexes show near quantitative agreement concerning the optical excitations.

    6. PDECO: Parallel differential evolution for clusters optimization (pages 1046–1059)

      Zhanghui Chen, Xiangwei Jiang, Jingbo Li, Shushen Li and Linwang Wang

      Version of Record online: 9 MAR 2013 | DOI: 10.1002/jcc.23235

      Thumbnail image of graphical abstract

      A parallel differential evolution algorithm is presented for the optimization of atomic clusters. It combines a modified differential evolution algorithm with improved genetic operators and a parallel strategy with a migration operator to address the problems of numerous local optima and large computational demands. Results of Lennard–Jones clusters, Co clusters, and Pt clusters demonstrate its superior performance.

    7. Effective fragment potential method in Q-CHEM: A guide for users and developers (pages 1060–1070)

      Debashree Ghosh, Dmytro Kosenkov, Vitalii Vanovschi, Joanna Flick, Ilya Kaliman, Yihan Shao, Andrew T.B. Gilbert, Anna I. Krylov and Lyudmila V. Slipchenko

      Version of Record online: 15 JAN 2013 | DOI: 10.1002/jcc.23223

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      The effective fragment potential (EFP) method is implemented in the Q-CHEM electronic structure package. The implementation interfaces EFP with standard quantum mechanical methods such as Hartree–Fock, density functional theory, and coupled-cluster models as well as with methods for electronically excited and open-shell species.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Some case studies on application of “rm2” metrics for judging quality of quantitative structure–activity relationship predictions: Emphasis on scaling of response data (pages 1071–1082)

      Kunal Roy, Pratim Chakraborty, Indrani Mitra, Probir Kumar Ojha, Supratik Kar and Rudra Narayan Das

      Version of Record online: 8 JAN 2013 | DOI: 10.1002/jcc.23231

      Thumbnail image of graphical abstract

      The proposed rinline image metrics have found wide application in the recent QSAR literature to judge the predictive potential of regressionbased models. Some case studies of the validation of QSAR predictions using rm2 metrics suggest that emphasis should be given on scaling response data before rinline image calculation. A new, open access, web-based application, the “rinline image calculator” (accessible from http://aptsoftware.co.in/rmsquare/ and http://203.200.173.43:8080/rmsquare/), is introduced for judging the quality of QSAR predictions.

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