Journal of Computational Chemistry

Cover image for Vol. 35 Issue 23

September 5, 2014

Volume 35, Issue 23

Pages i–iv, 1665–1737

  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 23 (pages i–ii)

      Article first published online: 21 JUL 2014 | DOI: 10.1002/jcc.23695

      Thumbnail image of graphical abstract

      The reliability and accuracy of selfconsistent-charge density-functional tightbinding (SCCDFTB) models for describing the structure, energetics, charge distributions, and vibrational frequencies of anionic water clusters have been comprehensively evaluated by comparison of their predictions with results of MP2/aug-cc-pVTZ and CCSD(T)/aug-cc-pVQZ calculations. On page 1707 (DOI: 10.1002/jcc.23677), Soran Jahangiri, Lemin Cai, and Gilles H. Peslherbe report the SCC-DFTB model is found to perform particularly well, at a fraction of the computational cost, especially when recent corrections for hydrogen bonding and charge transfer are included.

    2. You have free access to this content
      Cover Image, Volume 35, Issue 23 (pages iii–iv)

      Article first published online: 21 JUL 2014 | DOI: 10.1002/jcc.23696

      Thumbnail image of graphical abstract

      Path coordinates are a useful construct to drive systems during the simulation of complex reactions involving many degrees of freedom to obtain the associated free energy changes. Kirill Zinovjev and Iñaki Tuñón report on page 1672 (DOI: 10.1002/jcc.23673) that consideration of the variable metric tensor results in well-behaved coordinates that provides good transition state ensembles for the processes under consideration. The application is illustrated with the analysis of an enzymatic reaction studied by means of QM/MM methods.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Improving the calculation of magnetic coupling constants in MRPT methods (pages 1665–1671)

      Mariano Spivak, Celestino Angeli, Carmen J. Calzado and Coen de Graaf

      Article first published online: 3 JUL 2014 | DOI: 10.1002/jcc.23672

      Thumbnail image of graphical abstract

      Taking into account the ionic state in the optimization procedure of the molecular orbitals results in slightly more delocalized magnetic orbitals, and hence, repairs the underestimation of the magnetic coupling commonly observed for multiconfigurational perturbation theory.

    2. Exploring chemical reactivity of complex systems with path-based coordinates: Role of the distance metric (pages 1672–1681)

      Kirill Zinovjev and Iñaki Tuñón

      Article first published online: 1 JUL 2014 | DOI: 10.1002/jcc.23673

      Thumbnail image of graphical abstract

      Path coordinates are a useful construct to drive systems during the simulation of complex reactions involving many degrees of freedom to obtain the associated free energy changes. The consideration of the variable metric tensor results in well-behaved coordinates that provides good transition state ensembles for the processes under consideration. The application is illustrated with the analysis of an enzymatic reaction studied by means of QM/MM methods.

    3. Replica exchange with guided annealing for accelerated sampling of disordered protein conformations (pages 1682–1689)

      Weihong Zhang and Jianhan Chen

      Article first published online: 4 JUL 2014 | DOI: 10.1002/jcc.23675

      Thumbnail image of graphical abstract

      Efficiency of temperature replica exchange is severely limited by share cooperative transitions. Previously proposed inclusion of guided annealing cycles can help the system to escape deep energy minima and allow better sampling, but also introduces systematic bias in the simulated ensembles. Nonetheless, the bias is small for disordered protein states. It is demonstrated that replica exchange with simulated annealing (RE-GA) can generate converged and largely correct ensembles of intrinsically disordered proteins with several fold efficiency enhancement.

    4. Valence state parameters of all transition metal atoms in metalloproteins—development of ABEEMσπ fluctuating charge force field (pages 1690–1706)

      Zhong-Zhi Yang, Jian-Jiang Wang and Dong-Xia Zhao

      Article first published online: 9 JUL 2014 | DOI: 10.1002/jcc.23676

      Thumbnail image of graphical abstract

      The parameters of reference charges, valence state electronegativities, and valence state hardnesses of atom-bond electronegativity equalization method (ABEEMσπ) are calibrated through linear regression and the least square method. These parameters can be used to calculate charge distributions of metalloproteins containing transition metal atoms (Sc-Zn, Y-Cd, and Lu-Hg). The linear correlations of charge distributions of ABEEMσπ method and ab initio method are shown.

    5. Performance of density-functional tight-binding models in describing hydrogen-bonded anionic-water clusters (pages 1707–1715)

      Soran Jahangiri, Lemin Cai and Gilles H. Peslherbe

      Article first published online: 8 JUL 2014 | DOI: 10.1002/jcc.23677

      Thumbnail image of graphical abstract

      The reliability and accuracy of self-consistent-charge density-functional tight-binding (SCC-DFTB) models for describing the structure, energetics, charge distributions, and vibrational frequencies of anionic water clusters have been comprehensively evaluated by comparison of their predictions with results of MP2/aug-cc-pVTZ and CCSD(T)/aug-cc-pVQZ calculations. The SCC-DFTB model is found to perform particularly well, at a fraction of the computational cost, especially when recent corrections for hydrogen bonding and charge transfer are included.

    6. Coupled-cluster frozen-density embedding using resolution of the identity methods (pages 1716–1724)

      Sebastian Höfener

      Article first published online: 8 JUL 2014 | DOI: 10.1002/jcc.23679

      Thumbnail image of graphical abstract

      Frozen-density embedding is combined with resolution of the identity (RI) Hartree–Fock and a RI-variant of a second-order approximate coupled-cluster singles and doubles (RI-CC2) in the quantum chemistry program KOALA. This enables the calculation of solvatochromic shifts for molecules solvated in different environments with total system sizes of about 2.5 nm diameter without applying molecular mechanics.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Implementation of the diagonalization-free algorithm in the self-consistent field procedure within the four-component relativistic scheme (pages 1725–1737)

      Marcela Hrdá, Tomáš Kulich, Michal Repiský, Jozef Noga, Olga L. Malkina and Vladimir G. Malkin

      Article first published online: 4 JUL 2014 | DOI: 10.1002/jcc.23674

      Thumbnail image of graphical abstract

      A recently developed diagonalization-free approach for improving the efficiency of self-consistent field methods has been adapted to four-component relativistic calculations. The method has been thoroughly analyzed and stability and efficiency are improved. The modified algorithm is tested in four-component calculations of several heavy-element complexes.

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