Journal of Computational Chemistry

Cover image for Vol. 35 Issue 2

15 January 2014

Volume 35, Issue 2

Pages i–iv, 95–180

  1. Cover Image

    1. Top of page
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    3. Full Papers
    1. You have free access to this content
      Cover Image, Volume 35, Issue 2 (pages i–ii)

      Version of Record online: 8 DEC 2013 | DOI: 10.1002/jcc.23511

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      The cover shows a calcium ion coordinating to aspartate in aqueous solution, used by Andreas Götz, Matthew Clark, and Ross Walker on page 95 to demonstrate features of a new interface to electronic structure programs for ab initio wave function theory and DFT-based QM/MM simulations with the AMBER software package. Data exchange between the programs is implemented by means of files and system calls or the message passing interface. The QM/MM equations governing the implementation are visible on the surface that extends to the horizon.

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

      Version of Record online: 8 DEC 2013 | DOI: 10.1002/jcc.23512

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      To accurately predict the adsorption of pollution gases (CO2, SO2, H2S, and CO) in a porous organic cage CC3, Wenliang Li and Jingping Zhang propose a general multi-scale simulation procedure on page 174. In detail, the B2PLYP-D3/def2-TZVPP method is validated by CCSD(T)/CBS and then used to produce reference data for fitting an intermolecular force field vdW3 that is subsequently used in grand canonical Monte Carlo (GCMC) simulations. There is good agreement of CO2 uptake between GCMC simulation results and experimental data. The low deviation for SO2, H2S, and CO makes the approach suitable for predicting gases in novel porous materials.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    1. An extensible interface for QM/MM molecular dynamics simulations with AMBER (pages 95–108)

      Andreas W. Götz, Matthew A. Clark and Ross C. Walker

      Version of Record online: 9 OCT 2013 | DOI: 10.1002/jcc.23444

      Thumbnail image of graphical abstract

      A new interface to electronic structure programs provides ab initio wave function theory and density functional theory for mixed quantum mechanical and molecular mechanical simulations with the AMBER software package. Data exchange between the programs is implemented by means of files and system calls or the message passing interface standard. Results for the free energy of binding of calcium ions to aspartate in aqueous solution are presented to demonstrate features of this interface.

    2. The photoisomerization of 11-cis-retinal protonated schiff base in gas phase: Insight from spin-flip density functional theory (pages 109–120)

      Panwang Zhou, Jianyong Liu, Keli Han and Guozhong He

      Version of Record online: 19 NOV 2013 | DOI: 10.1002/jcc.23463

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      An extensive theoretical study is presented on the photoisomerization of the 11-cis-retinal protonated Schiff base (PSB11) and its minimal model tZt-penta-3,5-dieniminium cation (PSB3) by using spin-flip density functional theory, including optimizations of ground and excited state geometries, calculations of absorption and emission spectra, locating the conical intersection points, and constructions of the photoisomerization reaction path.

    3. A new size extensive multireference perturbation theory (pages 121–129)

      Feiwu Chen and Zhihui Fan

      Version of Record online: 7 NOV 2013 | DOI: 10.1002/jcc.23471

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      A new multireference perturbation theory is derived with three promising features: it is size extensive, orbitally invariant, and as inexpensive as the single reference Møller–Plesset perturbation theory.

    4. Calibration of forcefields for molecular simulation: Sequential design of computer experiments for building cost-efficient kriging metamodels (pages 130–149)

      Fabien Cailliez, Arnaud Bourasseau and Pascal Pernot

      Version of Record online: 25 OCT 2013 | DOI: 10.1002/jcc.23475

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      A global strategy of force field parameters optimization makes use of intermediate mathematical models to reproduce molecular simulation results. Compared to classical methods, this allows a thorough exploration of parameter space and, thus, the defining of optimal parameter values that reproduce calibration properties and confidence intervals on these values. Such information, not available until now, is necessary for a global quantification of uncertainties on molecular simulation results.

    5. Hamiltonian replica-exchange simulations with adaptive biasing of peptide backbone and side chain dihedral angles (pages 150–158)

      Katja Ostermeir and Martin Zacharias

      Version of Record online: 31 OCT 2013 | DOI: 10.1002/jcc.23476

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      Efficient sampling of relevant conformational states is important in the simulation of conformational transitions of peptides and proteins. A new Hamiltonian replica exchange technique is developed based on the biasing of backbone and side chain dihedral angles along replica simulations (BP-REMD). The biasing levels are controlled and continuously adapted during simulations, which significantly improves the sampling performance compared to standard molecular dynamics simulations.

    6. Study of Cl(H2O)n (n = 1–4) using basin-hopping method coupled with density functional theory (pages 159–165)

      Shuai Jiang, Yi-Rong Liu, Teng Huang, Hui Wen, Kang-Ming Xu, Wei-Xiong Zhao, Wei-Jun Zhang and Wei Huang

      Version of Record online: 31 OCT 2013 | DOI: 10.1002/jcc.23477

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      Through the basin-hopping method coupled with density functional theory, the minima if the potential energy surface of Cl-(H2O)n (n = 1-4) are searched. The structures, energetics, thermodynamics, vertical detachment energies, and vibrational frequencies show good agreement with previously published data. The benchmark work for chloride solvation systems indicated the potential of DF-LMP2 (second-order Møller–Plesset perturbation theory using local and density fitting approximations) for optimizing larger systems.

    7. Exploring transition state structures for intramolecular pathways by the artificial force induced reaction method (pages 166–173)

      Satoshi Maeda, Tetsuya Taketsugu and Keiji Morokuma

      Version of Record online: 1 NOV 2013 | DOI: 10.1002/jcc.23481

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      Artificial force induced reaction (AFIR), an efficient automated transition state search method, is extended for intramolecular reaction pathways. This is achieved by the introduction of a systematic fragmentation scheme of a molecule and an automated path search algorithm using the AFIR method. This version is called single-component AFIR (SC-AFIR) to distinguish it from the original multi-component AFIR for intermolecular reactions. SC-AFIR enables systematic examinations of complex reaction mechanisms involving intramolecular reactions.

    8. Multiscale simulation of pollution gases adsorption in porous organic cage CC3 (pages 174–180)

      Wenliang Li and Jingping Zhang

      Version of Record online: 12 NOV 2013 | DOI: 10.1002/jcc.23486

      Thumbnail image of graphical abstract

      A general multiscale simulation procedure is proposed to accurately predict the uptake of pollutant gases such as CO2, SO2, H2S, and CO in porous organic cages CC3. The simulated CO2 loading is in good agreement with the experimental one, and there is low deviation in the fitting procedure for H2S and CO, demonstrating that the approach can predict gases in novel porous materials.

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