Journal of Computational Chemistry

Cover image for Vol. 34 Issue 7

15 March 2013

Volume 34, Issue 7

Pages i–iv, 523–610

  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 7 (pages i–ii)

      Article first published online: 12 FEB 2013 | DOI: 10.1002/jcc.23260

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      The article by Ananth P. Kaushik and Paulette Clancy on page 523 deals with the preference of superlattice symmetry of ligand-capped nanocrystals, i.e., BCC or FCC, and how the choice of the solvent affects this preference. The image shows a single ligand-capped PbSe nanocrystal above a sea of other nanocrystals drowning in an ocean of toluene (solvent). The preference of the superlattice symmetry depends on the length of the capping ligands as well as the choice of the solvent (hexane vs. toluene). In general, for a given size of the nanocrystal, longer ligands favor BCC symmetry and shorter ligands prefer FCC symmetry.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 7 (pages iii–iv)

      Article first published online: 12 FEB 2013 | DOI: 10.1002/jcc.23261

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      Explicit solvent protein simulations may be used to evaluate conformational properties of side chains with the image showing Ubiquitin with 9 Leucine residues in green. Alternatively, high computational demands associated with full protein simulations can be mitigated with the (Ala)4-Leu-(Ala)4 model peptide, shown in the bottom of the cycle. On page 593, Alexander D. MacKerell Jr. et al. evaluated correlations between conformational sampling in (Ala)4-X-(Ala)4, with its backbone constrained to different conformations, and full protein simulations. Results show that the model peptide with the backbone constrained to the C7eq or PPII conformations yields good agreement with full protein sampling indicating it to be of utility for iterative, optimization of side chain chi torsion parameters.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Solvent-driven symmetry of self-assembled nanocrystal superlattices—A computational study (pages 523–532)

      Ananth P. Kaushik and Paulette Clancy

      Article first published online: 29 OCT 2012 | DOI: 10.1002/jcc.23152

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      The preference of facetted Pb chalcogenide nanocrystals (NCs) to spontaneously choose a crystal habit for NC superlattices (FCC/BCC) is investigated using molecular simulation approaches. The key questions addressed here concern the thermodynamic stability of the superlattice, and its preference of symmetry as the length of the ligand chains and the choice of solvent are varied. The free energy difference between FCC and BCC NC superlattice symmetries is evaluated to determine the system's preference for either geometry.

    2. Insights into the dynamics of evaporation and proton migration in protonated water clusters from Large-scale Born–Oppenheimer direct dynamics (pages 533–544)

      Vladimir V. Rybkin, Anton O. Simakov, Vebjørn Bakken, Simen Reine, Thomas Kjærgaard, Trygve Helgaker and Einar Uggerud

      Article first published online: 29 OCT 2012 | DOI: 10.1002/jcc.23162

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      Large-scale Born–Oppenheimer molecular dynamics have been performed to study kinetics of dissociation and proton transfer in the magic (n = 21) and anti-magic (n = 20) number protonated water clusters (H2O)nH+.

    3. Rate coefficients of the CF3CHFCF3 + H [RIGHTWARDS ARROW] CF3CFCF3 + H2 reaction at different temperatures calculated by transition state theory with ab initio and DFT reaction paths (pages 545–557)

      Maggie Ng, Daniel K. W. Mok, Edmond P. F. Lee and John M. Dyke

      Article first published online: 1 NOV 2012 | DOI: 10.1002/jcc.23163

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      Reaction rate coefficients of an environmentally friendly fire extinguishant FM200 with hydrogen atom between 300 and 1500 K were computed using quantum chemical methods and variational transition state theory. This reaction is important in kinetic modeling and understanding of the fire suppression mechanisms of FM200. Results suggested that tunneling is significant at low temperatures (∼300 K). Accurate determinations of the barrier height and the imaginary frequency of the transition state are important in calculating the rate coefficients.

    4. Conventional strain energies of azetidine and phosphetane: Can density functional theory yield reliable results? (pages 558–565)

      Shelley A. Smith, Karen E. Hand, Melissa L. Love, Glake Hill and David H. Magers

      Article first published online: 29 OCT 2012 | DOI: 10.1002/jcc.23165

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      Previous attempts to calculate reliable conventional strain energies with density functional theory have met with limited success. Here, the conventional strain energies of azetidine and both conformations of phosphetane are calculated with 10 different functionals and these results are compared to MP2 and CCSD(T) values to illustrate that the right choice of functional can make the difference.

    5. An accurate and efficient method to predict the electronic excitation energies of BODIPY fluorescent dyes (pages 566–575)

      Jia-Nan Wang, Jun-Ling Jin, Yun Geng, Shi-Ling Sun, Hong-Liang Xu, Ying-Hua Lu and Zhong-Min Su

      Article first published online: 1 NOV 2012 | DOI: 10.1002/jcc.23168

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      The electronic excitation energies of 90 BODIPY derivatives were calculated by extreme learning machine neural network, which is more efficient and accurate than methods such as B3LYP, NN, and GANN. Four groups of descriptors were considered when building the predication model, and results showed that quantum chemical descriptions play most important role in predicting. A user-friendly web server, EEEBPre, was built for prediction, freely accessible to public.

    6. Calculating standard reduction potentials of [4Fe–4S] proteins (pages 576–582)

      Bradley Scott Perrin Jr., Shuqiang Niu and Toshiko Ichiye

      Article first published online: 1 NOV 2012 | DOI: 10.1002/jcc.23169

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      A method for calculating the reduction potential versus the standard hydrogen electrode, E°, of a metalloprotein is presented, in which the reduction of the redox site is calculated using density functional theory while the contribution of the protein and solvent is calculated by continuum electrostatics. The calculated E° for six homologous HiPIPs are shown to be in excellent agreement with experimental results.

    7. Water PMF for predicting the properties of water molecules in protein binding site (pages 583–592)

      Mingyue Zheng, Yanlian Li, Bing Xiong, Hualiang Jiang and Jingkang Shen

      Article first published online: 1 NOV 2012 | DOI: 10.1002/jcc.23170

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      Using the potential of mean forces (PMF) approach, a water PMF (wPMF) based on 3946 non-redundant crystal structures was constructued. The extracted wPMF potential was used to investigate the structure pattern of water, residue hydrophilicity, relationship with the B factor value of crystal water, and to predict the potential hydration sites of protein structure.

    8. (Ala)4-X-(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side-chain dihedral empirical force field parameters (pages 593–603)

      Jihyun Shim, Xiao Zhu, Robert B. Best and Alexander D. MacKerell Jr.

      Article first published online: 29 NOV 2012 | DOI: 10.1002/jcc.23178

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      When optimizing amino acid side-chain parameters their conformational properties in solution need to be considered. In this work, the (Ala)4-X-(Ala)4 peptide, where X is any amino acid, serves as model system that mimics the conformations of sidechains sampled in simulations of full proteins. Accordingly, (Ala)4-X-(Ala)4 represents a model system that will be of utility for the iterative parametrization of protein side-chain dihedral parameters.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. PaDEL-DDPredictor: Open-source software for PD-PK-T prediction (pages 604–610)

      Yuye He, Chin Yee Liew, Nitin Sharma, Sze Kwang Woo, Yi Ting Chau and Chun Wei Yap

      Article first published online: 1 NOV 2012 | DOI: 10.1002/jcc.23173

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      Prediction of PD-PK-T properties using in silico tools has become very important in pharmaceutical research to reduce cost and enhance efficiency. PaDEL-DDPredictor is an in silico tool for rapid prediction of PD-PK-T properties of compounds from their chemical structures. It is free and open-source software that has both graphical user interface and command line interface, can work on all major platforms (Windows, Linux, and MacOS), and supports more than 90 different molecular file formats.

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