Journal of Computational Chemistry

Cover image for Vol. 34 Issue 19

15 July 2013

Volume 34, Issue 19

Pages i–iv, 1611–1705

  1. Cover Image

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    3. Full Papers
    4. Software News and Updates
    1. You have free access to this content
      Cover Image, Volume 34, Issue 19 (pages i–ii)

      Version of Record online: 14 JUN 2013 | DOI: 10.1002/jcc.23358

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      To facilitate the computational study of proteins in the AlkB family and related α-ketoglutarate/Fe(II)-dependent dioxygenases, Xueqin Pang, Keli Han, and Qiang Cui on page 1620 test a simple modeling strategy for the non-heme Fe(II) site in which the iron is represented by a simple +2 point charge with Lennard–Jones parameters. Molecular dynamics simulations indicate that the crystal structure of AlkB-dsDNA undergoes significant structural relaxations in a solution. This explains why, unlike another member of the AlkB family also studied here, AlkB prefers ssDNA over dsDNA as the natural substrate for DNA repair.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 19 (pages iii–iv)

      Version of Record online: 14 JUN 2013 | DOI: 10.1002/jcc.23359

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      The photophysical properties of a series of naphthodithiophene-based dyes are systematically studied by Yu-Ai Duan, Yun Geng, Hai-Bin Li, Jun-Ling Jin, Yong Wu, and Zhong-Min Su on page 1611. Density functional theory calculations are used to evaluate their potential as a candidate of donor materials in heterojunction organic solar cells. Molecules with naphthobisthiadiazole as the acceptor fragment show excellent performance and may become a promising donor candidate.

  2. Full Papers

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    1. Theoretical characterization and design of small molecule donor material containing naphthodithiophene central unit for efficient organic solar cells (pages 1611–1619)

      Yu-Ai Duan, Yun Geng, Hai-Bin Li, Jun-Ling Jin, Yong Wu and Zhong-Min Su

      Version of Record online: 22 APR 2013 | DOI: 10.1002/jcc.23298

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      Donor materials with different acceptor units for solar cells are designed and characterized through density functional theory calculations. System 7 with naphthobisthiadiazole as the acceptor fragment may become a high-performance donor due to broad- and red-shifted photoresponse, low exciton binding energies, high open-circuit voltage, and small reorganization energies.

    2. A simple but effective modeling strategy for structural properties of non-heme Fe(II) sites in proteins: Test of force field models and application to proteins in the AlkB family (pages 1620–1635)

      Xueqin Pang, Keli Han and Qiang Cui

      Version of Record online: 13 MAY 2013 | DOI: 10.1002/jcc.23305

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      A simple molecular mechanics model for the non-heme Fe(II) site is developed and tested using molecular dynamics simulations for enzymes in the AlkB family. Although structural features for the ABH2-dsDNA complex are overall in good agreement with the crystal structure, the dsDNA and AlkB-dsDNA interface undergo substantial changes. The results highlight that crystal packing may have a significant impact on the structure of protein–DNA complexes and provide additional insight regarding substrate specificity of AlkB enzymes.

    3. Nonfitting protein–ligand interaction scoring function based on first-principles theoretical chemistry methods: Development and application on kinase inhibitors (pages 1636–1646)

      Li Rao, Igor Ying Zhang, Wenping Guo, Li Feng, Eric Meggers and Xin Xu

      Version of Record online: 16 MAY 2013 | DOI: 10.1002/jcc.23303

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      Accurate theoretical estimation of protein–ligand interaction is vitally important for the rational design of an effective drug. A nonfitting protein–ligand interaction scoring function is developed based on the divide-and-conquer strategy and first-principles methods. Good correlations on applications to cyclin-dependent kinase 2 and p21-activated kinase 1 inhibitor databases are found between the calculated scores and the experimental inhibitor efficacies with the square of the correlation coefficient R2 of 0.76–0.89.

    4. Cytochrome P450 compound I in the plane wave pseudopotential framework: GGA electronic and geometric structure of thiolate-ligated iron(IV)–oxo porphyrin (pages 1647–1660)

      Justin E. Elenewski and John C Hackett

      Version of Record online: 14 MAY 2013 | DOI: 10.1002/jcc.23311

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      The thiolate-ligated iron(IV)-oxo porphyrins, collectively known as thiolate compound I, are potent and ubiquitous oxidizing agents active in both the cytochrome P450 superfamily of enzymes and in several highly reactive synthetic complexes. This particular species is characterized for the first time in a plane wave density functional theory framework and benchmarked with respect to established localized basis calculations.

    5. Fast and accurate generation of ab initio quality atomic charges using nonparametric statistical regression (pages 1661–1671)

      Brajesh K. Rai and Gregory A. Bakken

      Version of Record online: 7 MAY 2013 | DOI: 10.1002/jcc.23308

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      A class of the partial atomic charge assignment method is introduced, providing an ab initio quality description of the electrostatics of bioorganic molecules. The method uses a set of models that neither have a fixed functional form nor require a fixed set of parameters, and therefore are capable of capturing the complexities of the charge distribution in great detail.

    6. Corrected small basis set Hartree-Fock method for large systems (pages 1672–1685)

      Rebecca Sure and Stefan Grimme

      Version of Record online: 14 MAY 2013 | DOI: 10.1002/jcc.23317

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      A newly developed HF-3c quantum chemical protocol combines a Hartree–Fock/small basis set calculation with three physically plausible atom pair-wise correction terms. It yields good results for noncovalent interactions, geometries of organic molecules, supramolecular complexes, and small proteins. For most test cases, its accuracy approaches the density functional theory (DFT)-dispersion correction scheme (D3), large basis set quality, which is obtained at a tiny fraction the of computational cost and can be applied to large molecular systems as an alternative to semiempirical methods.

    7. Accurate double many-body expansion potential energy surface by extrapolation to the complete basis set limit and dynamics calculations for ground state of NH2 (pages 1686–1696)

      Yongqing Li, Jiuchuang Yuan, Maodu Chen, Fengcai Ma and Mengtao Sun

      Version of Record online: 10 MAY 2013 | DOI: 10.1002/jcc.23310

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      A novel accurate potential energy surface and quantum wave packet dynamics calculations are reported for the ground state of NH2. The novel potential energy surface can both be recommended for dynamics studies of the N(2D) + H2 reaction and as building blocks for constructing the single-sheeted double many-body expansion/complete basis set (DMBE/CBS) potential energy surface of larger nitrogen/hydrogen-containing systems. This new surface can be used to study the Renner–Teller degeneracy of the 12A′ and 12A″ states of NH2.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. PHAISTOS: A framework for Markov chain Monte Carlo simulation and inference of protein structure (pages 1697–1705)

      Wouter Boomsma, Jes Frellsen, Tim Harder, Sandro Bottaro, Kristoffer E. Johansson, Pengfei Tian, Kasper Stovgaard, Christian Andreetta, Simon Olsson, Jan B. Valentin, Lubomir D. Antonov, Anders S. Christensen, Mikael Borg, Jan H. Jensen, Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg and Thomas Hamelryck

      Version of Record online: 26 APR 2013 | DOI: 10.1002/jcc.23292

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      A new software package for the simulation and inference of protein structure is presented. The PHAISTOS framework contains a range of novel sampling techniques and probabilistic models, constituting a versatile toolkit for efficient simulations of protein structure. The package provides tools for a variety of tasks, including reversible folding simulations and probabilistic inference of protein structure from experimental data. The source code is released under an open source license, and full documentation is available online.

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