Journal of Computational Chemistry

Cover image for Vol. 34 Issue 30

15 November 2013

Volume 34, Issue 30

Pages i–iv, 2577–2665

  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 30 (pages i–ii)

      Article first published online: 10 OCT 2013 | DOI: 10.1002/jcc.23467

      Thumbnail image of graphical abstract

      Kick3 is an extension of the Kick-fragment algorithm, defined as being paired with a computationally efficient method such as third-order self-consistent-charge densityfunctional tight-binding (DFTB3). In the study by Matthew A. Addicoat et al. on page 2591, arbitrary molecular fragments from a pre-described ordered list of an arbitrary number of different fragments are placed in a 3-dimensional space, in much the same manner as haphazard Legos. The structure generation algorithm is conformationally aware and will create conformational isomers by random rotations around pre-described rotatable bonds, which is useful, for example, for the side chains of ionic liquid ions.

    2. You have free access to this content
      Cover Image, Volume 34, Issue 30 (pages iii–iv)

      Article first published online: 10 OCT 2013 | DOI: 10.1002/jcc.23468

      Thumbnail image of graphical abstract

      GalaxyDock2 by Woong-Hee Shin et al. on page 2647 is a protein-ligand docking program that performs conformational space annealing (CSA) global optimization to find the optimal binding pose of a ligand both in the rigid-receptor mode and the flexiblereceptor mode. Compared to the earlier version, GalaxyDock2 is improved by the efficient generation of high-quality initial conformations for CSA using a predocking method based on a betacomplex derived from the Voronoi diagram of receptor atoms. The cover shows that docking in the flexible mode can be effectively performed using the beta-complex and global optimization. GalaxyDock2 is freely available at http://galaxy.seoklab.org/softwares/galaxydock.html.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Atomistic understanding of the C·T mismatched DNA base pair tautomerization via the DPT: QM and QTAIM computational approaches (pages 2577–2590)

      Ol'ha O. Brovarets' and Dmytro M. Hovorun

      Article first published online: 16 AUG 2013 | DOI: 10.1002/jcc.23412

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      The tautomerization of the cytosine·thymine (C·T) mismatched DNA base pair with cis-oriented N1H glycosidic bonds into the C*·T* mispair occurs via the concerted and asynchronous double proton transfer (DPT). The C·T [LEFT RIGHT ARROW] C*·T* tautomerization through the DPT is assisted by the O2…O2 van der Waals contact. The nine key points, describing the evolution of the C·T [LEFT RIGHT ARROW] C*·T* tautomerization, are detected and completely investigated along the intrinsic reaction coordinate.

    2. Stochastic structure determination for conformationally flexible heterogenous molecular clusters: Application to ionic liquids (pages 2591–2600)

      Matthew A. Addicoat, Syou Fukuoka, Alister J. Page and Stephan Irle

      Article first published online: 26 AUG 2013 | DOI: 10.1002/jcc.23420

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      Kick3 is a stochastic structure generator for conformationally flexible molecular fragments. Using third-order density functional tight binding (DFTB3), Kick3 is applied to the high-throughput screening of ionic liquid (IL) clusters. The DFTB3 results compare favorably with results gained using density functional theory, indicating that DFTB3 is a suitable screening tool for IL clusters.

    3. Two-dimensional replica-exchange method for predicting protein–ligand binding structures (pages 2601–2614)

      Hironori Kokubo, Toshimasa Tanaka and Yuko Okamoto

      Article first published online: 4 SEP 2013 | DOI: 10.1002/jcc.23427

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      A two-dimensional replica-exchange method is developed for the prediction of protein-ligand binding structures. Starting from the configuration in which the protein and the ligand are far away from each other, the method predicts the ligand-binding structures in excellent agreement with experimental data from the Protein Data Bank with the improved sampling efficiency. This method will be useful for drug design simulations.

    4. Molecular dynamics simulation of benzene in graphite and amorphous carbon slit pores (pages 2615–2624)

      Yu. D. Fomin

      Article first published online: 4 SEP 2013 | DOI: 10.1002/jcc.23429

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      Benzene is studied in graphite and amorphous carbon slit pores. In graphite pores that are small enough, the benzene molecules arrange parallel to the surface; whereas in amorphous carbon pores, the benzene molecules do not observe any strong ordering, even in small pores.

    5. Splitting multiple bonds: A comparison of methodologies on the accuracy of bond dissociation energies (pages 2625–2634)

      David Robinson

      Article first published online: 13 SEP 2013 | DOI: 10.1002/jcc.23433

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      A comparison of wavefunction theory and density functional theory approaches is used to calculate potential energy curves and calculate bond dissociation energies. These are quantitatively compared with the experiment to understand the level of theory required to describe multiple bond-breaking processes.

    6. HomoSAR: Bridging comparative protein modeling with quantitative structural activity relationship to design new peptides (pages 2635–2646)

      Mahesh R. Borkar, Raghuvir R. S. Pissurlenkar and Evans C. Coutinho

      Article first published online: 18 SEP 2013 | DOI: 10.1002/jcc.23436

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      HomoSAR is an integrated approach using the principles of homology modeling and the quantitative structural activity relationship (QSAR) formalism to predict and design new peptide sequences. Although homology modeling establishes a relationship between peptide sequences, structures, and function, it does not quantify the relationship with activity, which is the domain of QSAR. A union of the two approaches provides a novel means to understand quantitative variations in peptide sequences with biological activity.

    7. GalaxyDock2: Protein–ligand docking using beta-complex and global optimization (pages 2647–2656)

      Woong-Hee Shin, Jae-Kwan Kim, Deok-Soo Kim and Chaok Seok

      Article first published online: 23 SEP 2013 | DOI: 10.1002/jcc.23438

      Thumbnail image of graphical abstract

      GalaxyDock performs conformational space annealing (CSA) global optimization for protein–ligand docking both in the rigid-receptor mode and the flexible-receptor mode. Compared to the earlier version, GalaxyDock2 is improved by the efficient generation of high-quality initial conformations for CSA using a pre-docking method based on a beta-complex derived from the Voronoi diagram of receptor atoms. GalaxyDock2 is freely available at http://galaxy.seoklab.org/softwares/galaxydock.html.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. A new module for constrained multi-fragment geometry optimization in internal coordinates implemented in the MOLCAS package (pages 2657–2665)

      Victor P. Vysotskiy, Jonas Boström and Valera Veryazov

      Article first published online: 4 SEP 2013 | DOI: 10.1002/jcc.23428

      Thumbnail image of graphical abstract

      An effective optimization with respect to positions and orientations between two or more molecular fragments is developed and implemented in the MOLCAS program package. The optimization is carried out using Z-matrix coordinates and based on numerical energy derivatives. Since the total number of required energy evaluations scales with the number of fragments, the proposed geometry optimization can be afforded for the CASPT2 method. This capability is illustrated with the phorphyrin example.

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