Journal of Computational Chemistry

Cover image for Vol. 34 Issue 22

15 August 2013

Volume 34, Issue 22

Pages i–iv, 1881–1967

  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 22 (pages i–ii)

      Version of Record online: 8 JUL 2013 | DOI: 10.1002/jcc.23388

      Thumbnail image of graphical abstract

      A highly accurate and novel method for reconstructing protein backbones from alpha carbon traces is described by Benjamin Moore, Lawrence Kelley, James Barber, James Murray, and James MacDonald on page 1881. Gaussian mixture models are used to build a “structural alphabet”, in this case a library of short alpha carbon fragments aligned on a central peptide bond. These are then fitted to alpha carbon protein models to estimate the positions of the missing backbone atoms. The cover image depicts several of the “letters” that make up the alphabet, surrounding an alpha carbon trace and reconstructed protein model. The method is available as a C++ source code and a webserver implementation at www.sbg.bio.ic.ac.uk/~phyre2/PD2_ca2main/.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 22 (pages iii–iv)

      Version of Record online: 8 JUL 2013 | DOI: 10.1002/jcc.23389

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      The cover image, designed by Stanislav Standara, shows a snapshot from the molecular dynamics simulation of the Xe@C60 system enclosed in a box of benzene molecules. The graph represents fluctuations of the calculated 129Xe NMR chemical shift during the simulation. Combining molecular dynamics and quantum chemical calculations, Stanislav Standara, Petr Kulhánek, Radek Marek, and Michal Straka on page 1890 identify how different physical effects, such as relativity, dynamics, and explicit solvent, affect the 129Xe chemical shift of the Xe atom enclosed in the C60 cage. Developed computational protocol can be used for theoretical simulations of NMR parameters in Xe atom guest–host systems.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. High–quality protein backbone reconstruction from alpha carbons using Gaussian mixture models (pages 1881–1889)

      Benjamin L. Moore, Lawrence A. Kelley, James Barber, James W. Murray and James T. MacDonald

      Version of Record online: 24 MAY 2013 | DOI: 10.1002/jcc.23330

      Thumbnail image of graphical abstract

      A novel method of constructing protein backbones from Cα coordinates is implemented in a program named PD2 ca2main. The method uses Gaussian mixture models to model short peptide fragments and build a library of “letters” that make up a structural alphabet. Given a series of Cα, the best-fittingletters can then be used to insert missing backbone atoms. PD2 ca2main is available as C++ source code and a webserver.

    2. 129Xe NMR chemical shift in Xe@C60 calculated at experimental conditions: Essential role of the relativity, dynamics, and explicit solvent (pages 1890–1898)

      Stanislav Standara, Petr Kulhánek, Radek Marek and Michal Straka

      Version of Record online: 23 MAY 2013 | DOI: 10.1002/jcc.23334

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      The isotropic 129Xe NMR chemical shift for Xe@C60 dissolved in benzene is calculated by piecewise approximation to simulate the real experimental conditions and to evaluate the role of different physical factors influencing the 129Xe NMR chemical shift. The developed computational protocol serves as a prototype for calculations of 129Xe NMR in different Xe atom guest–host systems.

    3. Influence of variation of a side chain on the folding equilibrium of a β-peptide: Limitations of one-step perturbation (pages 1899–1906)

      Zhixiong Lin and Wilfred F. van Gunsteren

      Version of Record online: 24 MAY 2013 | DOI: 10.1002/jcc.23331

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      The one-step perturbation method is applied to tackle a challenging computational problem, that is, the calculation of the folding free enthalpies of six hepta-β-peptides with different, nonpolar, and polar, side chains at the fifth residue. Different reference states are designed to better sample the conformational space of the peptides. For the peptides with polar side chains, post simulation rotational sampling of the side chain torsional angles is carried out.

    4. Binding affinity of substituted ureido-benzenesulfonamide ligands to the carbonic anhydrase receptor: A theoretical study of enzyme inhibition (pages 1907–1916)

      Chandan Sahu, Kaushik Sen, Srimanta Pakhira, Bhaskar Mondal and Abhijit K. Das

      Version of Record online: 24 MAY 2013 | DOI: 10.1002/jcc.23335

      Thumbnail image of graphical abstract

      The interaction of the ureido-benzenesulfonamides inhibitor with the human carbonic anhydrase enzyme, including binding parameters, inhibition constant, thermodynamic parameters, and active site metal–ligand bonding nature are systematically studied by quantum mechanical/molecular mechanical (QM/MM) simulation, molecular docking, and natural bond orbital (NBO) analysis. Molecular docking predicts the best dock pose compared to X-ray crystallographic structure within the root mean square deviation (RMSD) range (<1.50 Å). These findings can be extended to other carbonic anhydrase isoforms with the possibility of designing new inhibitors.

    5. Activation of C–H bond in methane by Pd atom from the bonding evolution theory perspective (pages 1917–1924)

      Anton S. Nizovtsev

      Version of Record online: 7 JUN 2013 | DOI: 10.1002/jcc.23345

      Thumbnail image of graphical abstract

      The electron density redistribution underlying methane's C–H bond activation by the Pd atom is studied as a simple model for ubiquitous oxidative addition reactions. The (i) C–H bond breaking is accompanied by substantial reorganization of Pd's outer core maxima corresponding to N-shell electrons of the metal. The (ii) electron density from Pd flows in a subtle way involving all of its electron localization function outer core basins.

    6. A homology/ab initio hybrid algorithm for sampling near-native protein conformations (pages 1925–1936)

      Priyanka Dhingra and Bhyravabhotla Jayaram

      Version of Record online: 3 JUN 2013 | DOI: 10.1002/jcc.23339

      Thumbnail image of graphical abstract

      In an effort to perform a thorough sampling of protein conformational space by making the best use of available homology and fold recognition approaches together with ab initio modeling methods, Bhageerath-H Strgen, a homology/ab initio hybrid algorithm, is developed. The algorithm can sample near-native conformations in maximum instances, as demonstrated with different benchmark datasets.

    7. Parallelization of a multiconfigurational perturbation theory (pages 1937–1948)

      Steven Vancoillie, Mickaël G. Delcey, Roland Lindh, Victor Vysotskiy, Per-Åke Malmqvist and Valera Veryazov

      Version of Record online: 7 JUN 2013 | DOI: 10.1002/jcc.23342

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      Using high-performance computing (HPC), quantum chemists try to push the boundaries of size and complexity of the molecules they study. As individual computational resources are reaching their limits, HPC has shifted to the parallel use of those resources, typically using large computer clusters. A parallel approach to a method that has become widely successful as an accurate but relatively inexpensive method to treat transition states, diradicals, and heavy-metal systems is explored.

    8. Continuous development of schemes for parallel computing of the electrostatics in biological systems: Implementation in DelPhi (pages 1949–1960)

      Chuan Li, Marharyta Petukh, Lin Li and Emil Alexov

      Version of Record online: 3 JUN 2013 | DOI: 10.1002/jcc.23340

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      A newly developed parallel DelPhi program allows the Poisson–Boltzmann equation to be solved and the electrostatics of very large macromolecules and macromolecular complexes to be calculated. As a demonstration of the capability and efficiency of the parallelized DelPhi program, the potential map calculated for the system, which is made of a real macromolecule (barnase–barstar complex) and an artificial nano-object (Clemson Robot), of more than 30,000 charged atoms and 1000 é in size is shown.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. SIMPRE: A software package to calculate crystal field parameters, energy levels, and magnetic properties on mononuclear lanthanoid complexes based on charge distributions (pages 1961–1967)

      José J. Baldoví, Salvador Cardona-Serra, Juan M. Clemente-Juan, Eugenio Coronado, Alejandro Gaita-Ariño and Andrew Palii

      Version of Record online: 5 JUN 2013 | DOI: 10.1002/jcc.23341

      Thumbnail image of graphical abstract

      SIMPRE is a fortran77 code for magnetic rare earth complexes. The program uses an effective point charge model to calculate crystal field parameters, energy levels, wave functions, and the most common magnetic properties. The package has been successfully applied to several systems. Its usage is illustrated with two example studies: a) an ideal cubic structure coordinating a lanthanoid ion, and b) a system with slow relaxation of the magnetization, LiHoxY(1-x)F4.

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