Journal of Computational Chemistry

Cover image for Vol. 35 Issue 19

15 July 2014

Volume 35, Issue 19

Pages i–iv, 1411–1471

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    1. You have free access to this content
      Cover Image, Volume 35, Issue 19 (pages i–ii)

      Version of Record online: 12 JUN 2014 | DOI: 10.1002/jcc.23663

      Thumbnail image of graphical abstract

      Recent studies have proposed that enzymes involve networks of coupled residues throughout the protein that participate in motions accompanying the chemical barrier crossing. On page 1411 (DOI: 10.1002/jcc.23629), Daniel Roston et al. use QM/MM simulations to reproduce experimental rates for the wild type and distal mutants of Escherichia coli dihydrofolate reductase, and detail how residues remote from the active site affect the catalyzed chemistry. The distance matrix on the cover shows changes in the distance between α-carbons of each enzyme in going from the reactant to the transition states.

    2. You have free access to this content
      Cover Image, Volume 35, Issue 19 (pages iii–iv)

      Version of Record online: 12 JUN 2014 | DOI: 10.1002/jcc.23664

      Thumbnail image of graphical abstract

      The rough lipopolysaccharides membrane is an important component of the bacterial outer membrane. It has a complex structure composed of various chemical components and Ca2+ ions bridging phosphate groups. The structure on the cover was modeled by Roberta P. Dias et al. using molecular dynamics simulations with an explicit water model, and the electrostatic potential was calculated with a DelPhi Poisson-Boltzmann solver. The upper figure shows the electrostatic potential mapped onto the membrane surface. Thebottom figure shows the distribution of the electrostatic potential across the membrane. The figure was made with Chimera, with red representing negative potential and blue representing positive potential.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    1. Simulations of remote mutants of dihydrofolate reductase reveal the nature of a network of residues coupled to hydride transfer (pages 1411–1417)

      Daniel Roston, Amnon Kohen, Dvir Doron and Dan T. Major

      Version of Record online: 2 MAY 2014 | DOI: 10.1002/jcc.23629

      Thumbnail image of graphical abstract

      Recent experimental and theoretical studies have proposed that enzymes involve networks of coupled residues throughout the protein that participate in motions accompanying chemical barrier crossing. Here, QM/MM simulations are used to reproduce experimental rates for the wild type and distal mutants of Escherichia coli dihydrofolate reductase (ecDHFR), and provide detailed insight into how residues remote from the active site affect the catalyzed chemistry.

    2. Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: The MEMPOT algorithm implemented in DelPhi (pages 1418–1429)

      Roberta P. Dias, Lin Li, Thereza A. Soares and Emil Alexov

      Version of Record online: 5 MAY 2014 | DOI: 10.1002/jcc.23632

      Thumbnail image of graphical abstract

      The rough lipopolysaccharides (LPS) membrane is an important component of the bacterial outer membrane. To investigate the distribution of the electrostatic potential across LPS membranes, molecular dynamics simulations and Poisson–Boltzmann calculations with an implicit water model are performed on four different chemotypes of the rough LPS. A tool termed MEMPOT (MEMbrane POTential) is developed in the DelPhi program to calculate the average membrane crossing electrostatic potential.

    3. Transformation between α-helix and β-sheet structures of one and two polyglutamine peptides in explicit water molecules by replica-exchange molecular dynamics simulations (pages 1430–1437)

      Hsin-Lin Chiang, Chun-Jung Chen, Hisashi Okumura and Chin-Kun Hu

      Version of Record online: 16 MAY 2014 | DOI: 10.1002/jcc.23633

      Thumbnail image of graphical abstract

      Transformation pathways and peptide conformations of a system with two polyglutamine peptides and 3129 water molecules are obtained by replica-exchange molecular dynamics simulations. When the interpeptide distance gets shorter, α-helix structure decreases and the interpeptide β-sheet structure increases. The intrapeptide β-sheet structure appears as an intermediate state in the α-helix to interpeptide β-sheet transformation.

    4. Efficient parameterization of torsional terms for force fields (pages 1438–1445)

      Steven K. Burger, Paul W. Ayers and Jeremy Schofield

      Version of Record online: 16 MAY 2014 | DOI: 10.1002/jcc.23636

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      Two-dimensional potential energy surfaces of the dihedral angles of methyl L-lactate are presented. The “QM Scan” surface is done with MP2/cc-pVTZ, while the other three are constructed with molecular mechanical approximations. This work presents the Monte Carlo method, using importance sampling to efficiently sample the surface, from which the dihedral coefficients are fit. The method scales favorable with dimensionality and does not involve performing costly high-level ab initio scans.

    5. Reaction mechanism of Ru(II) piano-stool complexes: Umbrella sampling QM/MM MD study (pages 1446–1456)

      Zdeněk Futera and Jaroslav V. Burda

      Version of Record online: 28 MAY 2014 | DOI: 10.1002/jcc.23639

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      Free energy profiles of interactions of piano-stool ruthenium(II) complexes with ds-DNA hexadecamer are explored using the QM/MM-MD umbrella sampling approach. The Ru(II) complex and two guanines represent a quantum core. The whole reaction mechanism is divided into three phases: the hydration of the complex, the monoadduct formation between the aqua-Ru(II) complex and the N7 position of one guanine in the ds-DNA, and the formation of the intrastrand Ru(II) cross-link between two adjacent guanines.

    6. A Molecular modeling study of the changes of some steric properties of the precatalysts during the olefin metathesis reaction (pages 1457–1463)

      Frans T. I. Marx, Johan H. L. Jordaan, Gerhard Lachmann and Hermanus C. M. Vosloo

      Version of Record online: 28 MAY 2014 | DOI: 10.1002/jcc.23641

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      The productive self-metathesis of 1-octene with a series of new phosphine ligated Grubbs-type precatalysts is studied. The resulting structures are used to compare some steric properties of the new precatalysts with those of well-known precatalysts. The possibility of a-CC agostic stabilization, and the ability of the ligands to shield the metal is studied in order to gain insight into the mechanism.

    7. A comparison of low and high activity precatalysts: Do the calculated energy barriers during the self-metathesis reaction of 1-Octene correlate with the precatalyst metathesis activity? (pages 1464–1471)

      Frans T. I. Marx, Johan H. L. Jordaan, Gerhard Lachmann and Hermanus C. M. Vosloo

      Version of Record online: 27 MAY 2014 | DOI: 10.1002/jcc.23642

      Thumbnail image of graphical abstract

      The self-metathesis reactions of 1-octene with several known Grubbs-type precatalysts are studied with molecular modeling. The obtained Gibbs free energy values for all steps during the productive self-metathesis of 1-octene recompared to the values obtained for some low catalytic activity precatalysts. Comparing the Gibbs free energy values of highly active precatalysts to those of low catalytic activity precatalysts provides insight into the mechanism.

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