Journal of Computational Chemistry

Cover image for Vol. 35 Issue 5

15 February 2014

Volume 35, Issue 5

Pages i–vi, 343–413

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
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      Cover Image, Volume 35, Issue 5 (pages i–ii)

      Version of Record online: 22 JAN 2014 | DOI: 10.1002/jcc.23529

      Thumbnail image of graphical abstract

      Quantum topological atoms in the protein crambin provide atomic multipole moments to realize more accurate electrostatics, as shown by Yongna Yuan, Matthew Mills, and Paul Popelier on page 343. These atoms do not overlap; they have finite volumes and shapes that are primarily determined by the local environment. The cover, designed by Tim Hughes, shows critical points of the type (3,−1) (small purple spheres), marking special atom–atom interactions with their associated atomic interaction lines (solid and dashed).

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      Cover Image, Volume 35, Issue 5 (pages iii–iv)

      Version of Record online: 22 JAN 2014 | DOI: 10.1002/jcc.23530

      Thumbnail image of graphical abstract

      Peptoids are a class of bioinspired polymers that differ from peptides in respect to where their sidechains (green) are placed on the backbone. To enable the predictive molecular simulation of peptoids, which has applications in drug design and molecular self-assembly, Dina Mirijanian, Ranjan Mannige, Ronald Zuckermann, and Stephen Whitelam present on page 360 a first-generation CHARMM-based atomistic forcefield designed for peptoids. The cover shows forcefield calculations of the flexibility of a peptoid backbone (Ramachandran plot), which agree with quantum mechanical calculations of the same.

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      Cover Image, Volume 35, Issue 5 (pages v–vi)

      Version of Record online: 22 JAN 2014 | DOI: 10.1002/jcc.23531

      Thumbnail image of graphical abstract

      The endo selectivity of the archetypal Diels–Alder cycloaddition between cyclopentadiene and maleic anhydride is caused by an unfavorable steric arrangement in the transition-state region of the exo pathway, as shown on the back cover. The methylene moiety of cyclopentadiene runs into the oxygen lone-pair electrons of maleic anhydride, which translates into a more destabilizing activation strain. Neither the donor–acceptor orbital interactions nor the total interaction between the deformed reactants contributes to the endo selectivity, as detailed by Israel Fernández and F. Matthias Bickelhaupt on page 371.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Multipolar electrostatics for proteins: Atom–atom electrostatic energies in crambin (pages 343–359)

      Yongna Yuan, Matthew J. L. Mills and Paul L. A. Popelier

      Version of Record online: 29 OCT 2013 | DOI: 10.1002/jcc.23469

      Thumbnail image of graphical abstract

      The status quo of using point charges in biomolecular modeling, if not overtuned, will harm the quality of current and future predictions. Fortunately, nucleus-centered multipole moments provide more realistic electrostatics. The protein crambin demonstrates the behavior of multipolar electrostatic interaction at the atomistic level. The conclusions are important in the construction of a novel multipolar protein force field.

    2. Development and use of an atomistic CHARMM-based forcefield for peptoid simulation (pages 360–370)

      Dina T. Mirijanian, Ranjan V. Mannige, Ronald N. Zuckermann and Stephen Whitelam

      Version of Record online: 29 NOV 2013 | DOI: 10.1002/jcc.23478

      Thumbnail image of graphical abstract

      Experiments and quantum mechanical calculations are used to develop an atomistic CHARMM-based forcefield for peptoids, technologically important positional isomers of peptides.

    3. Origin of the “endo rule” in Diels–Alder reactions (pages 371–376)

      Israel Fernández and F. Matthias Bickelhaupt

      Version of Record online: 25 NOV 2013 | DOI: 10.1002/jcc.23500

      Thumbnail image of graphical abstract

      The image represents what happens as the methylene moiety of cyclopentadiene runs into the oxygen lone-pair electrons of maleic anhydride in the [4 + 2] cycloaddition reaction between the two molecules. Density functional computations show that this steric mechanism, not a difference in orbital interactions, causes the endo selectivity in this Diels–Alder reaction.

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      Comparing distance metrics for rotation using the k-nearest neighbors algorithm for entropy estimation (pages 377–385)

      David J. Huggins

      Version of Record online: 5 DEC 2013 | DOI: 10.1002/jcc.23504

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      Computing the distance between two different orientations of a molecule is useful for statistical mechanical applications. A number of distance metrics have been used, and this study considers the utility of different distance metrics in entropy estimation using the k-nearest neighbors algorithm. The results identify quaternion metrics as superior to a metric based on the Euler angles and demonstrate their superiority over a histogram method.

    5. Halogen bonds with benzene: An assessment of DFT functionals (pages 386–394)

      Alessandra Forni, Stefano Pieraccini, Stefano Rendine and Maurizio Sironi

      Version of Record online: 13 DEC 2013 | DOI: 10.1002/jcc.23507

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      The interaction of DCl and DBr (D = H, HCC, F, and NC) with the aromatic system of benzene is investigated, testing the performance of an extensive set of DFT functionals against CCSD(T) results extrapolated to the complete basis set limit. Double hybrid functionals explicitly including dispersion (B2PLYPD and mPW2PLYPD) provide the best agreement with the CCSD(T)/CBS results.

    6. TiS2 and ZrS2 single- and double-wall nanotubes: First-principles study (pages 395–405)

      Andrei V. Bandura and Robert A. Evarestov

      Version of Record online: 10 DEC 2013 | DOI: 10.1002/jcc.23508

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      The structure and stability of TiS2 and ZrS2 nanolayers and nanotubes are studied by hybrid DFT. A small but noticeable deviation of the cross-section of the external walls is found in the armchair-like double-wall nanotubes from the completely cylindrical shape. The comparison of sulfide-based and oxide-based nanotubes with hexagonal morphology shows that the formation energy of the disulfide nanotubes is less than the formation energy of the dioxide nanotubes.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. You have full text access to this OnlineOpen article
      New faster CHARMM molecular dynamics engine (pages 406–413)

      Antti-Pekka Hynninen and Michael F. Crowley

      Version of Record online: 2 DEC 2013 | DOI: 10.1002/jcc.23501

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      A new, faster molecular dynamics engine is introduced into the CHARMM software package. The new engine dramatically improves CHARMM molecular dynamics performance both in serial (single CPU core) and in parallel (multiple CPU cores). The image shows the performance of the GlnBP protein system with 61157 atoms, in nanoseconds of simulation time per day. The maximum productivity improves from 2 ns/day to 31 ns/day for 256 CPU cores.

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