Journal of Computational Chemistry

Cover image for Vol. 34 Issue 28

30 October 2013

Volume 34, Issue 28

Pages i–iv, 2403–2492

  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 28 (pages i–ii)

      Version of Record online: 23 SEP 2013 | DOI: 10.1002/jcc.23441

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      On page 2403, Masashi Daido, Yukio Kawashima, and Masanori Tachikawa perform classical hybrid Monte Carlo (HMC) and path integral hybrid Monte Carlo (PIHMC) simulations to analyze the nuclear quantum effect on the hydrogenbonded structure of Watson–Crick-type adenine–thymine (A–T) and guanine–cytosine (G–C) pairs. The cover shows a schematic illustration of A–T and G–C pairs at 300 K in a path integral simulation using 16 beads. The characteristic widespread picture of bead expansion shows that the nuclear quantum effect of hydrogen atoms plays a key role in the hydrogen-bonded structure of these base pairs.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 28 (pages iii–iv)

      Version of Record online: 23 SEP 2013 | DOI: 10.1002/jcc.23442

      Thumbnail image of graphical abstract

      The cover shows the retinal π-conjugated system in the wild-type (top) and hS186W mutant (bottom) of human rhodopsin. On page 2460, Erix Wiliam Hernández- Rodríguez, Ana Lilian Montero-Alejo, Rafael López, Elsa Sánchez-García, Luis Alberto Montero-Cabrera, and José Manuel García de la Vega use the method of deformed atoms in molecules (DAM) to study the electron distribution in 11-cis-retinal in wild-type rhodopsin and two mutations associated with retinitis pigmentosa disease: hM207R and hS186W. The apparition of an electron density gap in mutants is related to a loss of charge delocalization. The planarity of Schiff-base regions of the retinal chain in rhodopsin is affected by changes in the electron density.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of base pairs (pages 2403–2411)

      Masashi Daido, Yukio Kawashima and Masanori Tachikawa

      Version of Record online: 5 AUG 2013 | DOI: 10.1002/jcc.23399

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      The ratio of buckle mode (PC1) for Watson–Crick–type guanine–cytosine pairs with quantum simulation decreases compared to that with classical simulation, whereas that of propeller mode (PC2) with quantum simulation increases. Nonplanar structures of base pairs become stable due to the nuclear quantum effect.

    2. Efficient lookup table using a linear function of inverse distance squared (pages 2412–2420)

      Jaewoon Jung, Takaharu Mori and Yuji Sugita

      Version of Record online: 12 AUG 2013 | DOI: 10.1002/jcc.23404

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      A new lookup table for short-range interaction in the particle-mesh Ewald (PME) method is developed by defining energy and gradient as a linear function of inverse distance squared. In this lookup table approach, densities of table points are inversely proportional to squared pair distances, enabling the accurate evaluation of energy and gradient at small pair distances. The new lookup table scheme allows fast pairwise non-bonded calculations due to efficient usage of cache memory.

    3. Bond fukui indices: Comparison of frozen molecular orbital and finite differences through mulliken populations (pages 2421–2429)

      Patrick Bultinck, Sofie Van Damme and Andrés Cedillo

      Version of Record online: 12 AUG 2013 | DOI: 10.1002/jcc.23405

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      Chemical reactions are usually accompanied by a reorganization of the chemical bonds in the molecule. Fukui functions are introduced to describe changes in chemical bonding under removal or addition of an electron using only first order density matrices. Atom-condensed Fukui functions are yielded by straightforward integration.

    4. A computational methodology for accurate predictions of rate constants in solution: Application to the assessment of primary antioxidant activity (pages 2430–2445)

      Annia Galano and Juan Raúl Alvarez-Idaboy

      Version of Record online: 13 AUG 2013 | DOI: 10.1002/jcc.23409

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      A computational methodology designed to be a reliable tool in the kinetic study of radical-molecule reactions in solution is presented and validated by comparison with experimental results. Its uncertainties are no larger than those arising from experiments. The methodology is applied to the study of the free radical scavenging activity of chemical compounds.

    5. Porting ONETEP to graphical processing unit-based coprocessors. 1. FFT box operations (pages 2446–2459)

      Karl Wilkinson and Chris-Kriton Skylaris

      Version of Record online: 26 AUG 2013 | DOI: 10.1002/jcc.23410

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      The Order–N Electronic Total Energy Package (ONETEP) linear-scaling quantum chemistry code is ported on GPU coprocessorbased architectures in a manner that is highly portable, while maintaining the full functionality of the code.

    6. Electron density deformations provide new insights into the spectral shift of rhodopsins (pages 2460–2471)

      Erix Wiliam Hernández-Rodríguez, Ana Lilian Montero-Alejo, Rafael López, Elsa Sánchez-García, Luis Alberto Montero-Cabrera and José Manuel García de la Vega

      Version of Record online: 26 AUG 2013 | DOI: 10.1002/jcc.23414

      Thumbnail image of graphical abstract

      The method of deformed atoms in molecules is used to study the electron distribution in 11-cis-retinal in bovine and human wild-type rhodopsins and two mutations associated with retinitis pigmentosa disease: M207R and S186W. The apparition of an electron density gap in hM207R and hS186W rhodopsins is related to a loss of charge delocalization. This perturbation provides new insights into the spectral shift of rhodopsins. Changes in the electron density affect the behavior of the bond length alternation, the blue shifts of vertical excitation energies, and the effect of the planarity of Schiff-base regions of the retinal chain in rhodopsins and mutants.

    7. Computational protein design: The proteus software and selected applications (pages 2472–2484)

      Thomas Simonson, Thomas Gaillard, David Mignon, Marcel Schmidt am Busch, Anne Lopes, Najette Amara, Savvas Polydorides, Audrey Sedano, Karen Druart and Georgios Archontis

      Version of Record online: 26 AUG 2013 | DOI: 10.1002/jcc.23418

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      Using the Proteus computation design software and Monte Carlo simulations, D-tyrosine is titrated into the active site of a wild type and a redesigned tyrosyl-tRNA synthetase, displacing L-tyrosine and obtaining binding free energy differences similar to experiments.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. Batch tautomer generation with MolTPC (pages 2485–2492)

      Thorsten Will, Michael C. Hutter, Johann Jauch and Volkhard Helms

      Version of Record online: 2 AUG 2013 | DOI: 10.1002/jcc.23397

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      Besides their conformational degrees of freedom, drug-like molecules and natural products often undergo tautomeric interconversions. Compared to the huge efforts made in the experimental investigation of tautomerism, open and free algorithmic solutions for prototropic tautomer generation are surprisingly rare and often limit their output to a subset of the configurational space. MolTPC provides an adjustable, fully automatic tautomer enumeration approach, which is freely available and incorporates the detection of ring-chain variants.

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