Journal of Computational Chemistry

Cover image for Vol. 34 Issue 10

5 April 2013

Volume 34, Issue 10

Pages i–iv, 803–891

  1. Cover Image

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    1. You have free access to this content
      Cover Image, Volume 34, Issue 10 (pages i–ii)

      Version of Record online: 14 MAR 2013 | DOI: 10.1002/jcc.23274

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      Erythropoeitin (Epo) is a treatment for anemia that elicits an immune response in some patients. The figure (from pdb id 1eer, rendered by PyMol) shows Epo (ribbon) and its receptor (surface), highlighting by color and ribbon thickness the locations of predicted T-cell epitopes within Epo. The computational method by Yoonjoo Choi, Karl E. Griswold, and Chris Bailey-Kellogg on page 879 redesigns such therapeutic proteins so as to have minimal predicted T-cell epitope content but still maintain native-like structural and sequence properties.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 10 (pages iii–iv)

      Version of Record online: 14 MAR 2013 | DOI: 10.1002/jcc.23275

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      Nuclear quantum effects are a recurring presence in computational chemistry— everyone knows they are present, but it is often difficult to quantify their spectroscopic fingerprints that would be observable in an experiment. Path integral molecular dynamics simulations and Monte Carlo calculations show distinct signatures of nuclear quantum delocalization in momentum profiles accessible via neutron Compton scattering experiments. As presented by Ole Schütt and Daniel Sebastiani on page 827, the image shows the inherent delocalization of the OH proton in a methanol molecule in the reference system of the CH3 group. This quantum delocalization is different from the classical rotation motion around the CO bond.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    1. Acceleration of coarse grain molecular dynamics on GPU architectures (pages 803–818)

      Ardita Shkurti, Mario Orsi, Enrico Macii, Elisa Ficarra and Andrea Acquaviva

      Version of Record online: 28 DEC 2012 | DOI: 10.1002/jcc.23183

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      Acceleration and optimization of a coarse grain (CG) molecular dynamics simulator is performed by porting its main computational kernels to graphic processing unit (GPU) architectures using CUDA language. A detailed analysis on CG features and their impact on the speed-up is reported for different GPUs, timestep size, and arithmetic precision. Accuracy and stability of the simulations are investigated. Simulations in recent GPU architectures showed more stable energy values compared to simulations in CPU.

    2. On the performance of long-range-corrected density functional theory and reduced-size polarized LPol-n basis sets in computations of electric dipole (hyper)polarizabilities of π-conjugated molecules (pages 819–826)

      Angelika Baranowska-Ła̧czkowska, Wojciech Bartkowiak, Robert W. Góra, Filip Pawłowski and Robert Zaleśny

      Version of Record online: 28 DEC 2012 | DOI: 10.1002/jcc.23197

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      Linear and nonlinear electric properties of six organic molecules are calculated using the recently developed LPol-n basis sets to assess their performance. Reference values of properties are obtained within the MP2 approximation using the Dunning's aug-ccpVTZ basis set and are supported by the CCSD(T)/aug-cc-pVDZ results. The performance of selected exchange-correlation functionals, including the long-range corrected ones, is investigated in this context.

    3. Spectroscopic fingerprints of toroidal nuclear quantum delocalization via ab initio path integral simulations (pages 827–835)

      Ole Schütt and Daniel Sebastiani

      Version of Record online: 28 DEC 2012 | DOI: 10.1002/jcc.23206

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      Nuclear momentum-space distributions can distinguish between localized, partially delocalized, and fully delocalized protons in molecular and condensed-phase systems, even if conventional spatial density distributions cannot. The differences in neutron Compton scattering profiles for differently delocalized protons at different temperatures are elucidated by first principles path integral molecular dynamics simulations.

    4. Simulating GTP:Mg and GDP:Mg with a simple force field: A structural and thermodynamic analysis (pages 836–846)

      Thomas Simonson and Priyadarshi Satpati

      Version of Record online: 28 DEC 2012 | DOI: 10.1002/jcc.23207

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      GTP and GDP exhibit several Mg coordination modes, including inner and outer sphere modes. The most important are explored with free energy simulations and a fixed charge force field, focussing on the GTP/GDP:Mg binding free energy difference.

    5. A numerically stable restrained electrostatic potential charge fitting method (pages 847–853)

      Juan Zeng, LiLi Duan, John Z.H. Zhang and Ye Mei

      Version of Record online: 28 DEC 2012 | DOI: 10.1002/jcc.23208

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      A numerically stable restrained electrostatic potential charge fitting method is proposed. The atomic charge is decomposed into two parts. The dominant part is fixed to a prede- fined value, and the residual part is to be determined by restrained fitting to residual electrostatic potential on grid points around the molecule. This can be used in quantum mechanical/molecular mechanics or similar studies, where quantum mechanical calculated electronic properties are frequently mapped to partial atomic charges.

    6. Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. Part I. Application of the Huzinaga equation (pages 854–861)

      György G. Ferenczy

      Version of Record online: 28 DEC 2012 | DOI: 10.1002/jcc.23210

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      A method is proposed to calculate the wavefunction in mixed quantum mechanics/molecular mechanics (QM/MM) approaches where the covalently bound subsystems are connected by localized frozen orbitals. The method automatically guarantees that the optimized orbitals are orthogonal to the frozen orbitals. Explicit orthogonalization of the basis set to the frozen orbitals, an approach commonly applied in related methods, is avoided. Properties calculated by the mixed QM/MM method with a small quantum subsystem well reproduce standard QM results.

    7. Calculation of wave-functions with frozen orbitals in mixed quantum mechanics/molecular mechanics methods. II. Application of the local basis equation (pages 862–869)

      György G. Ferenczy

      Version of Record online: 3 JAN 2013 | DOI: 10.1002/jcc.23209

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      A method is proposed to calculate the wave-function in mixed quantum mechanics/molecular mechanics (QM/MM) approaches where the covalently bound subsystems are connected by localized frozen orbitals. The method calculates nonorthogonal orbitals in a self-consistent field procedure. Wave-function deformation near the subsystem boundary is studied. The application of a QM/QM system with localized orbitals in the outer layer is proposed. Properties calculated by mixed methods with a small central quantum subsystem well reproduce standard QM results.

    8. Assessment of density functional methods for reaction energetics: Iridium-catalyzed water oxidation as case study (pages 870–878)

      Andranik Kazaryan and Evert Jan Baerends

      Version of Record online: 30 DEC 2012 | DOI: 10.1002/jcc.23212

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      Kohn-Sham density functional theory is fundamentally a one-electron (molecular orbital) method, and therefore believed to be less sensitive to basis set quality than explicitly correlated methods. Basis set effects are still large, leading to underestimation of the activation energy in this case study by about 10 kcal/mol with 6-31G** basis and still about 6 kcal/mol with def2-TZVPP(metal)/6-31G**(first row atoms).

    9. Structure-based redesign of proteins for minimal T-cell epitope content (pages 879–891)

      Yoonjoo Choi, Karl E. Griswold and Chris Bailey-Kellogg

      Version of Record online: 8 JAN 2013 | DOI: 10.1002/jcc.23213

      Thumbnail image of graphical abstract

      A computational method is presented to redesign therapeutic proteins so as to have minimal predicted T-cell epitope content while preserving native-like levels of predicted energy, packing quality, core hydrophobicity, and charge, and while maintaining a level of sequence identity to the wild-type proteins comparable to that of non-deimmunized designs.

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