Journal of Computational Chemistry

Cover image for Vol. 34 Issue 27

15 October 2013

Volume 34, Issue 27

Pages i–iv, 2313–2402

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Erratum
    5. Corrigendum
    1. You have free access to this content
      Cover Image, Volume 34, Issue 27 (pages i–ii)

      Article first published online: 19 SEP 2013 | DOI: 10.1002/jcc.23439

      Thumbnail image of graphical abstract

      The cover shows a polycationic spermine guest, which gets “stuck” on the way out of a high-affinity host molecule, cucurbit[6]uril. High free energy barriers for dissociation can lead to irreversibilities due to “stick–slip friction” in steered dynamics dissociation simulations, and due to convergence challenges in umbrella sampling calculations. The fluctuation-guided pulling method proposed by Camilo Velez-Vega and Michael K. Gilson on page 2360 helps resolve these issues.

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      Inside Cover, Volume 34, Issue 27 (pages iii–iv)

      Article first published online: 19 SEP 2013 | DOI: 10.1002/jcc.23440

      Thumbnail image of graphical abstract

      The cover shows a unit cell of 8.124 × 5.681 × 4.730 Å of N-methylaceticamide used for developing van der Waals parameters. Steven K. Burger and G. Andrés Cisneros on page 2313 present an approach to optimize the parameters by using ab initio dimer energies and condensed phase properties. The approach avoids the computational challenges of searching the parameter space by using an extrapolation method to obtain a reliable difference quotient for the parameter derivatives based on the central difference. The algorithm is tested on 12 compounds and is shown to reduce the error for a number of bulk properties.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Erratum
    5. Corrigendum
    1. Efficient optimization of van der Waals parameters from bulk properties (pages 2313–2319)

      Steven K. Burger and G. Andrés Cisneros

      Article first published online: 5 JUL 2013 | DOI: 10.1002/jcc.23376

      Thumbnail image of graphical abstract

      When developing a force field for a compound, fitting van der Waals (vdW) terms is often avoided because of the computational complexity involved. This article provides a novel approach for efficiently optimizing vdW terms, based on both ab initio dimer energies and condensed phase properties. The approach avoids the challenges of exhaustively searching the parameter space by using an extrapolation method to obtain derivatives.

    2. Ab initio study of the high-temperature phase transition in crystalline GeO2 (pages 2320–2326)

      Volker L. Deringer, Marck Lumeij, Ralf P. Stoffel and Richard Dronskowski

      Article first published online: 19 JUL 2013 | DOI: 10.1002/jcc.23387

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      Ab initio thermochemical computations are performed to probe the phase transition of crystalline germanium dioxide: from the low-temperature rutile type to the high-temperature α-quartz type polymorph. The compound is a good test case that illustrates the possibilities, but also the limitations, of modern density functional theory methods in the regime above 0 Kelvin.

    3. Spin-component-scaled double hybrids: An extensive search for the best fifth-rung functionals blending DFT and perturbation theory (pages 2327–2344)

      Sebastian Kozuch and Jan M. L. Martin

      Article first published online: 26 AUG 2013 | DOI: 10.1002/jcc.23391

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      An extensive search for the most accurate, dispersion-corrected, spin-component-scaled, double hybrid (DSD) density functional theory functionals is reported. Performance only mildly depends on the choice of underlying generalized gradient approximations exchange and correlation functionals; even DSD-LDA performs respectably. Only a handful of empirical parameters are involved. Our best choices, DSD-PBEP86 and DSD-PBEhB95, achieve accuracy comparable to composite ab initio methods for a wide variety of thermochemical, kinetic, and spectroscopic properties.

    4. Finite-field method with unbiased polarizable continuum model for evaluation of the second hyperpolarizability of an open-shell singlet molecule in solvents (pages 2345–2352)

      Tomoya Inui, Yasuteru Shigeta, Katsuki Okuno, Takeshi Baba, Ryohei Kishi and Masayoshi Nakano

      Article first published online: 1 AUG 2013 | DOI: 10.1002/jcc.23395

      Thumbnail image of graphical abstract

      The second hyperpolarizability γ of complexes composed of the open-shell singlet 1,3-dipole molecule containing a boron atom and a water molecule in aqueous phase are investigated by the finite-field (FF) method combined with a standard polarized continuum model (PCM) and a newly proposed unbiased PCM (UBPCM). The FF-PCM method remarkably overshoots the γ value in comparison to full quantum-mechanical (QM), QM/molecular-mechanical, and molecular-dynamics (QM/MM MD) ones, while the FF-UBPCM method reproduces QM/MM MD results.

    5. Long-range corrected density functionals combined with local response dispersion: A promising method for weak interactions (pages 2353–2359)

      Rahul Kar, Jong-Won Song, Takeshi Sato and Kimihiko Hirao

      Article first published online: 1 AUG 2013 | DOI: 10.1002/jcc.23396

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      Calculations with the S66 intermolecular complexes at equilibrium and nonequilibrium geometries suggest that LC−BOP12+LRD and LCgau−BOP+LRD methods are well-balanced, lower-cost alternatives to other high-level methods.

    6. Overcoming dissipation in the calculation of standard binding free energies by ligand extraction (pages 2360–2371)

      Camilo Velez-Vega and Michael K. Gilson

      Article first published online: 26 AUG 2013 | DOI: 10.1002/jcc.23398

      Thumbnail image of graphical abstract

      The challenge of computing the reversible inline image from steered molecular dynamics and umbrella sampling/Bennett acceptance ratio (BAR) simulations is examined for two host–guest complexes. For both methods, the choice of artificial pulling/restraining points strongly influences the degree of irreversibility in the computed work. The fluctuation-guided pulling (FGP) scheme is proposed and tested, efficiently identifying low-dissipation pathways from which greatly improved values of the reversible work can be obtained, either by direct calculation of the potential of mean force (PMF) or through the use of these FGP pathways as guiding routes for equilibrium umbrella sampling/BAR simulations.

    7. Accurate relativistic adapted gaussian basis sets for francium through ununoctium without variational prolapse and to be used with both uniform sphere and gaussian nucleus models (pages 2372–2379)

      Tiago Quevedo Teodoro and Roberto Luiz Andrade Haiduke

      Article first published online: 2 AUG 2013 | DOI: 10.1002/jcc.23400

      Thumbnail image of graphical abstract

      Prolapse-free relativistic adapted Gaussian basis sets for francium up to ununoctium atoms are developed to be employed with the uniform sphere and Gaussian nuclei. The largest basis set size is 33s30p19d14f functions for 7p block elements, and the errors do not exceed 15.4 miliHartree, which implies a good balance between computational cost and accuracy for relativistic calculations.

    8. Contributions of pauli repulsions to the energetics and physical properties computed in QM/MM methods (pages 2380–2388)

      Yingdi Jin, Erin R. Johnson, Xiangqian Hu, Weitao Yang and Hao Hu

      Article first published online: 6 AUG 2013 | DOI: 10.1002/jcc.23401

      Thumbnail image of graphical abstract

      Without interfragment Pauli repulsions, the electrons of a quantum mechanical (QM) fragment penetrate into the space of neighboring molecular mechanical (MM) fragments, leading to incorrect electron density and consequently incorrect electrostatic and magnetic properties in conventional QM/MM methods.

    9. Convergence in the QM-only and QM/MM modeling of enzymatic reactions: A case study for acetylene hydratase (pages 2389–2397)

      Rong-Zhen Liao and Walter Thiel

      Article first published online: 1 AUG 2013 | DOI: 10.1002/jcc.23403

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      Quantum-mechanics-only and quantum mechanics/molecular mechanics calculations, with the quantum mechanics region ranging from 408 atoms to 657 atoms, are performed. The convergence behavior of quantum-mechanics-only and quantum mechanics/molecular methods in the modeling of enzymatic reactions is assessed.

  3. Erratum

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Erratum
    5. Corrigendum
    1. You have free access to this content
    2. You have free access to this content
      Erratum: On-the-path random walk sampling for efficient optimization of minimum free energy path (page 2400)

      M. E. Chen and W. Yang

      Article first published online: 14 AUG 2013 | DOI: 10.1002/jcc.23411

      This article corrects:

      On-the-path random walk sampling for efficient optimization of minimum free-energy path

      Vol. 30, Issue 11, 1649–1653, Article first published online: 21 MAY 2009

  4. Corrigendum

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Erratum
    5. Corrigendum
    1. You have free access to this content
      Corrigendum: Inter- and intramolecular dispersion interactions (pages 2401–2402)

      M. Swart, M. Solà and F. M. Bickelhaupt

      Article first published online: 19 JUL 2013 | DOI: 10.1002/jcc.23386

      This article corrects:

      Inter- and intramolecular dispersion interactions

      Vol. 32, Issue 6, 1117–1127, Article first published online: 4 NOV 2010

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