Journal of Computational Chemistry

Cover image for Vol. 34 Issue 23

5 September 2013

Volume 34, Issue 23

Pages i–iv, 1969–2054

  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 23 (pages i–ii)

      Article first published online: 23 JUL 2013 | DOI: 10.1002/jcc.23392

      Thumbnail image of graphical abstract

      The picture shows the density of the binding 6s orbital combination for the most stable predicted planar D2h Au10 cluster, presented by Daniel A. Götz, Rolf Schäfer, and Peter Schwerdtfeger on page 1975. The bonding molecular orbital lies deep within the 5d space of gold due to relativistic effects stabilizing planar structures. The isomeric three-dimensional C2v structure lies close by in energy, making a prediction for the most stable geometric structure very difficult for quantum chemical methods.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 23 (pages iii–iv)

      Article first published online: 23 JUL 2013 | DOI: 10.1002/jcc.23393

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      A versatile method for calculating solvation thermodynamic quantities for molecules is developed by Yuichi Harano, Roland Roth, and Shuntaro Chiba on page 1969. The thermodynamic quantities are estimated as a linear combination of four fundamental geometric measures of the atomic species, which are defined by Hadwiger's theorem and the coefficients reflecting their solvation properties. This theoretical treatment enables the solvation free energy to be calculated with high accuracy, despite the limited computational load. The method can be applied to an all-atom molecular model, allowing the stability of these molecules' structures in solution to be evaluated.

  2. Full Papers

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    1. A morphometric approach for the accurate solvation thermodynamics of proteins and ligands (pages 1969–1974)

      Yuichi Harano, Roland Roth and Shuntaro Chiba

      Article first published online: 18 JUN 2013 | DOI: 10.1002/jcc.23348

      Thumbnail image of graphical abstract

      The thermodynamic quantities are estimated as a linear combination of four fundamental geometric measures of the atomic species, which are defined by Hadwiger's theorem, and the coefficients reflecting their solvation properties. This treatment enables the calculation of the solvation free energy with high accuracy, despite the limited computational load.

    2. The performance of density functional and wavefunction-based methods for 2D and 3D structures of Au10 (pages 1975–1981)

      Daniel A. Götz, Rolf Schäfer and Peter Schwerdtfeger

      Article first published online: 29 MAY 2013 | DOI: 10.1002/jcc.23338

      Thumbnail image of graphical abstract

      Can current quantum chemical methods correctly predict the energetic sequence between different gold clusters and the transition from 2D (shown on the left for the purely bonding orbital) to 3D (shown on the right) structures? The result is perhaps discouraging and best answered with a “no,” given the limited computer power available. This illustrates the current dilemma of correctly describing (near) metallic systems with close-lying isomeric structures.

    3. First principle and ReaxFF molecular dynamics investigations of formaldehyde dissociation on Fe(100) surface (pages 1982–1996)

      Takahiro Yamada, Donald K. Phelps and Adri C. T. van Duin

      Article first published online: 26 JUN 2013 | DOI: 10.1002/jcc.23320

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      Detailed formaldehyde adsorption and dissociation reactions on an Fe(100) surface are studied using first principle calculations and molecular dynamics simulations, and results are compared with available experimental data. The study includes formaldehyde, formyl radical, and CO adsorption and dissociation energy calculations on the surface; complete potential energy diagram construction; simulation of formaldehyde adsorption and dissociation reaction on the surface using reactive force fields (ReaxFF); and reaction rate calculations of adsorbates using transition state theory.

    4. The α-effect exhibited in gas-phase SN2@N and SN2@C reactions (pages 1997–2005)

      Yi Ren, Xi-Guang Wei, Si-Jia Ren, Kai-Chung Lau, Ning-Bew Wong and Wai-Kee Li

      Article first published online: 19 JUN 2013 | DOI: 10.1002/jcc.23356

      Thumbnail image of graphical abstract

      Calculations at G2(+)M theory show the enhanced reactivity exhibited by six α-oxy-Nus in the gas-phase SN2 reactions toward NR2Cl (R = H, Me) and RCl (R = Me, i-Pr). The magnitude of the α-effect in the SN2@N reactions is generally smaller than that in the SN2@C counterparts, but their variation trend with the identity of the α-atom is very similar. The origin of the α-effect of the SN2@N reactions largely arises from transition state stabilization.

    5. The ORP basis set designed for optical rotation calculations (pages 2006–2013)

      Angelika Baranowska-Łączkowska and Krzysztof Z. Łączkowski

      Article first published online: 5 JUN 2013 | DOI: 10.1002/jcc.23347

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      A basis set tailored for optical rotation calculations is presented and successfully used in calculations carried out for 32 test systems. The ORP basis set is shown to outperform larger basis sets, among them the aug-cc-pVTZ and the aug-pc-2 basis sets.

    6. Polarization functions for the modified m6-31G basis sets for atoms Ga through Kr (pages 2014–2019)

      Alexander V. Mitin

      Article first published online: 18 JUN 2013 | DOI: 10.1002/jcc.23353

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      Polarization functions are important for ab initio calculations, which take into account correlation energy. This article presents 2df polarization functions for the modified m6-31G basis for third-row atoms, and advantages of this basis over the known 6-31G and other similar basis sets. The figure shows relative average absolute deviation percentages of calculated harmonic frequencies from experimental values for different basis sets.

    7. A high-accuracy theoretical study of the CHnP Systems n = 1–3 (pages 2020–2031)

      Ringo Rey-Villaverde, Hubert Cybulski, Jesús R. Flores and Berta Fernández

      Article first published online: 26 JUN 2013 | DOI: 10.1002/jcc.23357

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      High-level electronic structure computations on the important but experimentally elusive CHnP systems n = 1–3 are performed. The explicitly correlated RCCSD(T)-F12 method is employed for geometry optimizations and vibrational frequency calculations. Vibrational configuration interaction (VCI) theory is used to account for vibrational averaging and anharmonicity effects. Basis set limit extrapolations are carried out to determine accurate thermochemical quantities. Electronic excited states are studied with coupled cluster approaches and the multi-reference configuration interaction method (MRCI). The image shows the vibrationally averaged structure of H2CPH(1A') (in Å and °), computed at the RCCSD(T)-F12b/cc-CVTZ-F12 level.

    8. A polarizable ellipsoidal force field for halogen bonds (pages 2032–2040)

      Likai Du, Jun Gao, Fuzhen Bi, Lili Wang and Chengbu Liu

      Article first published online: 26 JUN 2013 | DOI: 10.1002/jcc.23362

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      Anisotropic effects and short-range quantum effects are essential characters in halogen bonds. In the proposed polarizable ellipsoidal force field (PEff), the anisotropic charge distribution is represented with the combination of a negatively charged sphere and a positively charged ellipsoid. The polarization energy is incorporated by the induced dipole model. The PEff model correctly reproduces the potential energy surface of halogen bonds at the MP2 level.

  3. Software News and Updates

    1. Top of page
    2. Cover Image
    3. Full Papers
    4. Software News and Updates
    1. CENCALC: A computational tool for conformational entropy calculations from molecular simulations (pages 2041–2054)

      Ernesto Suárez, Natalia Díaz, Jefferson Méndez and Dimas Suárez

      Article first published online: 8 JUN 2013 | DOI: 10.1002/jcc.23350

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      CENCALC estimates the conformational entropy of single molecules from extended molecular dynamics simulations using various methods based on the so-called mutual information expansion, which, in turn, is built upon the converged probability density functions of the individual torsion angles, pairs of torsions, and so forth. CENCALC implements the correlation-corrected multibody local approximation that retrieves the maximum amount of genuine correlation from the available sampling and that can be applied to relatively large molecules (e.g., polypeptides).

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