Journal of Computational Chemistry

Cover image for Vol. 35 Issue 15

5 June 2014

Volume 35, Issue 15

Pages i–iv, 1107–1164

  1. Cover Image

    1. Top of page
    2. Cover Image
    3. Rapid Communication
    4. Full Papers
    1. You have free access to this content
      Cover Image, Volume 35, Issue 15 (pages i–ii)

      Version of Record online: 26 APR 2014 | DOI: 10.1002/jcc.23626

      Thumbnail image of graphical abstract

      The cover shows a heterogeneous anisotropic network model based on the alpha shape theory (αHANM), which is constructed using the crystal structure of bovine pancreatic trypsin inhibitor (PDB ID: 5PTI). The right part of the figure illustrates the decision making process to add harmonic springs between the coarse grained beads. The full connections between the beads are added when the circumcircles of the triangles (2D) or tetrahedrals (3D) do not include another bead. Otherwise, a corresponding spring is removed. This αHANM is parameterized by the progressive fluctuation matching method for accurately reproducing experimental B-factors, as presented by Fei Xia et al. on page 1111 (DOI: 10.1002/jcc.23587).

    2. You have free access to this content
      Cover Image, Volume 35, Issue 15 (pages iii–iv)

      Version of Record online: 26 APR 2014 | DOI: 10.1002/jcc.23627

      Thumbnail image of graphical abstract

      The study by Solen Ekesan, Seyit Kale, and Judith Herzfeld on page 1159 (DOI: 10.1002/jcc.23612) demonstrates that context-independent, pairwise interactions can describe the aufbau of diverse elements, including Hund's rule, the energies of electron transfers between atoms, and the spatial disposition of electrons according to orbital hybridization. The cover foreground shows chlorine in several oxidation states, as described by an explicit electron model. The background shows a graph of the pairwise potentials that provide these descriptions.

  2. Rapid Communication

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    2. Cover Image
    3. Rapid Communication
    4. Full Papers
    1. Toward product control in ring-opening oligomerization of 9H-9-borafluorenes (pages 1107–1110)

      Hui Zhu and Zheng-Wang Qu

      Version of Record online: 7 FEB 2014 | DOI: 10.1002/jcc.23555

      Thumbnail image of graphical abstract

      The remarkable substituent effects of the bulky tert-butyl-substitution on the ring-opening oligomerization reactivity of 9H−9-borafluorene compounds are mainly due to the evidently increased trimerization barrier from intermediate G on substitution. Both G and H are actually formed from ring-opening aryl exchange through double B[BOND]C[BOND]B bridges and, thus, cannot support the Köster's postulate. Experimentally desired polymerization channels are expected at a controlled heating, opening the way toward higher oligomers with improved thermal stability.

  3. Full Papers

    1. Top of page
    2. Cover Image
    3. Rapid Communication
    4. Full Papers
    1. Identifying essential pairwise interactions in elastic network model using the alpha shape theory (pages 1111–1121)

      Fei Xia, Dudu Tong, Lifeng Yang, Dayong Wang, Steven C. H. Hoi, Patrice Koehl and Lanyuan Lu

      Version of Record online: 19 MAR 2014 | DOI: 10.1002/jcc.23587

      Thumbnail image of graphical abstract

      The image shows a comparison of the elastic networks generated by the conventional cutoff-based approach (top) and alpha shape theory (bottom). The protein-s Protein Data Bank code is 1LTU. The figure shows detailed spring connections for the protrusion part of the protein, as elastic network models based on cutoffs have difficulty in accurately reproducing experimental B-factors in this region. Excellent agreement with the experimental B-factor is achieved after removing a few pairwise connections in accordance with the alpha shape theory.

    2. gWEGA: GPU-accelerated WEGA for molecular superposition and shape comparison (pages 1122–1130)

      Xin Yan, Jiabo Li, Qiong Gu and Jun Xu

      Version of Record online: 11 APR 2014 | DOI: 10.1002/jcc.23603

      Thumbnail image of graphical abstract

      A graphic processing unit (GPU)-accelerated weighted Gaussian algorithm for shape and/or pharmacophore features-based molecular superimposing is reported. The algorithm can search more than 55 million three-dimensional structures per second with multiple GPU nodes.

    3. Toward the understanding of the environmental effects on core ionizations (pages 1131–1139)

      Adèle D. Laurent, Vitaly N. Glushkov, Thibaut Very and Xavier Assfeld

      Version of Record online: 18 APR 2014 | DOI: 10.1002/jcc.23604

      Thumbnail image of graphical abstract

      A systematic methodology is used to evaluate core ionization energies of amino acids in the gas phase or in part of the human serum albumin protein. This is performed with the help of QM/MM tools and, more precisely, with the asymptotic projection formalism, accounting for orthogonality constraints between states. This work shows that environment effects are not trifling when computing core ionization energies, as they might be as large as 10 eV.

    4. SN1-SN2 and SN2-SN3 mechanistic changes revealed by transition states of the hydrolyses of benzyl chlorides and benzenesulfonyl chlorides (pages 1140–1148)

      Shinichi Yamabe, Guixiang Zeng, Wei Guan and Shigeyoshi Sakaki

      Version of Record online: 14 APR 2014 | DOI: 10.1002/jcc.23607

      Thumbnail image of graphical abstract

      Transition states of hydrolysis reactions Z[BOND]C6H4[BOND]X[BOND]Cl are investigated with specific water molecules (n = 6, 9, 11, 17, 23, and 29), where X = CH2, and SO2 and Z = O2N, Cl, H, H3C, and H3CO. In the case of a large n value and an electron-donating Z group, the hydrolysis reaction occurs through a SN2 mechanism. However, the combination of a small n value and an electron-withdrawing Z group converts the reaction mechanism to SN3.

    5. Using operators to expand the block matrices forming the Hessian of a molecular potential (pages 1149–1158)

      Martin Carlsen

      Version of Record online: 16 APR 2014 | DOI: 10.1002/jcc.23609

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      Compact expressions for the derivatives of a molecular potential are important in theoretical and practical applications. In this work, the second-order derivatives are expanded in terms of operators. This leads to a new set of formulas that can be implemented efficiently in high-level programming languages.

    6. Transferable pseudoclassical electrons for aufbau of atomic ions (pages 1159–1164)

      Solen Ekesan, Seyit Kale and Judith Herzfeld

      Version of Record online: 21 APR 2014 | DOI: 10.1002/jcc.23612

      Thumbnail image of graphical abstract

      The development of force fields with explicit electrons is motivated by the computational difficulty of quantum simulations of chemical reactions. This study demonstrates that context-independent, pairwise interactions can describe the aufbau of diverse elements, including Hund's rule, the energies of electron transfers between atoms, and the spatial disposition of electrons according to orbital hybridization. In effect, LEWIS• constitutes a pointillist approach to density functional theory, providing an efficient route to reactive simulations.

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