Journal of Computational Chemistry

Cover image for Vol. 34 Issue 31

5 December 2013

Volume 34, Issue 31

Pages i–iv, 2667–2756

  1. Cover Image

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    3. Rapid Communication
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    1. You have free access to this content
      Cover Image, Volume 34, Issue 31 (pages i–ii)

      Version of Record online: 23 OCT 2013 | DOI: 10.1002/jcc.23479

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      By following the scheme of the grid empowered molecular simulator (GEMS), Leonardo Pacifici, Marco Verdicchio, Noelia Faginas Lago, Andrea Lombardi, and Alessandro Costantini on page 2668 calculate an extended set of high-level abinitio electronic energy values. The calculated values are fitted using a many-body expansion technique and a full-dimensional N2 + N2 potential energy surface (PES), also allowing the N atom exchange to be produced. Plots of the obtained PES show the change of the intermediate geometry from reactants to products.

    2. You have free access to this content
      Inside Cover, Volume 34, Issue 31 (pages iii–iv)

      Version of Record online: 23 OCT 2013 | DOI: 10.1002/jcc.23480

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      The reaction dynamics of ethylene adsorption onto the Si(001) surface is studied by Yung Ting Lee and Jyh Shing Lin on page 2697 by combining density functional theory (DFT)-based molecular dynamics simulations with a molecular adsorption sampling scheme for investigating reaction pathways and corresponding populations. The major reaction pathway is indirect adsorption, in which ethylene forms the π-bond with the Si dimer and then turns into di-σ-bonded C2H4(ads). The spectrogram, constructed by the short-time Fourier transform of the structural coordinate autocorrelation function (STFT-SCAF), illustrates that the C[DOUBLE BOND]C stretching mode of π-bonded C2H4(ads) shifts to the C–C stretching mode of di-σ-bonded C2H4(ads).

  2. Rapid Communication

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    1. The RTAM electronic bibliography, version 17.0, on relativistic theory of atoms and molecules (page 2667)

      Pekka Pyykkö

      Version of Record online: 4 OCT 2013 | DOI: 10.1002/jcc.23454

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      Relativistic effects strongly influence the properties of heavier atoms and molecules. The RTAM bibliography is a collection of 16,566 references on the topic, starting from Sommerfeld (1916).

  3. Full Papers

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    4. Full Papers
    1. A high-level ab initio study of the N2 + N2 reaction channel (pages 2668–2676)

      Leonardo Pacifici, Marco Verdicchio, Noelia Faginas Lago, Andrea Lombardi and Alessandro Costantini

      Version of Record online: 26 AUG 2013 | DOI: 10.1002/jcc.23415

      Thumbnail image of graphical abstract

      An extended set of high-level ab initio electronic energy values is calculated by following the scheme of the grid empowered molecular simulator. The calculated values are fitted using a many-body expansion technique. A full dimensional N2 + N2 potential energy surface, including the N exchange reaction, is produced. This allows some key features of the various channels of the process to be investigated, and the routine needed to perform dynamical calculations to be built. The image shows the MRPT2/CCSD(T) isoenergetic contour plots for the X arrangement.

    2. The F130L mutation in streptavidin reduces its binding affinity to biotin through electronic polarization effect (pages 2677–2686)

      Juan Zeng, Xiangyu Jia, John Z. H. Zhang and Ye Mei

      Version of Record online: 2 SEP 2013 | DOI: 10.1002/jcc.23421

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      The F130L mutation-induced binding loss of biotin to streptavidin is investigated through molecular simulations and an end-point free energy method. With the AMBER03 charge, the binding pattern cannot be maintained, and the loss of binding free energy is underestimated. When the polarized protein-specific charge is used, binding structures and the loss of binding free energy are more in line with the experimental observations.

    3. Molecular modeling for Cu(II)-aminopolycarboxylate complexes: Structures, conformational energies, and ligand binding affinities (pages 2687–2696)

      Marina Ćendić, Zoran D. Matović and Robert J. Deeth

      Version of Record online: 16 SEP 2013 | DOI: 10.1002/jcc.23437

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      Aminopolycarboxylate ligands are promising for new treatments for copper-related conditions like Wilson's disease. Computational chemistry can play a significant role in the design of new chelators, but drug discovery involves too many calculations for density functional theory (DFT) to be viable. A classical force field based on ligand field molecular mechanics is designed for open-shell metal centers and captures the DFT result for these strongly Jahn–Teller-active Cu(II) complexes at a small fraction of the computational cost.

    4. Ab Initio molecular dynamics study of ethylene adsorption onto Si(001) surface: Short-time fourier transform analysis of structural coordinate autocorrelation function (pages 2697–2706)

      Yung Ting Lee and Jyh Shing Lin

      Version of Record online: 16 SEP 2013 | DOI: 10.1002/jcc.23434

      Thumbnail image of graphical abstract

      The reaction dynamics of ethylene adsorption onto the Si(001) surface is studied by combining density functional theory-based molecular dynamics simulations with a molecular adsorption sampling scheme to investigate reaction pathways and corresponding populations. The major reaction pathway is indirect adsorption, in which ethylene forms a π-bond with the Si dimer and then turns into di-σ-bonded C2H4(ads).

    5. Comparison of the capillary wave method and pressure tensor route for calculation of interfacial tension in molecular dynamics simulations (pages 2707–2715)

      Stella Nickerson, Denzil S. Frost, Harrison Phelan and Lenore L. Dai

      Version of Record online: 30 SEP 2013 | DOI: 10.1002/jcc.23443

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      Molecular dynamics simulations provide a unique tool for examining interfacial phenomena, allowing for a molecular-resolution view of the interface and its dynamics. Because of this, it is important to accurately and precisely calculate interfacial tension from molecular dynamics. This article examines two methods, the capillary wave method and the more commonly used pressure tensor route, and compares these methods with respect to both precision and accuracy.

    6. Modeling disordered morphologies in organic semiconductors (pages 2716–2725)

      Tobias Neumann, Denis Danilov, Christian Lennartz and Wolfgang Wenzel

      Version of Record online: 30 SEP 2013 | DOI: 10.1002/jcc.23445

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      Organic thin films are essential for many diverse electronic applications, including light-emitting diodes and organic photovoltaics. Modeling their properties on the basis of detailed molecular structures requires the generation of mostly amorphous representative morphologies. To solve the computational problem of slow time-scales for the formation of the morphology, a linear-scaling Monte-Carlo-based method is developed, which generates morphologies by the simulation of vapor deposition of molecular films.

    7. Absolute free energies of biomolecules from unperturbed ensembles (pages 2726–2741)

      Gevorg Grigoryan

      Version of Record online: 16 OCT 2013 | DOI: 10.1002/jcc.23448

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      Most methods for computing free-energy differences between conformational states integrate over paths connecting them. If it were possible to estimate absolute free energies of end states, the difference would emerge directly, regardless of how complex a path connecting the two might be. A method for computing absolute free energies provides enough accuracy (in reasonable amounts of simulation time) to enable quantitative comparisons of very different structural states.

    8. Monte carlo simulations of proteins at constant pH with generalized born solvent, flexible sidechains, and an effective dielectric boundary (pages 2742–2756)

      Savvas Polydorides and Thomas Simonson

      Version of Record online: 5 OCT 2013 | DOI: 10.1002/jcc.23450

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      The image shows titration curves for 12 sidechains in a bovine pancreatic trypsin inhibitor, obtained from constant-pH Monte Carlo simulations with a fixed backbone, flexible sidechains, and a generalized Born implicit solvent. To overcome the many-body character of the solvent model, a very efficient “native environment” approximation is used for the solvation radii. For 12 proteins and 167 titratable sidechains, the best rms pKa error is 1.1 units using a physically reasonable protein dielectric constant of 4.

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