Journal of Computational Chemistry

Cover image for Vol. 35 Issue 10

15 April 2014

Volume 35, Issue 10

Pages i–vi, 765–828

  1. Cover Image

    1. Top of page
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    1. You have free access to this content
      Cover Image, Volume 35, Issue 10 (pages i–ii)

      Version of Record online: 10 MAR 2014 | DOI: 10.1002/jcc.23581

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      LUMPAC (LUMinescence PACkage) was developed with the aim of enabling the user-friendly and computationally-efficient theoretical study of luminescent systems that contain lanthanide ions. This software, presented by José Diogo L. Dutra et al. on page 772, will contribute to the use and diffusion of theoretical methods among groups who are focused on understanding and designing lanthanide-based luminescent devices.

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      Cover Image, Volume 35, Issue 10 (pages iii–iv)

      Version of Record online: 10 MAR 2014 | DOI: 10.1002/jcc.23582

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      The computation of root mean square deviations (RMSDs) is an important core function in structural bioinformatics. In many scenarios, such as the clustering of docking results, structural variations are often dominated by rigid transformations of the molecule. RMSDs resulting from rigid transformations can be computed in constant time from the molecule's covariance matrix, which can be precomputed in linear time, as demonstrated by Anna K. Hildebrandt et al. on page 765. The cover illustrates clustering as it occurs in a docking context.

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      Cover Image, Volume 35, Issue 10 (pages v–vi)

      Version of Record online: 10 MAR 2014 | DOI: 10.1002/jcc.23583

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      The (H2—H2)+ system exhibits a mixed-valence character when the two hydrogen dimers are sufficiently apart, with the hole localized on the dimer with the longest bond. The cover shows energies of the two lowest electronic states (dashed lines) as a function of a reaction coordinate ξ that connects the two ground-state minima. On page 802, Gian Luigi Bendazzoli et al. find that the total position-spread tensor Λ is a powerful indicator of the electron delocalization within the two molecules. A spectacular peak of Λ is found for both the ground and the excited states in the transition state region.

  2. Full Papers

    1. Top of page
    2. Cover Image
    3. Full Papers
    1. Efficient computation of root mean square deviations under rigid transformations (pages 765–771)

      Anna K. Hildebrandt, Matthias Dietzen, Thomas Lengauer, Hans-Peter Lenhof, Ernst Althaus and Andreas Hildebrandt

      Version of Record online: 19 DEC 2013 | DOI: 10.1002/jcc.23513

      Thumbnail image of graphical abstract

      The computation of root mean square deviations (RMSDs) is an important core function in structural bioinformatics. If approached naively, each RMSD evaluation takes time linear in the number of atoms. In many scenarios, such as the clustering of docking results, structural variations are often dominated by rigid transformations of the molecule. RMSDs resulting from rigid transformations can be computed in constant time from the molecule's covariance matrix, which can be precomputed in linear time. The popular Ward distance can be computed in constant time from RMSDs, yielding a constant-time approach for Ward distances under rigid transformations.

    2. LUMPAC lanthanide luminescence software: Efficient and user friendly (pages 772–775)

      José Diogo L. Dutra, Thiago D. Bispo and Ricardo O. Freire

      Version of Record online: 14 FEB 2014 | DOI: 10.1002/jcc.23542

      Thumbnail image of graphical abstract

      The LUMinescence PACkage (LUMPAC) software is developed to enable the user-friendly and computationally efficient theoretical study of luminescent systems that contain lanthanide ions. This software contributes to the use and diffusion of theoretical methods that focus on the understanding and design of lanthanide-based luminescent devices.

    3. Fully atomistic molecular-mechanical model of liquid alkane oils: Computational validation (pages 776–788)

      Tsvetan K. Zahariev, Radomir I. Slavchov, Alia V. Tadjer and Anela N. Ivanova

      Version of Record online: 19 FEB 2014 | DOI: 10.1002/jcc.23546

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      Careful construction of explicit molecular models for fluid alkanes enables a deeper understanding of a number of processes at the oil–water interface or in a homogeneous hydrophobic environment. Atomistic molecular dynamics simulations of liquid normal pentane, hexane, and heptane are undertaken in this study, and the optimum simulation algorithm is proposed based on validation against a set of structural, thermodynamic, and transport experimental properties.

    4. A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons (pages 789–801)

      Oliwia M. Szklarczyk, Stephan J. Bachmann and Wilfred F. van Gunsteren

      Version of Record online: 19 FEB 2014 | DOI: 10.1002/jcc.23551

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      A polarizable force field for molecular dynamics simulations of hydrocarbons is reported. The polarizability of the compounds is introduced through the charge-on-spring or Drude's oscillator model. The model parameters are tested for structural, thermodynamic, dielectric, and dynamic properties. Good agreement with experimental data for a large set of properties for each considered system is obtained, resulting in a transferable set of polarizable force field parameters for CH2, CH3, and CH4 moieties.

    5. The total Position Spread in mixed-valence compounds: A study on the H4+ model system (pages 802–808)

      Gian Luigi Bendazzoli, Muammar El Khatib, Stefano Evangelisti and Thierry Leininger

      Version of Record online: 14 FEB 2014 | DOI: 10.1002/jcc.23557

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      The total position spread tensor, Λ, is applied to a mixed-valence model system. This tensor is a measure of the electron delocalization, and it is very sensitive to the change of the nature of the wavefunction, in particular if associated to a charge transfer. For class II systems, there are geometrical configurations where low-lying electronic states present avoided-crossing. At that moment, the Λ shows a marked peak, indicating that there is a strong delocalization of the wavefunction.

    6. Predicting adsorption enthalpies on silicalite and HZSM-5: A benchmark study on DFT strategies addressing dispersion interactions (pages 809–819)

      Cheng-chau Chiu, Georgi N. Vayssilov, Alexander Genest, Armando Borgna and Notker Rösch

      Version of Record online: 18 FEB 2014 | DOI: 10.1002/jcc.23558

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      Accuracy is evaluated for two DFT-based strategies for describing dispersive interactions when molecules adsorb in zeolites. For the adsorption of alkanes, alcohols, and water in HZSM-5/silicalite zeolites, the addition of an empirical force-field correction to a generalized gradient approximation functional (DFT-D) and the use of a nonlocal correlation functional (vdW-DF2) are compared with experimental data. Acceptable agreement between theory and the experiment is found for water and alcohol adsorption, whereas both methods overestimate the adsorption energies of alkane.

    7. Properties of atoms in electronically excited molecules within the formalism of TDDFT (pages 820–828)

      Eric Iván Sánchez-Flores, Rodrigo Chávez-Calvillo, Todd A. Keith, Gabriel Cuevas, Tomás Rocha-Rinza and Fernando Cortés-Guzmán

      Version of Record online: 15 FEB 2014 | DOI: 10.1002/jcc.23559

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      Time-dependent density functional theory (TDDFT) is used to obtain relaxed electron densities of excited states and thereby perform a subsequent topological analysis, in accordance with the quantum theory of atoms in molecules. This approach differs from previous work wherein DFT, rather than TDDFT, is used to determine the electron density of the excited state. Hopefully this new procedure will be useful in the study of different photochemical systems and processes.

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