Journal of Computational Chemistry

Cover image for Vol. 33 Issue 18

5 July 2012

Volume 33, Issue 18

Pages 1525–1585

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    1. Expanding molecular modeling and design tools to non-natural sidechains (pages 1525–1535)

      David Gfeller, Olivier Michielin and Vincent Zoete

      Article first published online: 14 APR 2012 | DOI: 10.1002/jcc.22982

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      Protein-protein interactions encode the wiring diagram of cellular signaling pathways and their deregulations underlie a variety of diseases, such as cancer. Inhibiting protein-protein interactions with peptide derivatives is a promising way to develop new biological and therapeutic tools. Here, we develop a general framework to computationally handle hundreds of non-natural amino acid sidechains and predict the effect of inserting them into peptides or proteins. Data generated in this work are all available at

    2. Placevent: An algorithm for prediction of explicit solvent atom distribution—Application to HIV-1 protease and F-ATP synthase (pages 1536–1543)

      Daniel J. Sindhikara, Norio Yoshida and Fumio Hirata

      Article first published online: 20 APR 2012 | DOI: 10.1002/jcc.22984

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      We have created an algorithm for automatically predicting the explicit solvent atom distribution of biomolecules using 3D-RISM. This procedure predicts optimal location of solvent molecules and ions given a rigid biomolecular structure and the solvent composition. Our results give excellent agreement with xperimental structure with an average prediction error of 0.39–0.65 Å. Our method can be performed directly on 3D-RISM output within minutes.

    3. Comparison of the electronic structure of different perylene-based dye-aggregates (pages 1544–1553)

      Volker Settels, Wenlan Liu, Jens Pflaum, Reinhold F. Fink and Bernd Engels

      Article first published online: 19 APR 2012 | DOI: 10.1002/jcc.22986

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      The efficiencies of organic devices strongly depend on the optoelectronic properties of the processed semiconductors. Examples are the absorption and emission band maxima or the exciton diffusion length, which strongly varies for diverse perylene-based materials. Our analysis reveals that variations result from differences in their geometrical arrangement in aggregates or crystals, as the corresponding electronic structures strongly resemble each other.

    4. First-principles calculations on thermodynamic properties of BaTiO3 rhombohedral phase (pages 1554–1563)

      Andrei V. Bandura and Robert A. Evarestov

      Article first published online: 19 APR 2012 | DOI: 10.1002/jcc.22988

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      Structural and electronic properties, as well as phonon frequencies were obtained for the rhombohedral phase of BaTiO3 crystal using hybrid PBE0 XC functionals. For the first time the bulk modulus, volume thermal expansion coefficient, heat capacity, and Grüneisen parameters in BaTiO3 rhombohedral phase have been estimated based on the results of first-principles calculations.

    5. GPU accelerated numerical simulations of viscoelastic phase separation model (pages 1564–1571)

      Keda Yang, Jiaye Su and Hongxia Guo

      Article first published online: 19 APR 2012 | DOI: 10.1002/jcc.22990

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      We introduce a complete implementation of viscoelastic phase separation model on a GPU. Our studies show that the GPU-based implementation can predict correctly the accepted results and provide about 190 times speedup over a single CPU core. Therefore, the GPU-based viscoelastic model is very promising for studying many phase separation processes of experimental and theoretical interests that often take place on the large length and time scales and are not easily addressed by a conventional CPU-based implementation.

  2. Software News and Updates

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    3. Software News and Updates
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      ERKALE—A flexible program package for X-ray properties of atoms and molecules (pages 1572–1585)

      Jussi Lehtola, Mikko Hakala, Arto Sakko and Keijo Hämäläinen

      Article first published online: 24 APR 2012 | DOI: 10.1002/jcc.22987

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      We present ERKALE, a novel software program for computing x-ray properties, such as ground-state electron momentum densities, Compton profiles, and core and valence electron excitation spectra of atoms and molecules. The program operates at Hartree-Fock or density-functional level of theory, and supports Gaussian basis sets of arbitrary angular momentum. ERKALE is written in an object oriented manner, making the code easy to understand and to extend to new properties while being ideal also for teaching purposes.