Journal of Computational Chemistry

Cover image for Vol. 36 Issue 20

Edited By: Charles L. Brooks III, Masahiro Ehara, Gernot Frenking, and Peter R. Schreiner

Impact Factor: 3.589

ISI Journal Citation Reports © Ranking: 2014: 36/157 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

Associated Title(s): International Journal of Quantum Chemistry, Wiley Interdisciplinary Reviews: Computational Molecular Science

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  1. You have full text access to this OnlineOpen article
    SDA 7: A modular and parallel implementation of the simulation of diffusional association software

    Michael Martinez, Neil J. Bruce, Julia Romanowska, Daria B. Kokh, Musa Ozboyaci, Xiaofeng Yu, Mehmet Ali Öztürk, Stefan Richter and Rebecca C. Wade

    Article first published online: 29 JUN 2015 | DOI: 10.1002/jcc.23971

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    SDA 7 is the latest release of the Simulation of Diffusional Association software, a Brownian dynamics simulation package for the modeling of biomolecular systems. This release has been fully rewritten in Fortran 90, using an object-oriented programming approach, with improved parallelization on multi-core shared memory architectures. It consolidates the previously separate versions used for simulations of bimolecular and many-molecule systems, and allows modeling of solute flexibility.

  2. Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling

    Chao Lv, Erick W. Aitchison, Dongsheng Wu, Lianqing Zheng, Xiaolin Cheng and Wei Yang

    Article first published online: 29 JUN 2015 | DOI: 10.1002/jcc.23982

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    The orthogonal space tempering simulation shows that hydrogen sulfide is amphipathic, and thus is favorably localized at the interface between the head-group and acyl chain regions. Because the membrane binding affinity of H2S is mainly governed by its small hydrophobic moiety and the barrier height inbetween the interfacial region and the membrane center is largely determined by its moderate polarity, the trans-membrane free energy barriers to encounter by this toxic molecule are very small.

  3. Is molecular alignment an indispensable requirement in the MIA-QSAR method?

    Stephen J. Barigye and Matheus P. Freitas

    Article first published online: 29 JUN 2015 | DOI: 10.1002/jcc.23992

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    The 2D-Discrete Fourier Transform is introduced as a strategy for creating a common base to construct multivariate images for chemical structures using their magnitude spectra. Thus, for the first time, the modeling of structurally diverse noncongruent chemical images in the Multivariate Image Analysis-Quantitative Structure Activity Relationship context is possible.

  4. Fragment-based similarity searching with infinite color space

    Jakub Gunera and Peter Kolb

    Article first published online: 29 JUN 2015 | DOI: 10.1002/jcc.23974

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    RedFrag is a fast and intuitive algorithm for similarity-based molecule screenings. It uses a reduced graph representation of molecules, with an infinite color space for each of the nodes. This makes it an evolved version of feature trees while retaining the efficiency of this concept. RedFrag is evaluated both retro- as well as prospectively, the latter leading to five novel binders of endothiapepsin.

  5. Statistical analysis of electronic excitation processes: Spatial location, compactness, charge transfer, and electron-hole correlation

    Felix Plasser, Benjamin Thomitzni, Stefanie A. Bäppler, Jan Wenzel, Dirk R. Rehn, Michael Wormit and Andreas Dreuw

    Article first published online: 29 JUN 2015 | DOI: 10.1002/jcc.23975

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    A new methodology for the analysis of electronic excitations is introduced. The formalism, which is based on a statistical analysis of the wavefunction of the electron-hole pair, allows to quantify the spatial location and compactness of electronic excitations, as well as giving new insight into charge transfer and correlation effects. A special focus is laid on different ways to quantify charge separation. In the figure, the hole (red) and electron (blue) densities are shown for a Rydberg state of cytosine. The hole size σh, the electron size σe, and the distance between the charge centroids inline image are marked.

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