Journal of Computational Chemistry

Cover image for Vol. 34 Issue 16

15 June 2013

Volume 34, Issue 16

Pages i–iv, 1363–1437

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      Cover Image, Volume 34, Issue 16 (pages i–ii)

      Version of Record online: 9 MAY 2013 | DOI: 10.1002/jcc.23336

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      NBO 6.0, the next generation in natural bond orbital methods, is released by Frank Weinhold, Eric Glendening, and Clark Landis on page 1429. NBO 6.0 includes link-free connectivity for interfaces to popular electronic structure programs, new methods of analysis, and numerous algorithmic enhancements. The cover image is made with the NBOView 2.0 program and shows the sigma-type, 3-center/2-electron bonding NBO of the cyclobutenyl cation that arises from the strong overlap of the vacant valence orbital at C1 with the C2–C3 bond. Automated multicenter bond searches are one of the many new features of the NBO program.

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      Inside Cover, Volume 34, Issue 16 (pages iii–iv)

      Version of Record online: 9 MAY 2013 | DOI: 10.1002/jcc.23337

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      Although phytochromes are a major family of photosensory proteins, there are fewer contributions to their characterization from computational modeling than for related photosensory proteins, which is likely because high-resolution structures of phytochromes are relatively scarce. Based on one such structure, Olle Falklöf and Bo Durbeej on page 1363 report hybrid quantum mechanics/molecular mechanics (QM/MM) calculations of UV-vis absorption spectra of a bacteriophytochrome. The calculations provide valuable information on how the choice of QM/MM methodology affects the resulting spectra, and they reveal how the protein tunes the absorption of its bilin chromophore relative to solvent and gas phase environments.

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    1. Modeling of phytochrome absorption spectra (pages 1363–1374)

      Olle Falklöf and Bo Durbeej

      Version of Record online: 1 MAR 2013 | DOI: 10.1002/jcc.23265

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      Hybrid quantum mechanics/molecular mechanics (QM/MM) methods are used to calculate UV-vis absorption spectra of a photosensory protein belonging to the phytochrome family. Besides providing valuable information on how the choice of QM/MM methodology affects the resulting spectra, the article also sheds new light on how the protein tunes the absorption of its bilin chromophore.

    2. On-the-fly reconstruction of free-energy profiles using logarithmic mean-force dynamics (pages 1375–1384)

      Tetsuya Morishita, Satoru G. Itoh, Hisashi Okumura and Masuhiro Mikami

      Version of Record online: 5 MAR 2013 | DOI: 10.1002/jcc.23267

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      Logarithmic mean-force dynamics (LogMFD) is a method for free energy calculation, which uses a logarithmic form of free energy to efficiently explore free energy landscapes. Using LogMFD, free energy profiles can be obtained on-the-fly without postprocessing. This guide to using LogMFD details practical issues concerning protocol for choosing parameters and reducing errors due to energy dissipation.

    3. Automated discovery of chemically reasonable elementary reaction steps (pages 1385–1392)

      Paul M. Zimmerman

      Version of Record online: 18 MAR 2013 | DOI: 10.1002/jcc.23271

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      A new method is proposed to find low barrier transition states starting from a single reactant complex. It operates by first generating chemically feasible structures and then uses a double-ended string method to locate reaction paths. The method in its current implementation is highly useful for main group chemistry.

    4. Multireference calculations for ring inversion and double bond shifting in cyclooctatetraene (pages 1393–1397)

      Axel Schild and Beate Paulus

      Version of Record online: 18 MAR 2013 | DOI: 10.1002/jcc.23273

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      In its electronic ground state, ring inversion and double bond shifting occur in cyclooctatetraene, as shown schematically in the picture. Multireference calculation methods are used to determine the relevant structures of the ground state potential energy surface for these processes. The level at which dynamical and static electron correlations have to be treated to allow faithful numerical results is also investigated.

    5. Free-energy differences between states with different conformational ensembles (pages 1398–1408)

      Jose Antonio Garate and Chris Oostenbrink

      Version of Record online: 23 MAR 2013 | DOI: 10.1002/jcc.23276

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      The potential of mean force along the glycosidic χ angle is calculated using the LE/US method at different λ points for the alchemical transformation GTP (λ = 0) to 8-Br-GTP (λ = 1). The population preference (syn–anti) shifts during the progress of the alchemical transformation.

    6. Common vertex matrix: A novel characterization of molecular graphs by counting (pages 1409–1419)

      Milan Randić, Marjana Novič and Dejan Plavšić

      Version of Record online: 26 APR 2013 | DOI: 10.1002/jcc.23300

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      The construction of a novel elementary matrix for graphs is outlined, which is of interest for the comparative study of molecules. The (i, j) matrix element of the novel matrix, referred to as the “Common Vertex Matrix,” is given by the count of vertices at equal distance from vertices i and j. Ordered row sums of the novel matrix (given as a sequence of integers) discriminate smaller acyclic molecular graphs quite well.

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      JACOB: An enterprise framework for computational chemistry (pages 1420–1428)

      Mark P. Waller, Thomas Dresselhaus and Jack Yang

      Version of Record online: 3 APR 2013 | DOI: 10.1002/jcc.23272

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      The implementation of an integrated framework for the future rapid development of computational chemistry applications is detailed. The multitiered infrastructure layer is based on enterprise programming paradigms. The code is available for download at www.wallerlab.org.

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      NBO 6.0: Natural bond orbital analysis program (pages 1429–1437)

      Eric D. Glendening, Clark R. Landis and Frank Weinhold

      Version of Record online: 9 MAR 2013 | DOI: 10.1002/jcc.23266

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      A new version of the natural bond orbital program (NBO 6.0) significantly expands the range of chemical applications through a new, link-free interface to host electronic structure systems, refined search algorithms, improved output labeling for exotic bonding motifs, and a broadened range of analysis options.

      Corrected by:

      Erratum: Erratum: NBO 6.0: Natural bond orbital analysis program

      Vol. 34, Issue 24, 2134, Version of Record online: 26 JUN 2013

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