Journal of Computational Chemistry

Cover image for Vol. 38 Issue 28

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

Impact Factor: 3.229

ISI Journal Citation Reports © Ranking: 2016: 53/166 (Chemistry Multidisciplinary)

Online ISSN: 1096-987X

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

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Recently Published Articles

  1. Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets

    William J. Allen, Brian C. Fochtman, Trent E. Balius and Robert C. Rizzo

    Version of Record online: 22 SEP 2017 | DOI: 10.1002/jcc.25052

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    De novo design methods aim to create new molecules, from scratch, with steric and electrostatic compatibility for the target system(s). In this work, we describe development, validation, and application of a new de novo design version of the program DOCK that allows assembly of small organic molecules in a binding site using fragment libraries consisting of scaffolds, linkers, and sidechains. The results highlight the potential utility for designing new molecules against a wide variety of important protein targets.

  2. Comparison of a quantum random number generator with pseudorandom number generators for their use in molecular Monte Carlo simulations

    Dario Ghersi, Abhishek Parakh and Mihaly Mezei

    Version of Record online: 18 SEP 2017 | DOI: 10.1002/jcc.25065

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    Four pseudorandom number generators were compared with a physical, quantum-based random number generator using the NIST suite of statistical tests. We then measured the effect of the five random number generators on various calculated properties in different Markov-chain Monte Carlo simulations. The results show that poor quality pseudorandom number generators produce results that deviate significantly from those obtained with the quantum-based random number generator. In contrast, the Mersenne Twister pseudorandom generator and a 64-bit Linear Congruential Generator with a scrambler produce results that are statistically indistinguishable from those obtained with the quantum-based random number generator.

  3. The influence of the metal cations and microhydration on the reaction trajectory of the N3 [LEFT RIGHT ARROW] O2 thymine proton transfer: Quantum mechanical study

    Filip Šebesta, Mateusz Z. Brela, Silvia Diaz, Sebastian Miranda, Jane S. Murray, Soledad Gutiérrez-Oliva, Alejandro Toro-Labbé, Artur Michalak and Jaroslav V. Burda

    Version of Record online: 18 SEP 2017 | DOI: 10.1002/jcc.24911

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    Intramolecular proton transfer (PT) process on thymine nucleobase between N3 and O2 atoms is explored in presence of hexacoordinated divalent metals cations Mg2+, Zn2+, and Hg2+. This PT proceeds as a two stages process. The first step involves the PT from one of the aqua ligands toward O2. The second stage is connected with the N3-proton abstraction. In the presence of the hexaaqua-cations, the activation barrier is at most 8 kcal/mol.

  4. σ-holes and π-holes: Similarities and differences

    Peter Politzer and Jane S. Murray

    Version of Record online: 6 SEP 2017 | DOI: 10.1002/jcc.24891

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    Computed electrostatic potentials on 0.001 au surfaces of FSBr (upper left) and SO2 (lower right) showing examples of σ-holes and π-holes, respectively. Color ranges, in kcal/mole: red, more positive than 20; yellow, between 20 and 10; green, between 10 and zero; blue, negative. Black hemispheres indicate locations of most positive potentials, the VS,max.

  5. On the existence of He[BOND]He bond in the endohedral fullerene Не2@C60

    Tymofii Yu. Nikolaienko, Eugene S. Kryachko and Grygoriy A. Dolgonos

    Version of Record online: 6 SEP 2017 | DOI: 10.1002/jcc.25061

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    Twenty years have already been passed since the endohedral fullerene's void ceaselessly attracts attention of both, experimentalists and theoreticians, computational chemists and physicists in particular, who direct their efforts on computer simulations of encapsulating atoms and molecules into fullerene void and on unraveling the arising bonding patterns. We review recent developments on the endohedral He2@C60 fullerene, on its experimental observation and on related computational works. The two latter are the main concerns in the present work: on the one hand, there experimentally exists the He dimer embedded into C60 void. On the other, computational side, each He atom exhibits a negligible charge transfer to C60 resulting in that altogether, the He dimer exists as a fractionally charged (He+δ)2. Whether there exists a bond between these two helium atoms is the key question of the present work. Since a bond is a two-body creature, we assert that it suffices to define the bond on the basis of Löwdin's postulate of a molecule which we invoke to investigate such formation of the He dimer in a given C60 void in terms of the He[BOND]He potential energy well. It is analytically demonstrated that this well enables to maintain at least one bound (ground) state, and, therefore, according to Löwdin's postulate which is naturally anticipated within quantum theory, we infer that (He+δ)2 is a molecule, a diatomic, where two heliums are bonded to each other. Using these arguments, we also propose to extend the concept of stability of endohedral fullerenes.