Journal of Computational Chemistry

Cover image for Vol. 38 Issue 3

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

Impact Factor: 3.648

ISI Journal Citation Reports © Ranking: 2015: 41/163 (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
    Electronic absorption spectra of pyridine and nicotine in aqueous solution with a combined molecular dynamics and polarizable QM/MM approach

    Marco Pagliai, Giordano Mancini, Ivan Carnimeo, Nicola De Mitri and Vincenzo Barone

    Version of Record online: 2 DEC 2016 | DOI: 10.1002/jcc.24683

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    The electronic absorption spectrum of nicotine in aqueous solution has been computed with an integrated protocol, performing time-dependent density functional theory calculations with a polarizable QM/MM scheme on a series of configurations extracted from molecular dynamics simulations. The protocol has been preliminary verified calculating the electronic absorption spectrum of the rigid aromatic moiety of nicotine (i.e., pyridine) in water.

  2. Residue-centric modeling and design of saccharide and glycoconjugate structures

    Jason W. Labonte, Jared Adolf-Bryfogle, William R. Schief and Jeffrey J. Gray

    Version of Record online: 30 NOV 2016 | DOI: 10.1002/jcc.24679

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    Carbohydrates are present everywhere in nature, possessing a vast array of structural diversity, yet historically, they have been challenging to model. RosettaCarbohydrate is a new tool for researchers studying the form and function of carbohydrate structures. The framework integrates with Rosetta's successful modeling and design suite and addresses challenges unique to glycans. This article describes the development of the framework and highlights its applications, including loop modeling and glyco-ligand docking.

  3. Anomerization reaction of bare and microhydrated d-erythrose via explicitly correlated coupled cluster approach. Two water molecules are optimal

    Marek Szczepaniak and Jerzy Moc

    Version of Record online: 29 NOV 2016 | DOI: 10.1002/jcc.24680

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    This comprehensive benchmark computational study has explored a complete path of the anomerization reaction of bare d-erythrose relating a pair of the low-energy α- and β-furanose anomers, the former of which was recently observed spectroscopically. The issue of the number of water molecules (n) required for optimal stabilization of the erythrose anomerization reaction rate-determining transition state is addressed by a systematic exploration of the potential energy surface of the ring opening in the α-anomer-(H2O)n and various β-anomer-(H2O)n (n = 1–3) clusters. The lowest free energy barrier of the erythrose ring opening is predicted for the doubly hydrated α-anomer.

  4. Conserving the linear momentum in stochastic dynamics: Dissipative particle dynamics as a general strategy to achieve local thermostatization in molecular dynamics simulations

    Peter P. Passler and Thomas S. Hofer

    Version of Record online: 26 NOV 2016 | DOI: 10.1002/jcc.24677

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    The stochastic dissipative particle dynamics (DPD) and Langevin thermostats for molecular dynamics simulations are compared with focus on the conservation of the linear momentum, which is inherently violated in the latter case. While structure and short-time correlated observables are not influenced, long-time correlation is shown to be highly sensitive to this shortcoming. Despite being able to conserve the linear momentum, DPD leads to similar ill-defined diffusive properties if friction and random components beyond the nearest neighbors are included. Furthermore, a sigmoid weighting is shown to be advantageous over the commonly used step- and linear weighting functions in the DPD approach.

  5. Applying strong external electric field to thiophene-based oligomers: A promising approach to upgrade semiconducting performance

    Xiaoling Zhan, Hu Shi, Hongguang Liu and Jin Yong Lee

    Version of Record online: 26 NOV 2016 | DOI: 10.1002/jcc.24684

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    This work is conducted to grasp the power of external electric fields, which could be utilized to address the challenges associated with organic semiconductors. By selecting a proper external field, we target on oligothiophenes with planarized backbone structures that exhibit attractive properties such as exceptionally low reorganization energies that are favorable for intermolecular hole transfer.

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