Journal of Computational Chemistry

Cover image for Vol. 38 Issue 21

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. Optimization and transferability of non-electrostatic repulsion in the polarizable density embedding model

    Dalibor Hršak, Jógvan Magnus Haugaard Olsen and Jacob Kongsted

    Version of Record online: 22 JUN 2017 | DOI: 10.1002/jcc.24859

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    In this study, we have optimized the scaling factor for the non-electrostatic repulsion in the polarizable density embedding (PDE) model. The nonscaled repulsion term is overestimated because the electron densities of the environment molecules are calculated for isolated fragments. The optimization was performed through PDE calculations of the interaction energy curves of four dimer complexes and they were compared to the reference results based on full QM description of the dimers. The PDE model with optimized factors has thereafter been applied to calculation of various molecular response properties.

  2. Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins

    Nguyen-Quoc-Khanh Le, Quang-Thai Ho and Yu-Yen Ou

    Version of Record online: 22 JUN 2017 | DOI: 10.1002/jcc.24842

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    In this study, we approach a deep learning technique generated from convolutional neural networks and position specific scoring matrix to identify the electron transport proteins, which is very important biological function. Our proposed technique can serve as a powerful tool for biologists to identify electron transport proteins. Moreover, this study provides a basis for further research that can enrich a field of applying deep learning in bioinformatics.

  3. Multistructural microiteration technique for geometry optimization and reaction path calculation in large systems

    Kimichi Suzuki, Keiji Morokuma and Satoshi Maeda

    Version of Record online: 22 JUN 2017 | DOI: 10.1002/jcc.24857

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    We propose a multistructural microiteration (MSM) method for geometry optimization and reaction path calculation in large systems. In this method, the surrounding part is described as the weighted sum of multiple structures to account for large-scale structural transitions along the reaction path. MSM gave lower energy profiles than the conventional QM/MM-microiteration method in all numerical tests with comparable computational costs.

  4. Gas adsorption in Mg-porphyrin-based porous organic frameworks: A computational simulation by first-principles derived force field

    Yujia Pang, Wenliang Li and Jingping Zhang

    Version of Record online: 19 JUN 2017 | DOI: 10.1002/jcc.24858

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    Recently, porphyrinic metal organic frameworks as a novel type of porous organic frameworks (POFs) have attracted great research attention. In this work, a series of designed diamond-like Mg-porphyrin-based POFs are obtained by the combination of organic fragments. The gas uptakes of CO2, H2, N2, and H2O in POF-Mgs are investigated. The good performance of POF-Mgs in the simulations inspires us to design novel porous materials experimentally for gas adsorption and purification.

  5. Simple computing of the viscosity of water–dioxane mixtures, according to a fluctuating SPC/E-Ih interstitial model

    Anis Ghazouani and Jalel M'halla

    Version of Record online: 17 JUN 2017 | DOI: 10.1002/jcc.24841

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    Cooperative dynamic jumps of water molecules from lattice sites toward adjacent holes into the fluctuating SPC/E-Ih network facilitate the viscous flow by lowering the Eyring's activity energy. In the case of the water–dioxane dilute mixture, dioxane molecules are incorporated according to a mechanism of substitution of the cluster “(H2O)6” by a “1,4-dioxane” molecule. This incorporation explains the quasi-linear variation of the global viscosity activation energy of the mixture with the molar fraction of dioxane.

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