カテゴリー: 未分類

[Published online Journal of Computer Chemistry, Japan Vol.18, 152-155, by J-STAGE]
<Title:> インフォマティクス手法を活用した結合エネルギー密度解析の開発
<Author(s):> 中村　海里, 清野　淳司, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> The bond energy density analysis (bond-EDA), which is one of the two-body energy decomposition schemes to obtain bond energies, was extended by revisiting the formula and the constraint conditions, and using the informatics technique. Numerical assessments of the present schemes were performed for 44 chemical bonds in 33 small molecules with covalent and ionic bonds involving second and third row atoms. The results show that the present scheme qualitatively reproduces the bond dissociation energies obtained by the direct evaluation scheme in quantum chemical calculations.
<Keywords:> Bond energy density analysis, Chemical bond, Bond energy, Bond dissociation energy, Quantum chemical calculation
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0026/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 150-151, by J-STAGE]
<Title:> マシンラーニングによる配座解析の時間短縮
<Author(s):> 﨑山　博史
<Corresponding author E-Mill:> saki(at)sci.kj.yamagata-u.ac.jp
<Abstract:> In the conformational analysis of [Mg(dmso)₆]²⁺ complex cation (dmso: dimethylsulfoxide), 130 candidates of the conformers were successfully narrowed down to 26 conformers by machine learning. As a result, the time required for the structural optimization turned out to be reduced to 1/8, and the machine learning was found to be effective in timesaving for conformational analysis.
<Keywords:> マシンラーニング, 配座解析, 正八面体型錯体, ディープニューラルネットワーク, 構造予測
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0020/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 156-158, by J-STAGE]
<Title:> 実験と計算によるイルソグラジン マレイン酸の結晶構造の予測
<Author(s):> 坂田　千夏, 岡本　有史, 梅田　大貴, 古石　誉之, 福澤　薫, 米持　悦生
<Corresponding author E-Mill:> k-fukuzawa(at)hoshi.ac.jp
<Abstract:> To improve the solubility of poorly water-soluble drugs, molecular complexes such as co-crystals and salts have been used. However, the huge number of combinations of drug substances and co-crystal former (coformer) makes experimental screening too expensive. In this study, with the subject of irsogladine maleate [1] whose crystal structure has already been reported, we investigated the predictability of the crystal structure using the computational method. In the experiment on irsogladine-maleic acid complex, single crystal X-ray structural analysis, powder X-ray diffraction (PXRD) method, and Fourier transform infrared spectroscopy (FT-IR) measurement have already been performed; lattice constant and interaction site were known and it is known to be a salt crystal. We used CONFLEX software and MMFF94S force field parameters for crystal structure prediction. As a result, it was possible to obtain a crystal structure consistent with the experimental structure.
<Keywords:> Crystal structure prediction, Salt crystal, Irsogladine maleate, Physical property improvement, CONFLEX
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0024/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 145-146, by J-STAGE]
<Title:> 分子動力学法によるS_N2反応の理論研究ー化学反応はいかにして起こるかー
<Author(s):> 松原　世明
<Corresponding author E-Mill:> matsubara(at)kanagawa-u.ac.jp
<Abstract:>
<Keywords:> S??sub??N??/sub??2 reaction, Molecular dynamics simulation, Requirement for the reaction, Solvent effect
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0011/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 142-144, by J-STAGE]
<Title:> ペロブスカイト太陽電池材料におけるポーラロン形成の量子力学的分子動力学シミュレーション
<Author(s):> 浦谷　浩輝, 周　建斌, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> Polarons, which are charge carriers in solids wearing a structural deformation, play a key role in photo-electronic devices such as solar cells. In this study, the polaron formation process in a lead halide perovskite, which is utilized in perovskite solar cells, was simulated using quantum mechanical molecular dynamics calculations. The simulations were performed in a several nanometers-scale model system to capture the spatial size of the polarons, with the use of the divide-and-conquer type density-functional tight-binding method, which is capable of fully quantum mechanical treatment of systems consisting of (tens of) thousands of atoms. The observed structural deformations and their process are discussed.
<Keywords:> Polaron, Perovskite solar cell, Divide-and-conquer method, Density-functional tight-binding method, Quantum mechanical molecular dynamics simulation
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0025/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 147-149, by J-STAGE]
<Title:> シクロフェニレン骨格での置換基の電子伝達機構
<Author(s):> 亮治 藤山, あゆみ 井上, 夢月 原田
<Corresponding author E-Mill:> fujiyama(at)kochi-u.ac.jp
<Abstract:> In order to examine the transmision of electronic effects in cyclophenylene framework, substituent effects on some cyclophenylene derivatives with primary carbocation CH₂⁺ were carried out. The substituent effects on the energy of isodesmic reactions were analyzed by the LSFE equation that separates the inductive and the resonance effects . The analysis results indicate that the counterclockwise and the clockwise resonances shown in the Figure are mainly important.
<Keywords:> Cyclophenylene, Substituent effect, LSFE equation, Resonance effect, Biphenylene
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0018/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, A6-A11, by J-STAGE]
<Title:> 相対論的量子化学計算プログラムRAQETの公開
<Author(s):> 五十幡　康弘, 吉川　武司, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> The “Relativistic And Quantum Electronic Theory (RAQET)” program was released for academic use. One-component (spin-free) and two-component (spin-dependent) relativistic calculations are possible based on the infinite-order Douglas-Kroll-Hess transformation and local unitary transformation. This review describes available features, registration/installation, and input/output of the RAQET program.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0022/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 123-125, by J-STAGE]
<Title:> 機械学習によるテキスト処理ツールの開発と応用
<Author(s):> 亘理　結香, 奥脇　弘次, 望月　祐志
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> We have developed a text processing tool consisting of several machine learning-related programs such as TreeTagger and Doc2Vec. This system was applied to a number of abstracts of a couple of physical chemistry journals (Chemical Physics Letters and American Journal of Physics). The degree of similarity of contents was then made evaluatable as a guide for papers to be checked for a certain topic.
<Keywords:> Text processing, Machine learning, Doc2Vec, Degree of similarity
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0012/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 129-131, by J-STAGE]
<Title:> ABINIT-MP Openシリーズの最新の開発状況について
<Author(s):> 望月　祐志, 秋永　宜伸, 坂倉　耕太, 渡邊　啓正, 加藤　幸一郎, 渡辺　尚貴, 奥脇　弘次, 中野　達也, 福澤　薫
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> We have been developing an original program named ABINIT-MP for fragment molecular orbital (FMO) calculations. Various functionalities for interaction analyses, e.g. PIEDA (Pair Interaction Energy Decomposition Analysis), have been augmented in Revision 10 and Revision 15 of the ABINIT-MP Open Series Version 1. In this Letter, we briefly describe such new features.
<Keywords:> キーワード：Fragment molecular orbital, FMO, ABINIT-MP, Interaction analysis, Correlation energy correction
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0016/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 126-128, by J-STAGE]
<Title:> Scratchを経由する機械学習教材の開発の試み
<Author(s):> 満野　仁美, 奥脇　弘次, 伊藤　雅仁, 望月　祐志
<Corresponding author E-Mill:> fullmoon(at)rikkyo.ac.jp
<Abstract:> We have been developing a Scratch-based educational program for machine learning in the chemistry context. This system has an interface with the DeepChem library set of Python. The solubility prediction of several molecules with SMILES notation was demonstrated as a preliminary application.
<Keywords:> キーワード：Scratch, Educational program, Machine learning, DeepChem, Solubility prediction
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0013/_article/-char/ja/