Journal of Computer Chemistry, Japan

[Published online Journal of Computer Chemistry, Japan Vol.18, 166-168, by J-STAGE]
<Title:> Pd触媒を用いたアリルウレタンの分子内ヒドロアミノ化反応機構の理論的解明
<Author(s):> 河田　悠太, 林　慶浩, 高田　十志和, 川内　進
<Corresponding author E-Mill:> kawauchi.s.aa(at)m.titech.ac.jp
<Abstract:> Intramolecular hydroamination of allylurethane using the Pd-centered macrocycle catalyst was reported as an efficient continuous modification of oligo-functional allylurethanes. To clarify the mechanism of the hydroamination, quantum chemical calculation was performed for the model reaction. As a result, the cyclization in the hydroamination occurs via the initial deprotonation from the urethane N-H. In addition, the deprotonation was suggested to be a driving force for the transfer of the macrocyclic catalyst.
<Keywords:> 分子内ヒドロアミノ化, 量子化学計算, 反応機構, ロタキサン
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0014/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 164-165, by J-STAGE]
<Title:> フォルステライトガラス表面における水分子の分解メカニズム
<Author(s):> 久保　文音, 西澤　隼哉, 深澤　倫子
<Corresponding author E-Mill:> fukazawa(at)meiji.ac.jp
<Abstract:> To investigate the decomposition mechanisms of adsorbed H₂O molecules as a monolayer on the surface of forsterite glass, we performed molecular dynamics calculations. The decomposition phenomenon of H₂O molecules is observed at temperatures above 200 K. The equilibrium rate of the decomposed H₂O increases as the temperature increases and approaches 1.0 at temperatures above 500 K. The decomposed hydrogen forms MgO_xH_y or SiO₄H_z structures with MgO_x or SiO_z units in forsterite glass. The processes of decomposition and reformation of the structure units on the surface of forsterite glass have important implications for chemical evolution in interstellar spaces.
<Keywords:> Molecular dynamics calculation, Forsterite glass, Amorphous ice, Surface
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0017/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 159-161, by J-STAGE]
<Title:> 粒子法による量子波束の数値解析
<Author(s):> 廣野　史明, 岩沢　美佐子, 狩野　覚, 善甫　康成
<Corresponding author E-Mill:> zempo(at)hosei.ac.jp
<Abstract:> The particle method has no restriction on the particle arrangement, where the calculation is performed. The purpose is, by using this feature, to develop the method to analyze the dynamics of the electronic state. In order to describe the time evolution of the electronic state, we have developed a new method to solve the time-dependent wave equation, using the Bohmian that is very compatible with the particle method. In this form, there is also numerical instability in the region, where the value of the wave function is very small. We have applied our technique to the wave packet dynamics on harmonic potential and the analysis of interference by double slits as a simple system with analytical solution and easy to compare accuracy, and realized that both results are in good agreement.
<Keywords:> Keyword Symmetric smoothed particle hydrodynamics, Electronic structure calculation, Real-space calculation, Gaussian wave packet, Wave packet dynamics, Double slits, Interference
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0015/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.18, 162-164, by J-STAGE]
<Title:> ルテニウム錯体における隣接アゴスティック相互作用の理論的解析
<Author(s):> 大橋　佐鳳子, 山中　聡美, 鷹野　景子
<Corresponding author E-Mill:> takano.keiko(at)ocha.ac.jp
<Abstract:> Abstract: Agostic interactions are covalent intramolecular interactions between a metal atom and a σ-bond in organometallic complexes. Sabo-Etienne et al. reported the Ru complex with two adjacent agostic interactions of C-H and B-H bonds in 2014. The objectives of the present study are to reveal whether the two adjacent agostic interactions have synergistic effects and to examine the difference between the C-H and B-H agostic bonds. Geometries were optimized for 11 Ru complexes (five reported complexes by Sabo-Etienne et al. and six model complexes) by density functional theory (DFT) calculations. Interaction energies based on natural bond orbital (NBO) analysis showed that the agostic interactions exhibit the multiplier effect and the B-H agostic bonds are less stable than the C-H ones. Bond lengths and vibrational frequencies of the bonds were consistent with the above results.
<Keywords:> Agostic Interaction, Organometallic Complexes, Density Functional Theory (DFT), Natural Bond Orbital (NBO) Analysis, Multiplier Effect
<URL:> https://www.jstage.jst.go.jp/article/jccj/18/3/18_2019-0019/_article/-char/ja/

[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/