Journal of Computer Chemistry, Japan

[Published online Journal of Computer Chemistry, Japan Vol.22, 5-7, by J-STAGE]
<Title:> 水酸基末端チタン二量体構造の電子状態
<Author(s):> 大古　善久, 長嶋　雲兵
<Corresponding author E-Mill:> y-ohko(at)aist.go.jp
<Abstract:> 酸化チタン光触媒の表面反応を理論計算で考察する時に，従来から用いられている平面型チタン二量体モデルの電子状態を調べた．用いた計算方法はB3LYP/6-311Gで，末端を水酸基化した初期構造(Ti₂O₆H₄)を最適化計算した．水酸基の初期の配向によって結果が異なり，非平面構造を取り易いことがわかった．また，HOMOとLUMOのエネルギー準位の比較から，光触媒反応の酸化力と還元力に水素の位置が重要であることがわかった．チタン二量体モデルのみでは電子状態の記述に無理があり，周辺構造を含めた新しい表面モデルの構築が必要であることが示唆された．
<Keywords:> TiO2 photocatalysis, Ti2O6H4, surface model, frequency, B3LYP/6-311G
<URL:> https://www.jstage.jst.go.jp/article/jccj/22/1/22_2022-0032/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 電子を描く(12) ― 炭素原子のsp³, sp², sp混成軌道
<Author(s):> 時田　澄男
<Corresponding author E-Mill:> sumio.tokita(at)gmail.com
<Abstract:> 炭素原子をはじめとする多電子原子を原子価結合法で取り扱い，原子価状態の軌道関数を表す方法である混成軌道が，原子軌道の線形結合によってどのような数式で表され，それらの数式を可視化するいろいろな方法によってどのように描かれるかを紹介した．
<Keywords:> Keywords many electron atom, atomic orbital, covalent bond, valence state, valence bond theory, molecular orbital method, valence state electron pair repulsion
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2022-0020/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 電子を描く(13) ― 混成軌道による分子の組立，σ結合とπ結合
<Author(s):> 時田　澄男
<Corresponding author E-Mill:> sumio.tokita(at)gmail.com
<Abstract:> 混成軌道を用いて，ルイスの電子対共有結合の概念にどのようにして同等性(等価性)や方向性を加味できるかを，簡単な分子を例にとって示す．σ電子とπ電子のちがい，π電子が核磁気共鳴スペクトルのケミカルシフトに及ぼす影響についても解説した．
<Keywords:> covalent bond, valence state, valence bond theory, molecular orbital method, hybrid orbital, resonance, difference electron density, NMR spectroscopy, ring current.
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2022-0021/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.9, -, by J-STAGE]
<Title:> Implementation of Wang-Landau Algorithm for Probing Thermodynamic Stable Configuration of Multi-Element Materials and Application to Multinary Alloy Nanoparticles
<Author(s):> Yusuke NANBA, Michihisa KOYAMA
<Corresponding author E-Mill:> nanba(at)shinshu-u.ac.jp
<Abstract:> With an increase in an element, the configurational entropy effect stabilizes the multi-element materials. However, the expansion of configuration space and heterogeneous surfaces such as nanoparticles preclude the analytical evaluation of configurational entropy. Then, we implemented the Wang-Landau algorithm, which is one of the Monte-Carlo algorithms, for evaluating the configurational entropy and probing the thermodynamic stable configuration of multi-element materials. The regression equation obtained by density functional theory calculation and multiple regression analysis is used in the energy estimation in the sampling. This method was applied to binary alloys in the bulk and ternary alloy nanoparticles and the obtained features of the stable configuration were discussed.
<Keywords:> High-entropy alloy, Wang-Landau algorithm, Monte Carlo algorithm, Multiple regression analysis, Density functional theory calculation
<URL:> https://www.jstage.jst.go.jp/article/jccjie/9/0/9_2022-0013/_html

[Published online Journal of Computer Chemistry, Japan Vol.21, 134-136, by J-STAGE]
<Title:> シトクロムcの複合体形成過程の再現シミュレーション
<Author(s):> 下山　紘充, 重田　育照
<Abstract:> A 3-dimensional domain swapping (3D-DS) phenomenon is a promising way to make a stable multimer because interactions in the multimer is about the same as that of a monomer; it would be useful to artificially design a functional protein’s multimer. In this study, molecular dynamics (MD) simulation of cytochrome c(cyt c) that is known to form a 3D-DS dimer (PDB ID: 3NBS) was performed to study factors that enhance 3D-DS structure sampling. Our results show a difficulty of 3D-DS structure sampling and a necessity of a method such as the generalized ensemble method. The results also show the importance of a loop-flexibility to sample 3D-DS structure; when the bond and torsion angle potential coefficients are less than 10% of secondary structure, 3D-DS structures become easy to sample.
<Keywords:> Cytochrome c, 3D-DS dimer, MD Simulation, Generalized ensemble method, Go-like model
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0014/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 129-133, by J-STAGE]
<Title:> 汎用ニューラルネットワークポテンシャルを用いた 三元系ナノ合金のCO吸着特性の評価
<Author(s):> 綾子 田村, Gerardo VALADEZ HUERTA, 優輔 難波, 馨 久間, 通久 古山
<Corresponding author E-Mill:> ayako_tamura(at)shinshu-u.ac.jp
<Abstract:> Multi-element alloy nanoparticles have attracted attention for their potentially high catalytic properties. However, a high degree of freedom in configurations of metal atoms within nanoparticle increases the distinct adsorption sites, making it difficult to theoretically analyze its catalytic properties because the first-principles calculation requires a considerable computational cost. In this study, we develop a sequential scheme to calculate hundreds of adsorption sites by employing a pre-trained universal neural network potential named PFP. Our automated scheme is applied to CO single-molecule adsorption of CO onto PtRuIr ternary alloy nanoparticles. The calculation results are first compared with DFT results to confirm the accuracy. Adsorption energies in the alloy systems are widely distributed in comparison with those of the monometal counterparts, indicating that the alloy nanoparticle includes adsorption sites with various catalytic activities.
<Keywords:> Alloy nanoparticle, Universal neural network potential, CO adsorption
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0016/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 126-128, by J-STAGE]
<Title:> グラフニューラルネットワークによる有機遷移金属反応の学習
<Author(s):> 酒井　基至, 金重　光典, 安田　耕二
<Corresponding author E-Mill:> yasudak(at)imass.nagoya-u.ac.jp
<Abstract:> 深層学習による反応予測は，人が識別パターンを設計する必要がないため最近注目されている．しかし有機遷移金属反応は一見複雑で，深層学習の適応例は殆どなかった．我々は，論文や特許などから集めた数万件の実験反応を，素反応に分解したデータベースを構築し，グラフニューラルネットワークを用いて学習させた．最高で97.1%の精度で反応が予測できた．
<Keywords:> Graph neural network, Forward synthesis prediction, Organo transition metal reactions
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0012/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 118-122, by J-STAGE]
<Title:> 中分子の膜透過性に対する計算手法の検討
<Author(s):> 高橋　輝行, Hengphasatporn　Kowit, 原田　隆平, 重田　育照
<Abstract:> We used computational methods to predict the cell membrane permeability of a medium molecular drug, Bottromycin A2. We compared the three calculation methods, electronic structure calculation, molecular dynamics (MD) simulation, and empirical method, and examined which method was the best. As a result, we found that the first one is the best method among three methods treated, and that a prediction with high accuracy can be expected by increasing the number of experimental data.
<Keywords:> Membrane permeability, Medium Molecular Drug, Bottromycin A2, Cyclic Peptide, LogP
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0007/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 123-125, by J-STAGE]
<Title:> 抗体軽鎖四量体の立体構造の理論解析
<Author(s):> Lian　Duan, Hengphasatporn　Kowit, 重田　育照
<Abstract:> In this study, the trajectories of the four protomers corresponding to the light chain tetramers of human antibodies were obtained from MD simulations. The four protomers, which should be symmetrically constructed, were not completely symmetrical in the simulations. The DSSP analysis and 2D-RMSD analysis of the four protomers showed that although the secondary structure of the four protomers is approximately the same, the deconvolution of part of the α helix leads to the asymmetry of the overall structure in the simulation. Although the number of interactions within the protomers decreases, that between the protomers increases, making the overall energy more stable. We hypothesize that the deconvolution is caused by the formation of the α helix fragment in the tetramer, and the hydrogen bonding and van der Waals forces between the protomers lead to the breakage of the hydrogen bond within the protomers, further leading to the disappearance of the α helix.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0005/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.21, 111-117, by J-STAGE]
<Title:> On the Thermodynamic Stability of Alloys: Combination of Neural Network Potential and Wang-Landau Sampling
<Author(s):> Tien Quang NGUYEN, Yusuke NANBA, Michihisa KOYAMA
<Corresponding author E-Mill:> quang(at)shinshu-u.ac.jp
<Abstract:> Thermodynamic properties and atomic configuration of PdRu alloy were investigated using Wang-Landau Monte Carlo method in combination with a newly-developed universal neural network potential. By using this new potential, excess energy of PdRu alloy was calculated. It is found that PdRu alloy in FCC lattice is unstable in the full range of alloy composition. This agrees with previous study based on density functional theory. The combined method was able to determine the configurational density of states, from which thermodynamic properties of the alloy were derived. It is found that when temperature increases, the excess free energy of the alloy is reduced, increasing the possibility of alloy mixing. Depending on the composition, transition peaks appear at finite temperatures where there are changes of preferable atomic arrangement due to the effect of temperature via the configurational entropy. In addition, the analyses on short-range order parameter and bond fraction show that PdRu alloy prefers to be in segregated form, where Pd and Ru are immiscible at low temperature, consistent with the experimental observations. The random mixing of Pd and Ru atoms in the form of solid-solution can occur at high temperature.
<Keywords:> Alloy stability, Wang-Landau sampling, Neural network potential, Short-range order parameter, Bond fraction
<URL:> https://www.jstage.jst.go.jp/article/jccj/21/4/21_2023-0015/_article/-char/ja/