カテゴリー: 未分類

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.9, -, by J-STAGE]
<Title:> Improvement of Blood-Brain Barrier Permeability Prediction Using Cosine Similarity
<Author(s):> Hiroshi SAKIYAMA, Ryushi MOTOKI, Takashi OKUNO, Jian-Qiang LIU
<Corresponding author E-Mill:> saki(at)sci.kj.yamagata-u.ac.jp
<Abstract:> Prediction of blood-brain barrier permeability for chemicals is one of the key issues in brain drug development. In this study, the effect of using training data relatively similar to the test data was investigated in order to improve the performance of machine learning methods in predicting blood-brain barrier permeability. The results showed that selecting training data with high cosine similarity to the test data improved prediction performance with a smaller number of training data. The best model in this study also showed improved scores on two external test sets to examine generalization performance, outperforming excellent existing models. The cosine similarity method is expected to be effective for predicting the properties of compounds with large diversity and a small number of data.
<Keywords:> Blood-brain barrier permeability, Prediction, Cosine similarity, Machine learning, Chemicals
<URL:> https://www.jstage.jst.go.jp/article/jccjie/9/0/9_2023-0017/_html

[Published online Journal of Computer Chemistry, Japan Vol.22, A2-A7, 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:> 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/22/1/22_2022-0020/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.22, A8-A15, 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/22/1/22_2022-0021/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.22, 1-4, by J-STAGE]
<Title:> 環状メタノール4分子クラスターの配座異性体
<Author(s):> 大古　善久, 長嶋　雲兵
<Corresponding author E-Mill:> y-ohko(at)aist.go.jp
<Abstract:> メタノール4分子の環状クラスター(CH₃OH)₄のOH基とCを同一面内に配置した初期構造から構造最適化計算を行った．HF/STO-3Gでは，初期構造のO-O間距離が2.7 以上の場合に最安定構造が高い頻度で得られる．O-O間距離が短い場合には他の安定な配座異性体が2種類得られる．この約2.7 の距離はOH基の水素結合力の範囲を示唆する．HF/6-31G (d)では，虚振動を持つ平面構造で収束する．B3LYP/6-31G (d)では，メチル基が環面外の同じ側に向いた構造で収束する．これらの結果は，酸素の非共有電子対の軌道の広がりによる安定化とメチル基の反発力の均衡から説明でき，配座異性体同士の変換傾向を反映する．計算過程で力定数を計算(calcall)すると初期O-O間距離に関わらず最安定構造が得られる．
<Keywords:> methanol, cyclic cluster, starting structure, hydrogen-bonding, conformers
<URL:> https://www.jstage.jst.go.jp/article/jccj/22/1/22_2022-0031/_article/-char/ja/

[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/