Journal of Computer Chemistry, Japan

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 化学勾配に駆動される膜興奮動態による単細胞生物ゾウリムシの障害物衝突に対する行動応答モデル
<Author(s):> 大嶺　志歩, 國田　樹
<Corresponding author E-Mill:> kunita(at)ie.u-ryukyu
<Abstract:> 　本研究は，生物の柔軟な行動を生み出す情報処理システムの本質的原理を化学勾配に基づく数理モデルで表現することを目的とした．単細胞生物の繊毛虫ゾウリムシが障害物に衝突した際の行動応答を生物実験により調べた結果，ゾウリムシは衝突後すぐに方向転換する行動と，障害物に沿って移動した後に方向転換する行動を示した．これらの行動を生じた時の衝突時の角度や速度は同じであったが，直前の角度変化の符号が異なっていた．ゾウリムシの行動は，体表に生えた繊毛運動によって制御され，それは細胞内外の化学勾配に従って生じる膜興奮動態によって調整される．この膜興奮動態と行動とを対応づける数理モデルを構成し，数値シミュレーション実験を行った．その結果，実験結果と同様にゾウリムシが障害物に衝突する前の角度変化の符号の違いで2つの行動を再現できた．つまり，ゾウリムシは同じ化学勾配状態でも，直前の角度変化という運動履歴の違いによって異なる行動を生じる柔軟性を有していた．
<Keywords:> membrane excitation dynamics, chemical gradients, Paramecium, ciliary movement, FitzHugh-Nagumo model
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2024-0026/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 36-38, by J-STAGE]
<Title:> Givens回転と誤差逆伝播法を組み合わせた自己無撞着場計算の高効率収束法の開発
<Author(s):> 大島　玲生, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> We have recently proposed a highly efficient convergence method for self-consistent (SCF) calculations combining Givens rotation and error back-propagation (EBP) algorithms, referred to as direct Givens rotation (DGR) method [J. Chem. Phys. 162, 014108 (2025)]. The Givens rotation corresponds to unitary transformations that guarantee the orthogonality of molecular orbitals. Complicated gradients constructed through sequential Givens rotations were computed using the EBP technique without deriving explicit forms. This article reviews the proposed DGR method and compares it with conventional methods such as the standard SCF procedure, the second-order SCF method, and the direct inversion in iterative subspace technique for H₂O molecule. The DGR method exhibited a convergence speed comparable to that of the SOSCF method while achieving a lower and more reliable energy.
<Keywords:> キーワード self-consistent field, direct minimization, Givens rotation, error back-propagation, Hartree-Fock, Kohn-Sham density functional theory
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2025-0003/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 18-24, by J-STAGE]
<Title:> 立体電子状態の定量評価による求核反応の面選択性の起源の解明
<Author(s):> 坂口　大門, 五東　弘昭
<Corresponding author E-Mill:> gotoh-hiroaki-yw(at)ynu.ac.jp
<Abstract:> 化学反応の反応性や選択性の起源の解明は学術的に興味深いだけでなく，反応を制御するうえでも重要である．我々は最近，環状ケトンの立体的な電子状態を定量評価して求核反応の面選択性を定量的に説明し解釈する新しい方法を提案した [1]．本稿では日本コンピュータ化学会2024年秋季年会での口頭発表の内容 [2] に基づき，化学反応と立体電子状態に関するこれまでの研究と，我々が開発した新しい方法について紹介する．
<Keywords:> Keywords ketone, nucleophilic addition, π-facial selectivity, QSSR, data-driven chemistry
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2024-0043/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 27-29, by J-STAGE]
<Title:> PdおよびAgRh合金ナノクラスターへの水素吸収と拡散に関する相対論的量子化学計算分子動力学シミュレーション
<Author(s):> 木村　愛花, 安藤　耕司
<Corresponding author E-Mill:> ando_k(at)lab.twcu.ac.jp
<Abstract:> Molecular dynamics simulations of hydrogen absorption and diffusion in Pd and AgRh alloy nanoclusters were performed. Parameters for atomic interaction potentials were determined from relativistic quantum chemical calculations. Although Rh is known not to absorb hydrogen in bulk, the Rh-H interaction strength obtained from the calculations was about 80% of that of the Pd-H. Using the parameters obtained, molecular dynamics simulations were performed. Molecular dynamics simulations of AgRh clusters with different Ag:Rh ratio have shown no significant difference in the Rh-Rh distance distribution at the nearest neighbor except for Ag₇₀Rh₃₀. However, at the second nearest neighbor the distance increased as the Ag fraction increased.
<Keywords:> Keywords Molecular dynamics simulation, Relativistic Quantum Chemical Calculations, Hydrogen-absorbing metal nanoclusters
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2024-0040/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 30-35, by J-STAGE]
<Title:> Predicting CO Adsorption on Multi-elemental Alloy through Machine Learning Analysis of Ternary Components
<Author(s):> Susan Menez ASPERA, Gerardo ALADEZ HUERTA, Yusuke NANBA, Kaoru HISAMA, Michihisa KOYAMA
<Corresponding author E-Mill:> aspera_susan(at)shinshu-u.ac.jp
<Abstract:> Surface-molecule interaction has always been an integral part in the analysis of reactions and surface reactivity in heterogenous catalysis. With the advent of computational resource advancement, the search for the next generation catalysts explores the combination of several metal elements in the multi-elemental nanoparticles (NP). However, with the complexity of the catalysts’ surface comes the difficulty of understanding surface-molecule interaction and methods to overcome this should be considered. In our previous study, we used metal-coordination to predict CO adsorption on the ternary alloy combinations. This method describes the adsorption site by the network of metal elements interacting with the site that contributes to the change in its electronic properties. Since this network considers up to the neighbor of the first nearest neighbor of the adsorption site, in this study, we considered to use the dataset of regression coefficient of ternary alloy combinations to predict molecular adsorption on a multi-elemental NP. We tested the method on CO molecular adsorption on the quaternary RuRhIrPt NP and used the regression coefficient obtained from RuRhPt, RhIrPt, RuIrPt and RuRhIr ternary alloy. Results show that the predicted values of CO adsorption energy on the RuRhIrPt NP have comparable values of coefficient of determination (R²) and mean absolute error (MAE) with the prediction of CO adsorption on ternary alloy. Thus, this method could pave the way for predicting molecular adsorption on multi-elemental NP using only the dataset of regression coefficient from ternary alloy combinations and the atomic configurational structure of the multi-elemental NP.
<Keywords:> Multi-elemental nanoparticle alloy, Machine learning, Generalized coordination number, Adsorption prediction
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2025-0002/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 20-26, by J-STAGE]
<Title:> Anion Intercalation and Selectivity in NiFe LDH: Insights from Neural Network-Enhanced Molecular Dynamics
<Author(s):> Tien Quang NGUYEN, Susan Me ez ASPERA, Yingjie CHEN, Kaoru HISAMA, Michihisa KOYAMA
<Corresponding author E-Mill:> quang(at)shinshu-u.ac.jp
<Abstract:> Molecular dynamics (MD) simulations, accelerated by a universal neural network potential, were employed to investigate the dynamic behaviors of ten inorganic anions (Br^–, Cl^–, F^–, OH^–_, NO₃^–_, H₂PO₂^–_, H₂PO₃^–_, HPO₄^2-_, CO₃^2- and SO₄^2-) intercalated into NiFe layered double hydroxide at varying hydration levels. Our results show that the lattice parameters along the layered double hydroxide (LDH) layers are minimally affected by the intercalated anions and water content, while the lattice parameter perpendicular to the layers, i.e., the basal spacing, is strongly influenced by the type of anion and hydration level. The basal spacing is closely correlated with the ionic radius and charge of the anions, as well as the amount of water uptake. Mean squared displacement (MSD) analysis reveals distinct behaviors of the anions under different hydration conditions. While some anions, such as NO₃^– and H₂PO₂^–, exhibit noticeable mobility, others remain largely immobilized, primarily due to strong electrostatic interactions with the LDH layers and water molecules. Hydration weakens the interaction between anions and the LDH but also restricts the mobility of anions due to the formation of hydration shells. These findings provide insights into anion dynamics and selectivity in NiFe LDH, which are critical for designing materials for anion removal applications.
<Keywords:> Layered-double hydroxides, Anion intercalation, Molecular dynamics, Neural network potential, Coulomb interactions
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2025-0001/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 17-19, by J-STAGE]
<Title:> アルキル鎖長が異なる有機半導体混合膜表面の分子動力学計算
<Author(s):> 鈴木　陸央, 宮田　稜, 井上　悟, 長谷川　達生, 松井　弘之
<Corresponding author E-Mill:> t231542d(at)st.yamagata-u.ac.jp
<Abstract:> A mixed solution of organic semiconductors Ph-BTBT-Cn with different alkyl chain length (n) forms a high-quality molecular bilayer by suppressing layer-by-layer stacking when the molar fraction of the longer chains (χ_L) is 0.1 0.6. In this study, we performed molecular dynamics simulations to investigate the dynamics of alkyl chains in the mixed bilayer. The order parameters and dihedral angles of the alkyl chains were analyzed as a function of χ_L. The results revealed that increasing χ_L enhances the ordering of the longer alkyl chains, thereby reducing their torsional motion. A stochastic model of the number of free surplus chains explains the molar fraction dependence of film morphology.
<Keywords:> キーワード Molecular dynamics, Organic semiconductor, Surface alkyl chain, Ordering, Interlayer frustration
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2024-0038/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 5-9, by J-STAGE]
<Title:> 光2重イオン化されたOCS分子のダイナミクスと隠される反応経路
<Author(s):> 神原　龍冬, 堤　拓朗, 古屋　謙治, 武次　徹也
<Corresponding author E-Mill:> take(at)sci.hokudai.ac.jp
<Abstract:> The global reaction route mapping (GRRM) strategy enables an exhaustive search of static chemical reaction pathways, providing deep insight into chemical reactions. On the other hand, ab initio molecular dynamics (AIMD) simulations explicitly account for the momenta of atoms, revealing the realistic dynamical motion of molecules. In this study, we constructed the reaction path network for the ground-state OCS²⁺ species, which has attracted significant interest from spectroscopists. Recently, a new dissociation mechanism of S⁺via the COS²⁺ isomer has been proposed. By referencing the results of AIMD simulations and focusing on the isomerization process, we emphasize the crucial role of dynamical effects and the concept of dynamically hidden reaction paths.
<Keywords:> Keywords Reaction path network, Ab initio molecular dynamics, Dynamically hidden reaction path
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2024-0044/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 10-13, by J-STAGE]
<Title:> 塩化亜鉛触媒を用いる芳香族ニトリルへのグリニャール付加反応の理論的研究
<Author(s):> 吉川　武司, 梅澤　美帆, 椿　紗穂里, 坂田　健, 波多野　学
<Corresponding author E-Mill:> takeshi.yoshikawa(at)phar.toho-u.ac.jp
<Abstract:> Alkylation reactions of aromatic nitriles using Grignard reagents produce ketones after hydrolysis. However, this addition reaction is slower than when using reactive organolithium(I) reagents. In the previous paper, we improved the reaction by using zinc(II)ates, which are generated in situ using Grignard reagents and zinc chloride (ZnCl₂). The corresponding ketones and amines were obtained in good yields under mild reaction conditions. In this study, the reaction mechanism was theoretically investigated by using density functional theory (DFT). The reactivity with ZnCl₂ was verified thorough orbital interaction analysis and non-covalent interactions analysis.
<Keywords:> キーワードGrignard reaction, Schlenk equilibrium, Zn(II)ate complex, Tetrahydrofuran solvent, Density functional theory
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2024-0037/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 1-9, by J-STAGE]
<Title:> ゆらぎの定理を利用した自由エネルギー計算に関する理論的背景と非平衡分子動力学シミュレーションへの応用
<Author(s):> 束村　晴, 菅波　祐介, 赤津　裕哉, 髙橋　颯人, 西村　好史, 中井　浩巳
<Corresponding author E-Mill:> nakai(at)waseda.jp
<Abstract:> Enhanced sampling methods have been applied to handle chemical reactions rarely observed in limited-scale molecular dynamics simulations. Some of these methods intentionally put the system in a nonequilibrium state. We focus on free energy calculation methods based on the fluctuation theorem to directly estimate free energy from simulations of nonequilibrium systems. In this paper, we derive Jarzynski’s equality and Bennett acceptance ratio method, and present their illustrative applications to free energy calculation.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2024-0033/_article/-char/ja/