月別: 2025年3月

[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.
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<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2024-0033/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.24, 1-4, by J-STAGE]
<Title:> ジメチルスルホキシドの水和構造評価:有効フラグメントポテンシャル-分子動力学計算
<Author(s):> 石郷岡　知里, 黒木　菜保子
<Corresponding author E-Mill:> kuroki.nahoko(at)ocha.ac.jp
<Abstract:> Dimethyl sulfoxide (DMSO), widely used as a cryoprotectant, drug, and oxidant, contains a hydrophilic S=O and hydrophobic CH₃ groups and is fully miscible with water in any ratio. In this study, intermolecular interactions in dilute aqueous DMSO solution were analyzed using effective fragment potential based molecular dynamics (EFP-MD) simulations. The analysis revealed that DMSO induced stable interactions with water molecules not only around its hydrophilic S=O group but also near the CH₃ groups. The interaction lifetimes suggested that the hydrogen bonding network in the first hydration shell is directional.
<Keywords:> キーワードHydration, Fragmentation, Quantum chemistry, Molecular dynamics, Intermolecular interaction
<URL:> https://www.jstage.jst.go.jp/article/jccj/24/1/24_2024-0042/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.23, 105-114, by J-STAGE]
<Title:> FMO法の相互作用情報を用いた相分離シミュレーションとの連携
<Author(s):> 奥脇　弘次, 土居　英男, 小沢　拓, 望月　祐志
<Corresponding author E-Mill:> okuwaki(at)rikkyo.ac.jp
<Abstract:> Recent efforts have focused on utilizing molecular interaction data from FMO calculations for phase separation simulations in materials design. Accurate prediction of phase separation, which is closely related to molecular affinity, has long been a challenge due to difficulties in calculating accurate interaction parameters. We have developed a framework for estimating effective interaction parameters between coarse-grained components using FMO calculations. In addition, a simulation scheme called FMO-DPD, which applies these parameters to dissipative particle dynamics (DPD) simulations, has demonstrated its effectiveness in various systems. These developments are discussed in this paper.
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<URL:> https://www.jstage.jst.go.jp/article/jccj/23/4/23_2024-0029/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan Vol.23, 115-125, by J-STAGE]
<Title:> 分子動力学法とFMO法を用いた非晶質固体分散体の吸湿安定性解析
<Author(s):> 松本　穂香, 奥脇　弘次, 東　顕二郎, 古石　誉之, 福澤　薫, 米持　悦生
<Corresponding author E-Mill:> okuwaki.koji(at)jsol.co.jp
<Abstract:> While Amorphous solid dispersion is an effective method for improving the solubility of pharmaceutical formulations, it presents stability challenges, as moisture absorption can accelerate crystallization. In this study, we employed a model system using four drug molecules (Droperidol, Nifedipine, Indomethacin, Ketoprofen) and the carrier polymer Polyvinylpyrrolidone, where molecular distribution was simulated using MD methods, and interaction energies were calculated using the FMO method. We analyzed the changes in interaction energies due to moisture absorption, clarifying the differences in crystallization tendencies and stability of the drugs.
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<URL:> https://www.jstage.jst.go.jp/article/jccj/23/4/23_2024-0031/_article/-char/ja/