Journal of Computer Chemistry, Japan

[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/

[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.
<Keywords:>
<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.
<Keywords:>
<URL:> https://www.jstage.jst.go.jp/article/jccj/23/4/23_2024-0031/_article/-char/ja/

[Advanced Published online Journal of Computer Chemistry, Japan, by J-STAGE]
<Title:> 結晶学を活用した結晶モデル作成支援ソフトウェア「壺車」の2024年更新版
<Author(s):> 洋陽 日沼
<Corresponding author E-Mill:> y.hinuma(at)aist.go.jp
<Abstract:> The author’s code for VASP POSCAR handling is updated with new methods developed in 2024. Size “1/N”supercells can be obtained to find identical or smaller size unit cells that may belong to a Bravais lattice with a lower degree of freedom if deviations from rigid requirements for each Bravais lattice are allowed. Sortable number “message digests” of the configuration of different species on a (sub)lattice can be derived, which is useful for eliminating identical configurations in exhaustive combinatorial searches of species distributions. A molecule containing a given atom can be extracted from, for example, a molecular crystal supercell with many molecules.
<Keywords:> Keywords Crystal model generation, 1/N-supercell, Bravais lattice, message digest, molecule detection
<URL:> https://www.jstage.jst.go.jp/article/jccj/advpub/0/advpub_2024-0034/_article/-char/ja/

[Published online Journal of Computer Chemistry, Japan -International Edition Vol.10, -, by J-STAGE]
<Title:> A Study of Deep Learning for Quantitative Analysis of Vitamin A in Cattle Blood
<Author(s):> Mizuki SHIBASAKI, Tetsuhito SUZUKI, Moriyuki FUKUSHIMA, Shin-ichi NAGAOKA, Yuichi OGAWA, Naoshi KONDO
<Corresponding author E-Mill:> nagaoka.shinichi.3c(at)kyoto-u.ac.jp
<Abstract:> Deep learning in combination with fluorescence excitation-emission spectroscopy was studied to quantitatively analyze vitamin A (retinol) in cattle blood. The neural network model being obtained with the deep learning predicted the vitamin-A levels with a coefficient of determination (R²) of 0.93 with respect to the experimental values. The combination of the deep learning and fluorescence excitation-emission spectroscopy has a potential to predict the vitamin-A level in the cattle blood accurately, rapidly and inexpensively and to improve production of marbled beef with maintaining cattle health. It could also be applied to quantitative vitamin-A assays of various biological tissues, foods and so on as well as to those of blood samples besides cattle.
<Keywords:> Deep learning, Neural network, Fluorescence excitation-emission spectroscopy, Vitamin A, Retinol, Cattle blood, random forest
<URL:> https://www.jstage.jst.go.jp/article/jccjie/10/0/10_2024-0012/_html