Journal of Computer Chemistry, Japan
Online ISSN : 1347-3824
Print ISSN : 1347-1767
ISSN-L : 1347-1767
Current issue
Special Issue: Selected Papers from the Annual Autumn Meeting 2024
Displaying 1-9 of 9 articles from this issue
Foreword
Commentary
Software News and Review
Letters (SCCJ Annual Meeting 2024 Autumn Poster Award Articles)
Letters (Selected Papers)
  • Takeshi YOSHIKAWA, Miho UMEZAWA, Sahori TSUBAKI, Ken SAKATA, Manabu HA ...
    2025 Volume 24 Issue 1 Pages 10-13
    Published: 2025
    Released on J-STAGE: March 29, 2025
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    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.

  • Ryo FUJIKI, Kowit HENGPHASATPORN, Yasuteru SHIGETA
    2025 Volume 24 Issue 1 Pages 14-16
    Published: 2025
    Released on J-STAGE: March 31, 2025
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    Molecular dynamics simulations combined with 3D-RISM theory provided new insights into how mutations influence the distribution of zinc ions in mutant ZIP8. When both Q58 and E221, which function as metal ion recognition filters, were replaced with histidine, the distance between residues 58 and 221 remained nearly unchanged compared to the wild type. However, the distance between the transmembrane domains on the intracellular side exhibited significant changes, suggesting a potential enhancement of zinc transport. This result aligns with experimental findings indicating that the mutation enhances zinc transport ability.

  • Rikuo SUZUKI, Ryo MIYATA, Satoru INOUE, Tatsuo HASEGAWA, Hiroyuki MATS ...
    2025 Volume 24 Issue 1 Pages 17-19
    Published: 2025
    Released on J-STAGE: April 01, 2025
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    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 (χL) 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 χL. The results revealed that increasing χL 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.

  • Tien Quang NGUYEN, Susan Meñez ASPERA, Yingjie CHEN, Kaoru HISAMA, Mic ...
    2025 Volume 24 Issue 1 Pages 20-26
    Published: 2025
    Released on J-STAGE: April 12, 2025
    JOURNAL FREE ACCESS FULL-TEXT HTML
    Supplementary material

    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-, HPO42-, CO32- and SO42-) 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.

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