分子動力学によるフラボノイド周囲の水和：溶媒の密度�?�双極子場�?�および拡散

Chem-Bio Informatics Journal

功刀 彰³  神谷 成敏¹  肥後 順一³  丸山 慶一朗³  �? 永淑³  横溝 剛² 

[1]大阪大学臨床医工学融合研究教育センター

[2]慶応大学理工学部

[3]東京薬科大学生命科学部

关键词: Hydration;    水和;    Solvent density;    分子配向;    Dipole;    場;    Diffusion;    分子動力学シミュレーション;    Molecular dynamics simulation;    断熱近似;   

DOI  :  10.1273/cbij.8.33

学科分类：生物化学/生物物理

来源: Chem-Bio Informatics Society

【 摘 要 】

References(36)Cited-By(1)We studied hydration of four types of small nonpeptidic molecule, flavonoid, by molecular dynamics simulations at 300 K with focusing on three physical quantities: solvent density, solvent site-dipole field, and solvent diffusion.The solvent site-dipole field is a quantity recently introduced by us to study directional ordering of water molecules around solute.The spatial patterns of these quantities showed strong site-dependency around the flavonoids.Common to the four flavonoids, high solvent-density sites around hydrophilic solute atoms were characterized by strong directional ordering of water molecule and by depressed solvent diffusive motions.Contrarily, high solvent-density sites around hydrophobic solute surface were characterized by weak directional ordering.The solvent site-dipole field showed specific ordering patterns of water molecules not only in the first solvent layer but also in the second solvent layer.The spatial patterns of the three quantities were conservative among the four flavonoids whether the intra-flavonoid flexibility was large or not.Thus, an adiabatic approximation, which has been assumed in various theoretical hydration studies, was satisfied well.The hydration at a site in the vicinity of solute was determined mainly by the physico-chemical property of the solute atom group nearest to the solvent site, which supports a phenomenological theorem that the solvent accessible surface area of a solute is proportional to the solvation free energy.

【 授权许可】

Unknown