Structural fluctuation and dynamics of ribose puckering in aqueous solution from first principles

Teppei Suzuki*, Hirotaka Kawashima, Hiromi Kotoku, Takayuki Sota

*この研究の対応する著者

研究成果: Article査読

6 被引用数 (Scopus)

抄録

Using the method of ab initio molecular dynamics, we examine the structural fluctuation and the low-frequency dynamics of β-ribofuranose puckering in aqueous solution. Our analysis suggests that the distance between the anomeric and hydroxymethyl oxygens is a simple relevant geometrical parameter that dynamically correlates with the phase angle in the north region. The time-frequency analysis using the Hilbert-Huang transform also confirms the correlation, and most of the instantaneous frequencies for the phase angle and the above distance are found to be concentrated on the region below about 100 cm-1. Our analysis of ab initio molecular dynamics trajectories suggests that the molecular origin of the hydration effects on the low-frequency dynamics of β-ribofuranose puckering is closely related to this correlation and thus primarily attributed to the relatively local interactions among the anomeric and hydroxymethyl oxygens and the surrounding water molecules near them. Additionally, we discuss the difference in the low-frequency dynamics of β-ribofuranose puckering between two hydroxymethyl rotamers.

本文言語English
ページ(範囲)12997-13005
ページ数9
ジャーナルJournal of Physical Chemistry B
109
26
DOI
出版ステータスPublished - 2005 7 7

ASJC Scopus subject areas

  • 物理化学および理論化学
  • 表面、皮膜および薄膜
  • 材料化学

フィンガープリント

「Structural fluctuation and dynamics of ribose puckering in aqueous solution from first principles」の研究トピックを掘り下げます。これらがまとまってユニークなフィンガープリントを構成します。

引用スタイル