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

Teppei Suzuki, Hirotaka Kawashima, Hiromi Kotoku, Takayuki Sota

    Research output: Contribution to journalArticle

    6 Citations (Scopus)

    Abstract

    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.

    Original languageEnglish
    Pages (from-to)12997-13005
    Number of pages9
    JournalJournal of Physical Chemistry B
    Volume109
    Issue number26
    DOIs
    Publication statusPublished - 2005 Jul 7

    Fingerprint

    ribose
    Ribose
    low frequencies
    aqueous solutions
    Molecular dynamics
    phase shift
    Oxygen
    molecular dynamics
    oxygen
    Hydration
    hydration
    Trajectories
    trajectories
    Molecules
    Water
    water
    molecules
    interactions

    ASJC Scopus subject areas

    • Physical and Theoretical Chemistry

    Cite this

    Structural fluctuation and dynamics of ribose puckering in aqueous solution from first principles. / Suzuki, Teppei; Kawashima, Hirotaka; Kotoku, Hiromi; Sota, Takayuki.

    In: Journal of Physical Chemistry B, Vol. 109, No. 26, 07.07.2005, p. 12997-13005.

    Research output: Contribution to journalArticle

    Suzuki, Teppei ; Kawashima, Hirotaka ; Kotoku, Hiromi ; Sota, Takayuki. / Structural fluctuation and dynamics of ribose puckering in aqueous solution from first principles. In: Journal of Physical Chemistry B. 2005 ; Vol. 109, No. 26. pp. 12997-13005.
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