Circular hydrogen bond networks on the surface of β-ribofuranose in aqueous solution

Teppei Suzuki, Takayuki Sota

    Research output: Contribution to journalArticle

    8 Citations (Scopus)

    Abstract

    This paper examines the hydration structure on the surface of β-ribofuranose in aqueous solution, using the ab initio molecular dynamics method. In particular, we focus on circular hydrogen bond networks involving two ribofuranose oxygens and three water molecules. In our simulations, the circular hydrogen bond networks near the ring oxygen of β-ribofuranose are found to be significantly influenced by the orientation of the hydroxymethyl group. The arrangements of hydrogen bonds observed in the circular hydrogen bond networks are both homodromic and antidromic. To explain these observations, we analyze the electronic properties of the first-hydration-shell water molecules and the OH groups of β-ribofuranose, using the centers of their maximally localized Wannier functions. The dipole moments of the proton-accepting first-hydration-shell water molecules in our well-defined circular hydrogen bond networks are found to increase by about 0.3 D compared with that of liquid water, indicating the relatively strong polarization effects created by the interactions between the OH groups of the solute and the surrounding water molecules. Our analysis also implies that circular H-bond networks cannot be fully explained from a simple geometrical point of view.

    Original languageEnglish
    Pages (from-to)12603-12611
    Number of pages9
    JournalJournal of Physical Chemistry B
    Volume109
    Issue number25
    DOIs
    Publication statusPublished - 2005 Jun 30

    Fingerprint

    Hydrogen bonds
    hydrogen bonds
    aqueous solutions
    Water
    Hydration
    hydration
    Molecules
    water
    molecules
    Oxygen
    Dipole moment
    oxygen
    Electronic properties
    Molecular dynamics
    Protons
    solutes
    dipole moments
    Polarization
    molecular dynamics
    Hydrogen

    ASJC Scopus subject areas

    • Physical and Theoretical Chemistry

    Cite this

    Circular hydrogen bond networks on the surface of β-ribofuranose in aqueous solution. / Suzuki, Teppei; Sota, Takayuki.

    In: Journal of Physical Chemistry B, Vol. 109, No. 25, 30.06.2005, p. 12603-12611.

    Research output: Contribution to journalArticle

    @article{8bbffa6ffe01454cb476f8fbead24e11,
    title = "Circular hydrogen bond networks on the surface of β-ribofuranose in aqueous solution",
    abstract = "This paper examines the hydration structure on the surface of β-ribofuranose in aqueous solution, using the ab initio molecular dynamics method. In particular, we focus on circular hydrogen bond networks involving two ribofuranose oxygens and three water molecules. In our simulations, the circular hydrogen bond networks near the ring oxygen of β-ribofuranose are found to be significantly influenced by the orientation of the hydroxymethyl group. The arrangements of hydrogen bonds observed in the circular hydrogen bond networks are both homodromic and antidromic. To explain these observations, we analyze the electronic properties of the first-hydration-shell water molecules and the OH groups of β-ribofuranose, using the centers of their maximally localized Wannier functions. The dipole moments of the proton-accepting first-hydration-shell water molecules in our well-defined circular hydrogen bond networks are found to increase by about 0.3 D compared with that of liquid water, indicating the relatively strong polarization effects created by the interactions between the OH groups of the solute and the surrounding water molecules. Our analysis also implies that circular H-bond networks cannot be fully explained from a simple geometrical point of view.",
    author = "Teppei Suzuki and Takayuki Sota",
    year = "2005",
    month = "6",
    day = "30",
    doi = "10.1021/jp050100x",
    language = "English",
    volume = "109",
    pages = "12603--12611",
    journal = "Journal of Physical Chemistry B Materials",
    issn = "1520-6106",
    publisher = "American Chemical Society",
    number = "25",

    }

    TY - JOUR

    T1 - Circular hydrogen bond networks on the surface of β-ribofuranose in aqueous solution

    AU - Suzuki, Teppei

    AU - Sota, Takayuki

    PY - 2005/6/30

    Y1 - 2005/6/30

    N2 - This paper examines the hydration structure on the surface of β-ribofuranose in aqueous solution, using the ab initio molecular dynamics method. In particular, we focus on circular hydrogen bond networks involving two ribofuranose oxygens and three water molecules. In our simulations, the circular hydrogen bond networks near the ring oxygen of β-ribofuranose are found to be significantly influenced by the orientation of the hydroxymethyl group. The arrangements of hydrogen bonds observed in the circular hydrogen bond networks are both homodromic and antidromic. To explain these observations, we analyze the electronic properties of the first-hydration-shell water molecules and the OH groups of β-ribofuranose, using the centers of their maximally localized Wannier functions. The dipole moments of the proton-accepting first-hydration-shell water molecules in our well-defined circular hydrogen bond networks are found to increase by about 0.3 D compared with that of liquid water, indicating the relatively strong polarization effects created by the interactions between the OH groups of the solute and the surrounding water molecules. Our analysis also implies that circular H-bond networks cannot be fully explained from a simple geometrical point of view.

    AB - This paper examines the hydration structure on the surface of β-ribofuranose in aqueous solution, using the ab initio molecular dynamics method. In particular, we focus on circular hydrogen bond networks involving two ribofuranose oxygens and three water molecules. In our simulations, the circular hydrogen bond networks near the ring oxygen of β-ribofuranose are found to be significantly influenced by the orientation of the hydroxymethyl group. The arrangements of hydrogen bonds observed in the circular hydrogen bond networks are both homodromic and antidromic. To explain these observations, we analyze the electronic properties of the first-hydration-shell water molecules and the OH groups of β-ribofuranose, using the centers of their maximally localized Wannier functions. The dipole moments of the proton-accepting first-hydration-shell water molecules in our well-defined circular hydrogen bond networks are found to increase by about 0.3 D compared with that of liquid water, indicating the relatively strong polarization effects created by the interactions between the OH groups of the solute and the surrounding water molecules. Our analysis also implies that circular H-bond networks cannot be fully explained from a simple geometrical point of view.

    UR - http://www.scopus.com/inward/record.url?scp=22744435440&partnerID=8YFLogxK

    UR - http://www.scopus.com/inward/citedby.url?scp=22744435440&partnerID=8YFLogxK

    U2 - 10.1021/jp050100x

    DO - 10.1021/jp050100x

    M3 - Article

    VL - 109

    SP - 12603

    EP - 12611

    JO - Journal of Physical Chemistry B Materials

    JF - Journal of Physical Chemistry B Materials

    SN - 1520-6106

    IS - 25

    ER -