Density functional study on core ionization spectra of cytidine and its fragments

Alexander Thompson, Saumitra Saha, Feng Wang, Takashi Tsuehimoehi, Ayako Nakata, Yutaka Imamura, Hiromi Nakai

    Research output: Contribution to journalArticle

    15 Citations (Scopus)

    Abstract

    The sugar-base correlation of cytosine (base) and deoxyribose (sugar) moieties of cytidine is investigated based on their inner-shell electronic structural information. A recently developed density functional theory (DFT) model, CV-B3LYP, with a Gaussian-type basis set of 6-311G**, and the DFT-LB94 model with a Slater-type basis set of TZ2P are employed to calculate inner shell ionization energies. The results reveal that the corresponding geometry of cytidine is not significantly different from its fragments, i.e., cytosine and deoxyribose. Changes in charge distribution of cytidine with respect to cytosine and deoxyribose concentrate on the local C sites in the base pyrimidine ring and sugar ring, as indicated by the atomic Hirshfeld charges. The O-K, N-K, and C-K spectra of cytidine inherit the aromatic signature in cytosine, suggesting that the role of the aromatic ring is a buffer to diffuse the changes brought in by the addition of the deoxyribose moiety. Formation of cytidine, however, substantially changes the C-K spectra of the deoxyribose moiety. In general, the correlated O-K, N-K, and C-K sites of cytidine exhibit small red shifts with respect to the cytosine base, whereas the O-K and C-K sites of cytidine show blue shifts in comparison with those of deoxyribose.

    Original languageEnglish
    Pages (from-to)187-195
    Number of pages9
    JournalBulletin of the Chemical Society of Japan
    Volume82
    Issue number2
    DOIs
    Publication statusPublished - 2009

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    Cytidine
    Deoxyribose
    Ionization
    Cytosine
    Sugars
    Density functional theory
    Ionization potential
    Charge distribution
    Buffers
    Geometry

    ASJC Scopus subject areas

    • Chemistry(all)

    Cite this

    Density functional study on core ionization spectra of cytidine and its fragments. / Thompson, Alexander; Saha, Saumitra; Wang, Feng; Tsuehimoehi, Takashi; Nakata, Ayako; Imamura, Yutaka; Nakai, Hiromi.

    In: Bulletin of the Chemical Society of Japan, Vol. 82, No. 2, 2009, p. 187-195.

    Research output: Contribution to journalArticle

    Thompson, Alexander ; Saha, Saumitra ; Wang, Feng ; Tsuehimoehi, Takashi ; Nakata, Ayako ; Imamura, Yutaka ; Nakai, Hiromi. / Density functional study on core ionization spectra of cytidine and its fragments. In: Bulletin of the Chemical Society of Japan. 2009 ; Vol. 82, No. 2. pp. 187-195.
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    AU - Nakai, Hiromi

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