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

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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 Mar 24

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ASJC Scopus subject areas

  • Chemistry(all)

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