Density functional study on core ionization spectra of cytidine and its fragments - Swinburne Research Bank : Open Access Repository

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Title: Density functional study on core ionization spectra of cytidine and its fragments
Author(s): Thompson, Alexander; Saha, Saumitra; Wang, Feng; Tsuchimochi, Takashi; Nakata, Ayako; Imamura, Yutaka; Nakai, Hiromi
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, CVB3LYP, 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 ill 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.
Publication Type: Journal article
Research Centre: Swinburne University of Technology. Faculty of Information and Communication Technologies. Centre for Molecular Simulation
Source: Bulletin of the Chemical Society of Japan, Vol. 82, no. 2 (Feb 2009), pp. 187-195
Publication Year: 2009
FOR Code(s): 020201 Atomic and Molecular Physics; 030402 Biomolecular Modelling and Design; 030702 Radiation and Matter
Keyword(s): Amino; Atoms; Cytidine; Electron binding-energies; Ionization spectra; Molecules; Nucleobases; Ray-absorption spectra; Signatures; Spectroscopy
Publisher: Chemical Society of Japan
Publisher URL: http://dx.doi.org/10.1246/bcsj.82.187
ISSN: 0009-2673
Peer Reviewed