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DFT study on conformational behavior of hydrogen ion abstractions of cytosine nucleosides: AIM and NBO analysis

Tehrani, Z. A ; Sharif University of Technology

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  1. Type of Document: Article
  2. DOI: 10.1142/S0219633611006797
  3. Abstract:
  4. In this paper, we explore theoretically energetic and structural properties of the possible cations formed via hydride ion abstraction at various sites of sugar part of cytosine nucleosides by employing B3LYP exchange-correlation functional with 6-311++G (d,p) orbital basis sets. In general, the hydride ion abstracted sugar cations of cytosine nucleosides have the following stability sequence: caH2′ > caH1′ > caH3′ > caH4′ > caH5′ for cytidine and caH1′ > caH4′ > caH3′ > caH5′ > caH2′ for deoxycytidine. Furthermore, the effect of solvent environment on the stability order of cations integral equation formalism of the polarized model (IEF-PCM) was employed to model aqueous solution. The natural bond orbital method was used for quantitative analysis of the electron delocalization donoracceptor interaction of various hydride ions abstracted centers of cytosine nucleosides. The role of CH⋯O and HO⋯H intramolecular hydrogen bonds in the stability of cations is investigated based on the results of topological properties of atom in molecule theory. Moreover, variations of significant structural parameters such as puckering amplitudes and phase angles of sugar parts of cytosine nucleosides after cation formation are also found
  5. Keywords:
  6. AIM theory ; DFT study ; Hydride ion abstraction ; NBO analysis ; Sugar puckering mode
  7. Source: Journal of Theoretical and Computational Chemistry ; Volume 10, Issue 6 , 2011 , Pages 803-817 ; 02196336 (ISSN)
  8. URL: http://www.worldscientific.com/doi/abs/10.1142/S0219633611006797