Vibrational Spectroscopy and Intramolecular Hydrogen Bond Network of (Didehydro)Deoxycytidine Nucleosides

Sugar puckering and hydrogen bond networks are the most important properties of nucleosides as either DNA functional moieties or antibiotics. This article studies such the relationship quantum mechanically for two cytidine nucleoside derivatives, 1’, 2’-didehydro-3’, 4’-deoxycytidine (I) and 2’-deoxycytidine (II) with respect to cytidine (III) in isolation. Vibrational infrared (IR) spectroscopy studied using density functional theory (DFT) models in addition to other properties such as potential energy surfaces (PES), geometries, molecular electrostatic potentials (MEP) and Fukui functions. The atomic site related Fukui function indicates that the sugar carbons are less chemically active in III but can be activated when losing the hydroxyl group at C(2’) as in II and can be significantly activated by forming a C=C double bond as in I. The simulated IR spectra indicate that the compounds are related structurally. Intramolecular hydrogen bond networks (as “spider webs”) of the biomolecules are revealed with IR red-shift and blue-shift. A detailed study in the region of C-H stretch in 2800-3300 cm-1 indicates that intramolecular H-bond networks cause IR spectral blue-shift.