Structures, electrophilic properties, and hydrogen bonds of cytidine, uridine, and their radical anions:...

Structures, electrophilic properties, and hydrogen bonds of the neutral and anionic monohydrated nucleoside, (cytidine)H2O, and (uridine)H2O have been systematically investigated using density functional theory. Various water-binding sites were predicted by explicitly considering the optimized monohydrated structures. Meanwhile, predictions of electron affinities and vertical detachment energies were also carried out to investigate their electrophilic properties. By examining the singly occupied molecular orbital and natural population analysis, we found the excess negative charge is localized on the cytidine and uridine moiety in anionic monohydrates. This may be the reason why the strength of hydrogen bonding undergoes an obvious change upon the extra electron attachment. Based on the electron density (ρ) and reduced density gradient (RDG), we present an approach to map and analyze the weak interaction (especially hydrogen bond) in monohydrated cytidine and uridine. The scatter plots of RDG versus ρ allow us to identify the different type interactions. Meanwhile, the maps of the gradient isosurfaces show a rich visualization of hydrogen bond, van der Waals interaction, and steric effect.