Influence of 2′-fluoro modification on glycosidic bond stabilities and gas-phase ion structures of protonated pyrimidine nucleosides

Abstract

The effects of 2′-fluoro substitution on the protonated gas-phase ions of the pyrimidine nucleosides are examined and compared with their previously reported canonical RNA and DNA forms. N-Glycosidic bond cleavage is the only collision-induced dissociation (CID) fragmentation pathway of protonated 2′-fluoro-2′-deoxycytidine, [Cydfl+H]+, and the major pathway of protonated 2′-fluoro-2′-deoxyuridine, [Urdfl+H]+. Based on energy-resolved CID and survival yield analysis, the N-glycosidic bond of [Cydfl+H]+ is more stable than that of [Urdfl+H]+. Further, the N-glycosidic bond stability of protonated pyrimidine nucleosides increases with increasing 2′-substituent electronegativity and follows the order F > OH > H. Gas-phase conformations of [Cydfl+H]+ and [Urdfl+H]+ are studied via infrared multiple photon dissociation (IRMPD) action spectroscopy coupled with theoretical calculations. IRMPD action spectra are measured over the IR fingerprint and hydrogen-stretching regions. Comparisons of theoretical and experimental spectra indicate that the experimentally accessed [Cydfl+H]+ and [Urdfl+H]+ conformers are highly parallel to those populated for their canonical counterparts. Evidence for gas-phase intramolecular O3′H⋯F2′ hydrogen-bonding in the IRMPD spectra of [Cydfl+H]+ and [Urdfl+H]+ allows for more definitive sugar puckering determinations than possible in the analogous canonical nucleosides.