Transition of the coordination modes in sodiated uridine radicals revealed by infrared multiphoton dissociation spectroscopy and theoretical calculations

Abstract

The stable generation and structural characterization of sodium cationized nucleic acid radicals at the molecular level have always been a difficult problem to solve. Herein, we produced the radical cation of [Urd + Na − H]˙⁺ through ultraviolet photodissociation (UVPD) of the precursor ion of [I − Urd + Na]⁺ in the gas phase and further studied its infrared multiphoton dissociation (IRMPD) spectrum in the region of 2750–3850 cm⁻¹. The comparison between the IRMPD spectra of the precursor and radical cations shows their common features at both 3445 and 3705 cm⁻¹ peaks, as well as the difference in the 3628 cm⁻¹ peak that exists only in the case of the latter. By combining with theoretical calculations, it is indicated that the bidentate coordination structure M–B(O2,O2′)-1 and the tridentate coordination structure R–T(O2,O′,O5′)–(C5H–C1′)-1 are dominantly populated for the precursor and the radical cations, respectively. After the homo-cleavage of the C–I bond using a UV laser, a multi-step hydrogen transfer process started from the C1′ position, followed by a rotation of the intramolecular C–N bond, resulting in the formation of the most stable isomer, characterized by its radical position at C1′ and its tridentate coordination mode. This result indicates that the generation of free radicals of metal cationized nucleic acids by UVPD may result in the hydrogen transfer from the sugar ring, as well as the accompanied change of its coordination mode of the attached metal ions.