The gas-phase structures of protonated uracil, thymine, and cytosine are probed by using mid-infrared multiple-photon dissociation (IRMPD) spectroscopy performed at the Free Electron Laser facility of the Centre Laser Infrarouge d'Orsay (CLIO), France. Experimental infrared (IR) spectra are recorded for ions that were generated by electrospray ionization, isolated, and then irradiated in a quadrupole ion trap; the results are compared to the calculated infrared absorption spectra of the different low-lying isomers (computed at the B3LYP/6-31++G(d,p) level). For each protonated base, the global energy minimum corresponds to an enolic tautomer, whose infrared absorption spectrum matched very well with the experimental IRMPD spectrum, with the exception of a very weak IRMPD signal observed at about 1800 cm(-1) in the case of the three protonated bases. This signal is likely to be the signature of the second-energy-lying oxo tautomer. We thus conclude that within our experimental conditions, two tautomeric ions are formed which coexist in the quadrupole ion trap.

The gas-phase reactivity of lead(II) ions towards uracil and thymine has been studied by means of mass spectrometry and theoretical calculations. Positive-ion electrospray spectra show that this reactivity gives rise to both singly and doubly-charged species. The singly charged [Pb(nucleobase) n-H] + (n=1-4) complexes are the most intense ions on spectra at low concentration and are produced notably by dissociative proton transfer within the doubly charged [Pb(nucleobase) m ] 2+ (m=6-12) complexes. The most abundant ion, [Pb(nucleobase)-H] + , has been extensively studied by MS/MS experiments. Results obtained with uracil and thymine are rigorously similar and show that this ion mainly dissociates by elimination of isocyanic acid, and by formation of a [PbNCO] + ion. According to labeling experiments, the N3, C2 and O2 centers are exclusively expelled and complexed, respectively. Our experimental data suggest that the complex may correspond to a mixture of several structures. This is supported by stability of the most stable minima which are close in energy. Comparison with the geometry of neutral and deprotonated nucleobases indicates that lead cationization induces significant geometrical modifications, and more particularly an important activation of the N3-C4 bond, which accounts for the observed fragmentations.

The structure of the [Pb(UMP)-H](+) (UMP = uridine-5'-monophosphate) complex was studied in the gas phase by combining electrospray ionization (ESI), tandem mass spectrometry, and mid-infrared multiple photon dissociation (IRMPD) spectroscopy. The results obtained show that Pb(2+) ions interact not only with the deprotonated phosphate group but also with a carbonyl group of the nucleobase moiety by folding of the mononucleotide, resulting in macrochelates that are not likely to be present in solution. Comparison between the IRMPD and DFT-computed spectra suggests that the ESI-generated complex likely corresponds to a mixture of several structures, and establishes the enolic tautomers as the most abundant species for the [Pb(UMP)-H](+) ion, while the very weak IRMPD signal observed at ∼1763 cm(-1) points to a minor population of oxo forms. Our data also suggest that losing the nucleobase residue under CID conditions does not necessarily mean a lack of interaction between the metal and the nucleobase moiety, as commonly reported in the literature for large oligonucleotides.