Gas-phase conformations and energetics of protonated 2'-deoxyadenosine and adenosine: IRMPD action spectroscopy and theoretical studies.

The gas-phase conformations of protonated 2'-deoxyadenosine, [dAdo+H](+), and its RNA analogue protonated adenosine, [Ado+H](+), generated upon electrospray ionization are examined using infrared multiple photon dissociation (IRMPD) action spectroscopy techniques and supported by complementary theoretical electronic structure calculations. IRMPD action spectra are measured over the IR fingerprint region using the FELIX free-electron laser and the hydrogen-stretching region using an optical parametric oscillator/amplifier laser system. The measured IRMPD spectra are compared to linear IR spectra predicted for the stable low-energy conformations of [dAdo+H](+) and [Ado+H](+) computed at the B3LYP/6-311+G(d,p) level of theory to determine the preferred site of protonation and to identify the structures populated in the experiments. N3 is found to be the most favorable site of protonation for both [dAdo+H](+) and [Ado+H](+), whereas conformers protonated at the N1 and N7 positions are much less stable by >25 kJ/mol. The 2'-hydroxyl substituent of Ado does not lead to a significant change in the structure of the ground-state conformer of [Ado+H](+) as compared to that of [dAdo+H](+), except that it provides additional stabilization via the formation of an O2'H···O3' hydrogen bond. Therefore, [dAdo+H](+) and [Ado+H](+) exhibit highly parallel IRMPD spectral features in both the fingerprint and hydrogen-stretching regions. However, the additional 2'-hydroxyl substituent markedly affects the IRMPD yield of the measured IR bands. The spectral signatures in the hydrogen-stretching region provide complementary information to that of the fingerprint region and enable facile differentiation of the conformers that arise from different protonation sites. In spite of the relative gas-phase stabilities of the N3 and N1 protonated conformers, present results suggest that both are accessed in the experiments and contribute to the measured IRMPD spectrum, indicating that the relative stabilities in solution also influence the populations generated by electrospray ionization.