InfraredMultiple Photon Dissociation Action Spectroscopyof Proton-Bound Dimers of Cytosine and Modified Cytosines: Effectsof Modifications on Gas-Phase Conformations.

The gas-phase structures of proton-bounddimers of cytosine andmodified cytosines and their d6-analogues generated byelectrospray ionization are probed via infrared multiple photon dissociation(IRMPD) action spectroscopy and theoretical electronic structure calculations.The modified cytosines examined include the 5-methyl-, 5-fluoro-,and 5-bromo-substituted species. IRMPD action spectra of seven proton-bounddimers exhibit both similar and distinctive spectral features overthe range of ∼2600–3700 cm–1. TheIRMPD spectra of all of these proton-bound dimers are relatively simple,but exhibit obvious shifts in the positions of several bands thatcorrelate with the properties of the substituent. The measured IRMPDspectra are compared to linear IR spectra calculated for the stablelow-energy tautomeric conformations, determined at the B3LYP/6-31G*level of theory, to identify the conformations accessed in the experiments.Comparison of the measured IRMPD and calculated IR spectra indicatesthat only a single conformation, the ground-state structure, is accessedfor all proton-bound homodimers, whereas the ground-state and a smallpopulation of the first-excited tautomeric conformations are accessedfor all proton-bound heterodimers. In all cases, three hydrogen-bondinginteractions in which the nucleobases are aligned in an antiparallelfashion analogous to that of the DNA i-motif areresponsible for stabilizing the base pairing. Thus, base modificationssuch as 5-methyl- and 5-halo-substitution of cytosine should not alterthe structure of the DNA i-motif. [ABSTRACT FROM AUTHOR]