The gas phase acidities of a series of uracil derivatives (1-methyluracil, 3-methyluracil, 6-methyluracil, 5,6-dimethyluracil, and 1,3-dimethyluracil) have been bracketed to provide an understanding of the intrinsic reactivity of uracil. The experiments indicate that in the gas phase, uracil has four sites more acidic than water. Among the uracil analogs, the N1-H sites have ⌬H acid values of 331-333 kcal mol Ϫ1 ; the acidity of the N3 sites fall between 347-352 kcal mol Ϫ1 . The vinylic C6 in 1-methyluracil and 3-methyluracil brackets to 363 kcal mol Ϫ1 , and 369 kcal mol Ϫ1 in 1,3-dimethyluracil; the C5 of 1,3-dimethyluracil brackets to 384 kcal mol Ϫ1 . Calculations conducted at B3LYP/6-31ϩG* are in agreement with the experimental values. The bracketing of several of these sites involved utilization of an FTMS protocol to measure the less acidic site in a molecule that has more than one acidic site, establishing the generality of this method. In molecules with multiple acidic sites, only the two most acidic sites were bracketable, which is attributable to a kinetic effect. The measured acidities are in direct contrast to in solution, where the two most acidic sites of uracil (N1 and N3) are indifferentiable. The vinylic C6 site is also particularly acidic, compared to acrolein and pyridine. The biological implications of these results, particularly with respect to enzymes for which uracil is a substrate, are discussed. (J Am Soc Mass Spectrom 2002, 13, 985-995)

We have shown for the first time experimentally that the O2 and O4 sites of uracil have different proton affinities, and as implied in previous computational studies, the O4 is more basic and would be energetically preferred in an orotate ribose 5'-monophosphate decarboxylase catalysis mechanism involving proton transfer to oxygen.