Influence of methylation on the properties of uracil and its noncovalent interactions with alkali metal ions: Threshold collision-induced dissociation and theoretical studies

Abstract

The influence of methylation on the properties of uracil and its noncovalent interactions with alkali metal ions is investigated both experimentally and theoretically. Threshold collision-induced dissociation (CID) of M +( xMeU) with Xe is studied in a guided ion beam mass spectrometer. M + include the following alkali metal ions: Li +, Na +, and K +. Five methylated uracils are examined, xMeU = 1-methyluracil, 3-methyluracil, 6-methyluracil, 1,3-dimethyluracil, and 5,6-dimethyluracil. In all cases endothermic loss of the intact nucleobase is the dominant reaction pathway, while ligand exchange to produce MXe + is observed as a minor reaction pathway. The threshold regions of the cross sections are interpreted to extract 0 and 298 K bond dissociation energies (BDEs) for M + xMeU after accounting for the effects of multiple ion-neutral collisions, kinetic and internal energies of the reactants, and dissociation lifetimes. Ab initio calculations at the MP2(full)/6–31 G* level of theory are used to determine the structures of these complexes and provide molecular constants required for the thermochemical analysis of the experimental data. Theoretical bond dissociation energies are determined from single point energy calculations at the MP2(full)/6–311 + G(2d,2p) level using the MP2(full)/6–31 G* geometries. Excellent agreement between theory and experiment is found for the Na + and K + systems, while theory systematically underestimates the strength of binding in the Li + systems. Theoretical calculations are also performed to examine the influence of methylation on the acidities, proton affinities, and Watson–Crick base pairing energies. The present results are compared to earlier studies of uracil and 5-methyluracil to more fully elucidate the influence of methylation on the properties of uracil, its noncovalent interactions with alkali metal ions, and nucleic acid stability.