Noncovalent Interactions of Nucleic Acid Bases (Uracil, Thymine, and Adenine) with Alkali Metal Ions. Threshold Collision-Induced Dissociation and Theoretical Studies

Threshold collision-induced dissociation of M⁺L (M⁺ = Li⁺, Na⁺, and K⁺; L = uracil, thymine, and adenine) with xenon is studied using guided ion beam mass spectrometry. In all cases, the primary product formed corresponds to endothermic loss of the intact neutral molecule. The only other product observed is the result of ligand exchange processes to form MXe⁺. Cross-section thresholds are interpreted to yield 0 and 298 K bond dissociation energies for M⁺−L after accounting for the effects of multiple ion−molecule collisions, internal energy of the reactant ions, and dissociation lifetimes. Ab initio calculations at the MP2(full)/6-311+G(2d,2p)//MP2(full)/6-31G* level of theory are used to determine the structures and relative energetics of several conformers of these complexes and to provide molecular constants necessary for the thermodynamic analysis of the experimental data. We find that all of the complexes are very nearly planar. Calculated M⁺−L bond dissociation energies compare favorably to the experimentally determined bond energies for Na⁺ and K⁺ binding to uracil and thymine, while theoretical values for Li⁺ to all three bases and adenine with all three metal ions are systematically low (by 16 ± 8 kJ/mol). Comparisons with previous values determined by the kinetic method are reasonable, except in the case of Na⁺(adenine). A key observation in this work is that the metal ions bind most strongly to adenine at the N7 site coupled with chelation to the amino group. The magnitude of the interaction with the amino group is estimated to be sufficient to disrupt hydrogen bonding in A:T (A:U) nucleic acid base pairs for Li⁺, Na⁺, and probably transition metal ions and multiply charged ions.