Low-energy collision-induced dissociation of deprotonated dinucleotides: determination of the energetically favored dissociation pathways and the relative acidities of the nucleic acid bases

Abstract

Fourier transform ion cyclotron resonance mass spectroscopy has been used to examine the collision-induced dissociation pathways of all 16 of the possible deprotonated dinucleotides. These quasimolecular ions were generated by cesium ion bombardment of a mixture of triethanolamine, ammonium hydroxide and the dinucleotide. Collisional activation using continuous off-resonance excitation permits observation of energetically-favorable dissociation pathways. Dissociation products were examined over the range of center of mass energies from 0 to the minimum energy required to bring about complete dissociation of the reactant ion which did not exceed 7.7eV for deprotonated parent ions and 8.8eV for fragment ions in any of the systems. Semiempirical calculations were performed using the PM3 method, a variant of the AM1 method, to obtain gas-phase model structures and energies of the deprotonated dinucleotides and their collision-induced dissociation fragments. The acidities of the nucleic acid bases and dimethyl phosphate were calculated using the AM1 method. The deprotonated quasimolecular ions dissociate to yield several characteristic products. The major products formed in all systems are the deprotonated 5′-terminus base, the ion resulting from loss of the neutral 5′-terminus base, or the metaphosphate anion, PO − 3. Insight into the relative stabilities of the fragment ions is gained by comparing the product distributions observed in each of the systems. The relative yields of products involving either the 3′- or 5′-end of the molecule suggest the 3′-terminus base is stabilized through hydrogen bonding interaction with the phosphate group. The relative strength of this stabilization follows the order guanine > thymine > cytosine > adenine. Additionally, the relative abundances of the deprotonated nucleic acid fragments suggest that the relative acidities of the nucleic acid bases follow the order adenine > thymine > guanine > cytosine. Only minor yields of sequence ions in which one of the phosphate diester linkages is cleaved are observed with these quasimolecular ions. Reaction mechanisms which account for the observed products are proposed.