Ammonia elimination from protonated nucleobases and related synthetic substrates

The results are reported of mass-spectrometric studies of the nucleobases adenine 1h ( 1 , R = H), guanine 2h , and cytosine 3h . The protonated nucleobases are generated by electrospray ionization of adenosine 1r ( 1 , R = ribose), guanosine 2r , and deoxycytidine 3d ( 3 , R = deoxyribose) and their fragmentations were studied with tandem mass spectrometry. In contrast to previous EI-MS studies of the nucleobases, NH 3 elimination does present a major path for the fragmentations of the ions [ 1h + H] + , [ 2h + H] + , and [ 3h + H] + . The ion [ 2h + H − NH 3 ] + also was generated from the acyclic precursor 5-cyanoamino-4-oxomethylene-dihydroimidazole 13h and from the thioether derivative 14h of 2h (NH 2 replaced by MeS). The analyses of the modes of initial fragmentation is supported by density functional theoretical studies. Conjugate acids 15 – 55 were studied to determine site preferences for the protonations of 1h , 2h , 3h , 13h , and 14h . The proton affinity of the amino group hardly ever is the substrate’s best protonation site, and possible mechanisms for NH 3 elimination are discussed in which the amino group serves as the dissociative protonation site. The results provide semi-direct experimental evidence for the existence of the pyrimidine ring-opened cations that we had proposed on the basis of theoretical studies as intermediates in nitrosative nucleobase deamination.