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, NH3 elimination does present a major path for the fragmentations of the ions [1h + H]+, [2h + H]+, and [3h + H]+. The ion [2h + H - NH3]+ also was generated from the acyclic precursor 5-cyanoamino-4-oxomethylene-dihydroimidazole 13h and from the thioether derivative 14h of 2h (NH2 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 NH3 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.




National Institutes of Health (U.S.)


This study was supported by the United States National Institutes of Health (GM61027).

Keywords and Phrases

Density Functional Theory; Electrospray Ionization; Ion Sources; Mass Spectrometry; Proton Transfer; Protonation; Dissociative Protonation Site; Fragmentations; Nucleobase Deamination; Nucleobases; Protonated Nucleobases; Ammonia; Adenosine; Deoxycytidine; Deoxyribose; Guanosine; Nucleic Acid Base; Pyrimidine; Sulfide; Chemical Structure; Density Functional Theory; Electrospray; Excretion; Mass Fragmentography; Proton Transport; Tandem Mass Spectrometry; Adenine; Cytosine; Guanine; Protons; Spectrometry; Mass; Electrospray Ionization

International Standard Serial Number (ISSN)

1044-0305; 1879-1123

Document Type

Article - Journal

Document Version

Accepted Manuscript

File Type





© 2007 Springer Verlag, All rights reserved.

Publication Date

01 Nov 2007

PubMed ID


Included in

Chemistry Commons