Identification of ion fragments produced from thymine and deuterated thymine by low energy ion impact in films and electron impact in the gas phase

The chemical composition of charged fragments desorbing from thymine-methyl-d3-6-d (Td) films during 10-200 eV Ar+ ion irradiation is studied by mass spectrometry of positive and negative ions. The resulting mass spectra are compared to those obtained from similar films of thymine (T), and from 70 eV electron impact on both T and Td in the gas phase. Ion impact on T and Td films produces numerous positive and negative ion fragments via endocyclic and exocyclic bond cleavage, even at ion energies well below 60 eV. The major cations desorbing from T films are identified as HNCH+, HN(CH)CCH3+, [T-OCN]+, OCNH2+, CxHy+ (x = 1-3 and y = 0-4), and [T + H]+. While ion impact on T and Td films produces a new fragment [T-O]+, [Td-O]+, not seen in gas phase electron impact, the latter yields CO+ fragments that are not observed during ion impact on the films. Anion desorption is dominated by H−, O−, CN−, OCN−, and [T-H]− formation, with lesser dissociation channels leading to desorption of C2−, C2H−, C2CN−, NC3H2−, HNC3H3−, OC3H3−, C2OCN−, and C3Hx− (x = 2 and 3). Measurements of the primary ion energy dependence of the fragment desorption yields show that positive ion fragments appear at energies near 15-20 eV, while generally the endocyclic fragments appear at lower energies than the exocyclic (anion and cation) fragments. Our results show that even at very low ion energies, thymine is sensitive to complete fragmentation, whereby the loss of the HNCH (or HNCD from Td) fragment, i.e., ring cleavage involving the N1 and C6 atoms, dominates; in cellular DNA, this would correspond to complete loss of the base.