Structures, fragmentation, and protonation of trideoxynucleotide CCC mono- and dianions

Both quantum chemical calculations and ESI mass spectrometry are used here to explore the gas-phase structures, energies, and stabilities against collision-induced dissociation of a relatively small model DNA molecule-a trideoxynucleotide with the sequence CCC, in its singly and doubly deprotonated forms, (CCC - H)- and (CCC - 2H)2-, respectively. Also, the gas-phase reactivity of these two anions was measured with HBr, a potential proton donor, using an ESI/SIFT/QqQ instrument. The computational results provide insight into the gas-phase structures of the electrosprayed (CCC - 2H)2- and (CCC - H)- anions and the neutral CCC, as well as the proton affinities of the di- and monoanions. The dianion (CCC 2H)2- was found to dissociate upon CID by charge separation via two competing channels: separation into deprotonated cytosine (C - H)- and (CCC - (C - H) - 2H)-, and by wi /a2 cleavage of the backbone. The monoanion (CCC - H)- loses a neutral cytosine upon CID, and an H/D-exchangeable proton, presumably residing on one of the phosphate groups, is transferred to the partially liberated (C - H)_ before dissociation. This was confirmed by MS/MS experiments with the deuterated analog. The reaction of (CCC - 2H)2- with HBr was observed to be rapid, k = (1.4 0.4) X 10-9 cm' molecule' s-', and to proceed both by addition (78%) and by proton transfer (22%) while (CCC - H)_ reacts only by HBr addition, k = (7.1 2. 1) X 10-11 CM3 molecule' s-1. This is in accord with the computed proton affinities of (CCC - 2H)2- and (CCC - H)- anions that bracket the known proton affinity of Br.