UV-Vis Action Spectroscopy Reveals Structures of DNA Codon Trinucleotide Cation Radicals

We report a comprehensive spectroscopic study of gas-phase cation radicals and dication radicals derived from DNA trinucleotide codons AAA, AAC, AAT, ATA, and TAA that was augmented by computational analysis of protomer and conformer structures, energies, excited states, and vibronic spectra for AAA, AAC, and AAT cation radicals and AAA and AAC dication radicals. Multiply charged noncovalent complex ions of codons with dibenzo-18-crown-6 ether (DBCE) were generated by electrospray protonation, selected by mass, and used for electron transfer dissociation to cleanly generate codon cation radicals, dication radicals, and doubly reduced ions upon DBCE elimination. Complexes of AAA and AAC formed both doubly and triply charged ions that upon gas-phase reduction and loss of DBCE yielded the respective stable hydrogen-rich cation radicals (AAA + 2H)^+• and (AAC + 2H)^+• and dication radicals (AAA + 3H)^2+• and (AAC + 3H)^2+•. The AAT, ATA, and TAA complexes formed doubly charged ions that were used to generate the respective (AAT + 2H)^+•, (ATA + 2H)^+•, and (TAA + 2H)^+• cation radicals. UV-vis photodissociation in the 210-700 nm region was employed to acquire action spectra that characterized valence-electron excitations in the ions. Ion structures were assigned by matching the action spectra with vibronic absorption spectra that were calculated by time-dependent density functional theory for multiple isomers. (AAA + 2H)^+• was found to assume a zwitterionic structure with protonated 5'- and 3'-adenine rings, a negative phosphate, and the radical residing at the middle adenine. In contrast, upon formation the (AAA + 3H)^2+• dication radical underwent exothermic hydrogen migration to C8 at the 5'-adenine. The different course of hydrogen atom migration was related to the different recombination energies of the dications and trications, and explained by Rice-Ramsperger-Kassel-Marcus theory calculations of rate constants that showed a substantial rate decrease by collisional cooling of the (AAA + 2H)^+• isomerization. (AAT + 2H)^+• ions that were produced by electron transfer underwent hydrogen atom migrations, forming dihydrothymine radicals and adenine cation radicals, as indicated by the action spectra. Single electron reduction of (AAC + 2H)²⁺ and (AAC + 3H)³⁺ resulted in hydrogen atom migrations between the nucleobases in the cation radicals and dication radicals. Upon formation, the (AAC + 2H)^+• cation radicals were found to undergo hydrogen migrations between the adenine rings, forming C8-dihydroadenine radicals, whereas cytosine radicals were indicated only weakly by the action spectra. Action and vibronic spectra of the (AAC + 3H)^2+• dication radicals indicated that the ions underwent exothermic isomerizations by hydrogen atom migrations, forming N3,C8-dihydroadenine cation radicals within the middle nucleobase. The action spectra of the doubly reduced ions, (AAA + 3H)⁺ and (AAC + 3H)⁺, showed no bands in the near UV and visible regions that would have indicated radical chromophores. This was consistent with hydrogen atom migrations after the first electron transfer that steered the second electron to recombine with cation-radical intermediates, forming closed-shell products.