Decay Pathways of Thymine and Methyl-Substituted Uracil and Thymine in the Gas Phase

Abstract

We report observations of a dark state in the decay pathways of thymine, 1,3-dimethyl thymine, 1,3-dimethyl uracil, and 1-methyl uracil in the gas phase. After initial excitation by a nanosecond laser, the excited molecules failed to return to the ground state but rather were trapped in a dark state for tens to hundreds of nanoseconds. This result contradicts those reported in water solutions. We therefore propose that the photochemistry of these pyrimidine bases is different in the gas phase from that in the liquid phase and that the dark state is effectively quenched in water solutions. Although we do not have a quantitative measure of the yield of this dark state, the fact that further ionization from this dark state has a high yield in the deep UV makes this pathway important in the chemistry of nucleic acid bases. This result further implies that the photostability of our genetic code may not be an inherent property of the bases themselves.

Internal conversion to the electronic ground state occurs via two distinct pathways for pyrimidine bases in aqueous solution

“…Reported lifetimes from photoelectron measurements for the 1 n * state are on the order of several hundred femtoseconds to several picoseconds for all of the pyrimidines (29,42,43). In contrast to these reports, Kong and coworkers (45,46) detected a state with a many-nanosecond lifetime upon electronic excitation of isolated Thy and Ura. They assigned this state to a 1 n * state, which they suggested would be undetectable in solution (46).…”

Multi-photon ionization and fragmentation of uracil: Neutral excited-state ring opening and hydration effects

“…3,4,17 He et al 10,18 observed access to long-lived (23-209 ns) dark states of thymine, methylated thymine, and methylated uracil, as well as a general tendency for longer lifetimes at lower excitation wavelengths (approx. range 290-220 nm) and higher degree of methyl substitution (up to two sites).…”

Characterizing the dark state in thymine and uracil by double resonant spectroscopy and quantum computation

“…This entire deactivation mechanism still proceeds on a pico-second timescale. However, an additional sub-nanosecond to nanosecond relaxation pathway to a nonfluorescent ("dark") state has been reported in many experimental studies 1,27,28 . This state was also observed for methylated derivatives of uracil and thymine 29,30 .…”

“…This state was also observed for methylated derivatives of uracil and thymine 29,30 . Several candidates for the dark state have been suggested, including the vibrationally "hot" ground state, the S 1 state of 1 (nπ*) character, and the T 1 state of 3 (ππ*) or 3 (nπ*) character [27][28][29][30][31][32][33] . The involvement of different tautomeric forms of thymine was ruled out by Schultz and co-workers on the basis of theoretical calculations 28 .…”