To explore the origin of the differences in UV photochemistry of uracil (RNA) and thymine (DNA) nucleobases, we have measured the UV resonance Raman spectra of uracil in aqueous solution at wavelengths throughout the lowest-energy absorption band and analyzed the resulting resonance Raman excitation profiles and absorption spectra using a time-dependent wave-packet formalism to obtain the initial excited-state structural changes. In contrast to thymine, which differs from uracil only by the presence of a methyl group at C(5), most of the resonance Raman intensity and resulting initial excited-state structural dynamics for uracil occur along in-plane hydrogen-bond angle deformation, ring stretching, and carbonyl vibrational modes. Weaker intensities and less significant structural dynamics are observed along the C=C stretching mode. These results suggest that the initial excited-state structural dynamics of uracil occur along a carbon pyramidalization coordinate. These dynamics are different from those of thymine, which distorts primarily along a C(5)=C(6) bond lengthening coordinate. These differences in initial excited-state structural dynamics can explain the different primary photoproducts observed for these two pyrimidine nucleobases.

5-Deuterouracil (5-d-U) is an analogue of uracil (RNA) and thymine (DNA), which differ only in the mass of their 5-substituent. Previous work has shown that the initial excited-state structural dynamics primarily lie along C5C6 bond lengthening in thymine, while these dynamics primarily lie along C5 and C6 pyramidalization in uracil. To test whether the 5-substituent mass determines these dynamics, the resonance Raman spectra of 5-d-U, with a 5-substituent mass intermediate between uracil and thymine, is measured at wavelengths throughout its 262 nm absorption band. The resulting spectrum of 5-d-U is intermediate between that of thymine and uracil, indicating both bond-lengthening and pyramidalization motions in the excited state. Self-consistent analysis of the resonance Raman excitation profiles and absorption spectra show that the initial excited-state structural dynamics of 5-d-U are indeed intermediate between those of thymine and uracil, supporting the mass-tuning model of initial excited-state structural dynamics in DNA and RNA pyrimidine nucleobases.

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