Abstract:

We obtained resonance Raman spectra and UV absorption spectra of 5-chlorouracil and uracil in methanol and in water. B3LYP/6-311+G(d,p), B3LYP-TD/6-311+G(d,p), and CIS/6-311+G(d,p) computations were carried out to predict their ground state geometries, ground state vibrational frequencies, electronic transition energies, and 1S2 excited state geometries for 5-chlorouracil and uracil. The resonance Raman spectra of 5-chlorouracil and uracil were assigned based on our FT-Raman and FT-IR measurements and density functional theory calculations. Their absorption cross-sections and absolute resonance Raman cross-sections were quantitatively simulated using the time-dependent wave packet formalism. Excited state structural dynamics associated with the lowest singlet 1(π, π*) state was obtained. Results indicate that the major feature of the initial excited state structural dynamics of 5-chlorouracil is along the C5=C6 stretch + C6H12 bending and N3H9/N1H7 bending + N1C6 stretch reaction coordinates, while that of uracil is mostly along the ring stretch + C5H11/C6H12/N1H7 bending and C4=O10 stretch reaction coordinates. We conclude that substitution of 5-Hby a Cl atom results in a p-πconjugation interaction between the pz orbital of the Cl atom and the π or π* orbital of the pyrimidine ring. This makes the vibrational reorganizational energies more partitioned into the ring bending vibrational modes and the C5=C6 vibrational mode for 5-chlorouracil. The major feature of the initial excited state structural dynamics of uracil in methanol is similar to that in water and the wave-packet motions along the C5H11/C6H12/N1H7 bending + N1C6 stretch (υ12) and the ring breathing (υ17) reaction coordinates of uracil are obviously enhanced in methanol relative to those in water.

Key words: Resonance Raman spectrum, Uracil, Dynamic structure, 5-Chlorouracil