Initial Excited-State Structural Dynamics of 6-Substituted Uracil Derivatives: Femtosecond Angle and Bond Lengthening Dynamics in Pyrimidine Nucleobase Photochemistry

Abstract

Substituents on the pyrimidine ring of nucleobases appear to play a major role in determining their initial excited-state structural dynamics and resulting photochemistry. To better understand the determinants of nucleobase initial excited-state structural dynamics, we have measured the absorption and resonance Raman excitation profiles of 6-deuterouracil (6-d-U) and 6-methyluracil (6-MeU). Simulation of the resonance Raman excitation profiles and absorption spectrum with a self-consistent, time-dependent formalism shows the effect of the deuterium and methyl group on the photochemically active internal coordinates, i.e. C5C6 stretch and C5X and C6X bends. The methyl group on either the C5 or C6 position of uracil equally increases the excited-state reorganization energies along the C5C6 stretch. However, a lower reorganization energy of the C5X + C6X bends in 6-MeU than uracil and 5-MeU shows that C6 methyl substituents reduce the bending reorganization energy. In addition, deuterium substitution at either C5 or C6 has a much smaller effect on the initial excited-state structural dynamics than methyl substitution, consistent with a mass effect. These results will be discussed in light of the resulting photochemistry of pyrimidine nucleobases.

Resonance Raman Intensities Demonstrate that C5 Substituents Affect the Initial Excited‐State Structural Dynamics of Uracil More than C6 Substituents

“…The addition of lithium sulfate did not noticeably change the absorption or resonance Raman spectra of 5,6‐ d 2 ‐U. The UV resonance Raman spectra of solutions containing 1 m m 5,6‐ d 2 ‐U and 0.3 m lithium sulfate internal standard were obtained at excitation wavelengths of 250, 257, 266, and 275 nm with laser powers of 5–12 mW, as previously described . Spectral slit widths were 5–7 cm −1 , and the total accumulation time was 20–30 min for each spectrum.…”

“…Previous elucidation of the initial excited‐state structural dynamics of C5‐and C6‐methylated uracil derivatives have shown that methyl substitution increases the initial excited‐state structural dynamics along the C5−C6 bond‐lengthening coordinate . Similarly, methyl substitution at C6 shows lower initial excited‐state distortional forces along the C5−X and C6−X in‐plane bends than substitution at C5 . We herein examine the initial excited‐state structural dynamics of 5,6‐dideuterouracil (5,6‐ d 2 ‐U) (Scheme ) by using resonance Raman and absorption spectroscopy to further test this model of C5/C6 substituent‐dependent initial excited‐state structural dynamics.…”

“…The initial excited‐state structural dynamics of nucleobases with short‐lived excited‐states can be obtained by using resonance Raman intensities, absorption spectra, and a self‐consistent time‐dependent wavepacket formalism. Such an analysis has been performed on numerous uracil derivatives in an attempt to elucidate photochemical mechanisms in DNA components. Previous elucidation of the initial excited‐state structural dynamics of C5‐and C6‐methylated uracil derivatives have shown that methyl substitution increases the initial excited‐state structural dynamics along the C5−C6 bond‐lengthening coordinate .…”

“…Such an analysis has been performed on numerous uracil derivatives in an attempt to elucidate photochemical mechanisms in DNA components. Previous elucidation of the initial excited‐state structural dynamics of C5‐and C6‐methylated uracil derivatives have shown that methyl substitution increases the initial excited‐state structural dynamics along the C5−C6 bond‐lengthening coordinate . Similarly, methyl substitution at C6 shows lower initial excited‐state distortional forces along the C5−X and C6−X in‐plane bends than substitution at C5 .…”

Initial excited‐state structural dynamics of uridine from resonance Raman spectroscopy

“…For example, the intensities of the resonance Raman peaks are proportional to the slopes of the excited‐state potential energy surface along each vibrational coordinate. The power of resonance Raman spectroscopy to probe the initial excited‐state structural dynamics of the molecules has been exploited by Loppnow et al in studying thymine, uracil, and their derivatives . The initial excited‐state structural dynamics of uracil in the photochemically relevant excited state is mostly directed along C5H and C6H bending modes, whereas it is oriented along the CC stretching mode in thymine …”