Role of Ribose in the Initial Excited State Structural Dynamics of Thymidine in Water Solution: A Resonance Raman and Density Functional Theory Investigation

Abstract

Resonance Raman spectra were obtained for thymidine and thymine with excitation wavelengths in resonance with the approximately 260 nm band absorption spectrum. The spectra indicate that the Franck-Condon (FC) region photodissociation dynamics of thymidine have multidimensional character with motion predominantly along the nominal C5=C6 stretch + C6-H bend nu17 (delta = 0.75, lambda = 468 cm(-1)), the nominal thymine ring stretch + C6-H bend + N1-C1, stretch nu29 (delta = 0.73, lambda = 363 cm(-1)), the nominal thymine ring stretch + C5-CH3/ N1-C1, stretch nu37 (delta = 0.69, lambda = 292 cm(-1)), and accompanied by the moderate and minor changes in the nu40, nu20 and nu23, nu55, nu60, nu61, nu63 modes. A preliminary resonance Raman intensity analysis was done, and these results for thymidine and thymine were compared to each other. The roles of ribose in the FC structure dynamics of thymidine were explored and the results were used to correlate to its lifetime constants tau1 and tau2 for two nonradiative decay channels. Spi/Sn conical intersection versus a distorted structure of Spi,min in the FC region was briefly discussed.

Photochemical and Photodynamical Properties of Sulfur‐Substituted Nucleic Acid Bases,

“…The covalent addition of a sugar moiety to the thiopyrimidine chromophore at the N1 position accelerates the rate of triplet decay to the ground state (B. Ashwood, M. Pollum, C. E. Crespo-Hern andez, unpublished results) (46,94), as has also been reported for the canonical nucleobases (55,(133)(134)(135)(136)(137)(138). Taras-Go sli nska reported a more than tenfold decrease in the intrinsic triplet lifetime of 2-thiothymine following N1-glycosylation in acetonitrile (94).…”

“…In addition to the excitation wavelength used, glycosylation of the thiopyrimidine chromophore at the N1 position affects the intersystem-crossing rate (47,96, B. Ashwood, M. Pollum, C. E. Crespo-Hern andez, unpublished results), as has been reported for the canonical nucleobases (55,(133)(134)(135)(136)(137)(138). Pollum et al (46) first reported that N1-glycosylation of 2-thiothymine leads to a considerable reduction in the intersystem-crossing lifetime from the singlet to triplet manifold in aqueous solution.…”

“…In addition to the excitation wavelength used, glycosylation of the thiopyrimidine chromophore at the N1 position affects the intersystem‐crossing rate (, B. Ashwood, M. Pollum, C. E. Crespo‐Hernández, unpublished results), as has been reported for the canonical nucleobases . Pollum et al .…”

Photochemistry of Nucleic Acid Bases and Their Thio- and Aza-Analogues in Solution

“…1 The covalent incorporation of the deoxyribose or ribose sugar group at the N1 position of the pyrimidine monomers has a significant effect on the excited-state dynamics of the nucleobase [129,140,155,156,158]. Hare et al [140] first reported that the magnitude of the 1 nπ* state lifetime increases significantly when the hydrogen in the N1 position of the pyrimidine bases is substituted by a sugar.…”

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

“…The results presented above show that uridine has similar resonance Raman peak frequencies to those of uracil, indicating that the presence of the sugar does not change the ground‐state vibrational structure of the nucleobase . Also, the fact that the relative resonance Raman intensities in the spectra of uracil and uridine are the same indicates that the relative proportion of initial excited‐state structural dynamics along each mode are the same in the two.…”