Thymine vibrational structure

As mentioned previously (Section III) IR and Raman spectroscopic studies have been carried out to elucidate the structure of the main tautomers of uracil and thymine. Although the vibrational spectra of the pyrimidine bases (e.g., refs 41, 50, 51, 55, 326, 354, 370) are difficult to interpret, a better understanding of the vibrational motions of these molecules has been possible over the past years.193,370-372 There have also been some quantum-mechanical attempts to interpret the vibrational spectra. 

The plots of the intensities of selected characteristic bands as a function of lateral position (so-called chemical maps) provide information on the amount of the respective molecules or molecular groups in the different morphological structures (Fig. 4.2). The band at 784 cm 1 can be assigned to out-of-plane deformation vibrational modes of the nucleobases cytosine, thymine and uracil and serves as an indicator for the presence of nucleic acids. At 483 cm-1, a C-C-C deformation of carbohydrate polymers such as starch or pectin is present in some of the spectra. To study the distribution of protein compounds, we analysed characteristic signals of the amino acid phenylalanine (1002 cm 1 ring breathe) as well as of the protein amide I band (1651 cm-1) that is brought about by vibrations of the protein backbones. The maximum of the phenylalanine signal co-localizes with a maximum in protein content... 

With this normal mode description, then, it is instructive to review the resonance Raman intensity-derived excited-state structural dynamics. The first UV resonance Raman study of thymine was not done until 1994 by Lagant, et al. [113], Although Raman and IR spectra of thymine had been recorded much earlier. Most earlier studies of nucleic acid components focussed on the nucleosides and nucleotides. Indeed, much of the earlier research on nucleic acid components was done by the groups of Peticolas and Spiro, working independently. Spiro focussed more on nucleosides and larger nucleic acid structures (see below), while Peticolas examined the nucleobases initially. Peticolas s approach was to combine ab initio computations of the ground-state and excited-state structures and vibrational frequencies, with... 

The UV resonance Raman spectrum of thymine was revisited in 2007, with a slightly different approach, by Yarasi, et al. [119]. Here, the absolute UV resonance Raman cross-sections of thymine were measured and the time-dependent theory was used to experimentally determine the excited-state structural dynamics of thymine. The results indicated that the initial excited-state structural dynamics of thymine occurred along vibrational modes that are coincident with those expected from the observed photochemistry. The similarity in a DFT calculation of the photodimer transition state structure [29] with that predicted from the UV resonance Raman cross-sections demonstrates that combining experimental and computational techniques can be a powerful approach in elucidating the total excited-state dynamics, electronic and vibrational, of complex systems. 

Hrouda, V., Florian, J., and Hobza, R, Structure, energetics and harmonic vibrational spectra of the adenine-thymine and adenine -thymine base pairs Gradient nonempirical and semi-empirical study, J. Phys. Chem. 97, 1542-1557 (1993). 

Microwave measurements of uracil in a heated cell suggested the diketo form as the most abundant [54]. Brown et al. reported the first microwave measurements in a seeded molecular beam and also concluded that the diketo form was predominant [55]. Viant et al. reported the first rotationaUy resolved gas phase IR spectra of uracil [28]. This work employed a slit nozzle, an IR diode laser, and a multipass arrangement to obtain high resolution IR absorption spectra of the out-of-phase V(, C2—0, 4=0) stretching vibration. The rotational analysis unambiguously assigned the species to the diketo tautomer. Brown et al. also observed the diketo form of thymine in a seeded molecular beam, based on the hyperfine structure in the 14440-133,11 transition [56]. 

Raman bands of nucleic acids originate from inplane vibrations of the nucleic acid bases (adenine, guanine, cytosine, thymine and uracil) and from the furanose-phosphate backbone. In general, Raman spectra of DNA or RNA reveal structural... 

Nucleobases, such as cytosine, thymine, and uracil are the most important pyrimidine derivatives. In a recent gas-phase study [64], three low-energy tautomers were identified on the basis of CCSD(T)/cc-pVQZ energy calculations andMP2/6-311++G(2d,2p) estimation ofthe vibrational frequencies. The authors emphasize the importance of the high-level estimation of the frequencies and the related thermal correction in order to obtain rehable AG within a 0.7 kcal mol free energy range of the tautomers at T = 450 K. The lowest-free-energy structure is the canonical hydroxy-amine form of cytosine. 

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