Thymine quantum mechanical studies

Cytosine was the first nucleobase whose radiationless decay was studied with quantum mechanical methods. Nevertheless, its first excited states are not so clearly separated as in uracil and thymine, and this causes complications in the computational studies of the photophysics. So, many computational studies have been reported to elucidate the mechanisms for radiationless decay to the ground state but, not always with the same conclusions. 

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. 

It should be noted here that thymine photodimerization may occur by a non-concerted mechanism, involving free radical intermediates. Indeed, photoproducts other than cis-syn dimer, such as the next most abundant thymine dimer, so-called 6 4 adduct, were observed in irradiated DNA. However, the quantum yield of cis-syn photodimer formation (r/j 0.02) is more than an order of magnitude higher than that of the 6 4 adduct ( 0.0013) which in turn is an order of magnitude higher than the quantum yields for other thymine isomers [68]. This specificity can lead to the conclusion that the thymine photodimerization occurs predominantly via concerted 2 + 2 cycloaddition mechanism. A time-resolved study of thymine dimer formation demonstrated that thymine cyclobutane dimers are formed on a timescale of less than 200 nsec, while the 6 4 adduct is formed on a timescale of few milliseconds [69]. The delay in the formation of the latter was attributed to the mechanism of its formation through a reactive intermediate. 

Based on the model studies discussed above, an analogous mechanism for the DNA-PL-catalyzed cleavage of pyrimidine dimers would occur via initial photoactivation of one or both of the enzyme cofactors, followed by electron transfer between the activated photosensitizer and enzyme-bound dimer. The studies by Joms indicated that only reduced flavin is required to initiate thymine dimer cleavage in the model reaction 162). This is consistent with the observation that the quantum yield for the blue semiquinone radical form of E. coli DNA-PL in vitro was found to be much lower than the in vivo values. Treatment of the isolated enzyme with dithionite to give fully reduced flavin cofactor then results in a 12- to 15-fold increase in the quantum yield, suggesting that the flavin cofactor is in the reduced oxidation state in vivo 163). 

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