In thymine

Experimentally the lowest peak in uracil corresponding to the bright nn states is observed in the gas phase at 5.1 eV [132], In thymine the first band maximum is at 4.8 eV [132], An extended table of available experimental results taken from absorption spectra and circular dichroism is given by Roos and coworkers [125] for both molecules. 

As discussed earlier, thymine is very similar to uracil in its excited states pattern. This is also true for its radiationless decay mechanism except from the fact that the excited state lifetime in thymine is somewhat longer than in uracil. Theoretically the mechanism for radiationless decay has been studied using CASPT2 electronic structure methods [150, 152],... 

The ab initio molecular dynamics study by Hudock et al. discussed above for uracil included thymine as well [126], Similarly to uracil, it was found that the first ultrafast component of the photoelectron spectra corresponds to relaxation on the S2 minimum. Subsequently a barrier exists on the S2 surface leading to the conical intersection between S2 and Si. The barrier involves out-of-plane motion of the methyl group attached to C5 in thymine or out-of-plane motion of H5 in uracil. Because of the difference of masses between these two molecules, kinematic factors will lead to a slower rate (longer lifetime) in thymine compared to uracil. Experimentally there are three components for the lifetimes of these systems, a subpicosecond, a picosecond and a nanosecond component. The picosecond component, which is suggested to correspond to the nonadiabatic S2/S1 transition, is 2.4 ps in uracil and 6.4 ps in thymine. This difference in the lifetimes could be explained by the barrier described above. 

Perun S, Sobolewski AL, Domcke W (2006) Conical intersections in thymine. J Phys Chem A 110 13238... 

This reaction has also been shown to occur in cytidine, cytidylic acid, uracil, uridine, and uridylic acid (found in RNA) but reportedly not in thymine, thymidine, or thymidylic acid/55 The photohydration has been found to be partially reversible, dehydration being nearly complete at extremes of temperature and pH. 

Most of the early methods for assigning isotopically labeled nucleic acids were developed using RNA samples, since 13C and 15N isotopes can be incorporated in RNA more easily than in DNA. While most of the magnetization transfer pathways in RNA and DNA are the same, the latter contains thymine rather than uracil. To remove the ambiguity of intra- and inter-residue H6-CH3 peak assignment in thymine, the HCCCH through-bond method was proposed [51] as a more sensitive alternative to NOE or ROE. 

Measurement of multiple acidic sites in thymine. Because we have already embarked on the study of uracil (see Preliminary Results), we will begin with thymine (4a, Figure 1), which is the 5-methyl-derivative of uracil. (From Lee, 2001)... 

The thymine anion is only a weak base = 6.9) [22]. This means that protonation of the anion may depend on the specific environment. The primary reduction product observed in the solid state in thymine derivatives is the C4-OH protonated anion [17]. This species exhibits significant spin density at C6 and 04. Here one must distinguish between two different situations. In single crystals of thymidine, the C4-OHp proton is out of the molecular plane which gives rise to an additional 33.1-MHz isotropic hyperfine coupling [31]. A similar situation is observed in single crystals of anhydrous thymine [32]. In 1-meThy, however, the C4—OHp proton is in the molecular plane. Consequently, the proton coupling is very small. 

The previous section outlined the typical e loss and e gain products observed in the nucleic acid bases in the solid state. These studies can be applied to the study of the radiation chemistry of DNA. The relevance of the study of model systems is shown by considering the following remarkable observations. Years ago, Ehrenberg et al. showed the EPR spectra of the 5,6-dihydrothymine-5-yl radical observed in thymine, thymidine, and DNA. The spectra are nearly identical [46]. The reduction product observed in cytosine monohydrate is the N3 protonated anion. In solution, this reduction product gives rise to a 1.4-mT EPR doublet. The same feature is present in irradiated DNA at 77 K. Likewise, the result of e loss in guanine bases is characterized by a broad EPR singlet. The same feature is also evident in the EPR spectrum of DNA irradiated and observed at 77 K. 

An electron trapping reaction analogous to that in thymine might be expected for cytosine Cyt + Cyt(C6 + H) (see Fig. le for structures). But this reaction is not... 

Fig. 11. Net w-charges in thymine calculated by different methods (from top to bottom w-HMO,140 wSCF MO,388 CNDO/2,214 and nonempirical219,220,384). For the nonempirical charge distributions in anionic forms of thymine, see ref.364. The symbols NH, CH, or CH3 indicate that the charge for the whole group of atoms is given.

Fig. 17. Hydration sites in thymine.252 Energies in kilocalories per mole. Heavy lines, preferred hydration sites full lines, coplanar arrangement of water and base half-dashed lines, perpendicular arrangement of water with respect to the plane of the base.

Miles et a/.418 to be of the n — it type and correlated with the B2u, Blu, and Elu bands of benzene. The absorption at 180 nm in uracil, according to Miles et aZ.,418,421 covers a fifth it -> n transition. A recent study405 of the influence of an electric field on the light absorption of uracil and thymine in solution confirms that in the region < 255 nm the long-wavelength band of uracil overlaps a second transition which is hidden in the absorption spectrum. Similarly, in thymine the second transition appears below 275 nm. In both cases, however, no conclusion as to the nature of the weak bands was given. 

Henriksen T, Snipes W (1970) Radiation-induced radicals in thymine ESR studies of single crystals. Radiat Res 42 255-269... 

It was first reported in 1941 that DNA can be damaged by exposure to UV light, which was initially attributed to depolymerization [18,19], Only in the 1960s was it recognized that dimerization of adjacent thymine bases in the DNA strands via photocycloaddition is a major factor in biological inactivation of exposed DNA [17]. As a result of this photoreaction the double carbon-carbon bonds in thymine moieties cyclizes with an adjacent thymine forming so-called cyclobutane thymine dimer as shown in Figure 13.2. The thymine photodimer was first isolated and analyzed in 1960 by Beukers and Berends [20] who experimented with frozen aqueous solutions of thymine. 

What is the difference between singlet and triplet states of the excited thymine molecule Why do triplet precursors play a more important role in thymine dimerization in solutions than in films ... 

The pyrimidine nucleobases have the highest quantum yields for photoreactivity, with thymine uracil > cytosine. The purine nucleobases have much lower quantum yields for photochemistry, but can be quite reactive in the presence of oxygen. As can be seen from Figure 9-3, thymine forms primarily cyclobutyl photodimers (ToT) via a [2ir + 2tt cycloaddition, with the cis-syn photodimer most prevalent in DNA. This is the lesion which is found most often in DNA and has been directly-linked to the suntan response in humans [65]. A [2Tr + 2Tr] cycloaddition reaction between the double bond in thymine and the carbonyl or the imino of an adjacent pyrimidine nucleobase can eventually yield the pyrimidine pyrimidinone [6 1]-photoproduct via spontaneous rearrangement of the initially formed oxetane or azetidine. This photoproduct has a much lower quantum yield than the photodimer in both dinucleoside monophosphates and in DNA. Finally, thymine can also form the photohydrate via photocatalytic addition of water across the C5 = C6 bond. 

The similarities between the main excited-state decay paths for cytosine and the remaining pyrimidine nucleobases, uracil and thymine, have been noticed by several authors. In all cases the energetically favored decay takes place at an ethylenic-type intersection, associated to torsion around a C=C double bond, which can be accessed along a low barrier in cytosine, and along barrierless paths in thymine and uracil [35]. The main difference between cytosine and the other two pyrimidinic bases is the presence of an additional low-lying decay path which involves the lone pair on N3 and torsion around the N3-C4 bond, both of which features are absent in uracil and thymine. 

The centrosymmetrical UU12 configuration (Fig. 16.2) occurs frequently as in thymine [THYMIN] thymine monohydrate [THYMMH] Dihydrouracil [DHU-RAC10] dihydrothymidine [DHTHYD10] 6-methyluracil-5-acetic acid [MUR-CAC] 5,6-dihydro-2-thiouracil [DHTURC] 6-methyl-5,6-dihydrouracil [MDH-URC10] 2,4-dithiouracil [DTURAC]. 

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