Thymine, tautomerism

Pyridones and other six-membered compounds (functional tautomerism). The pyridone /hydroxypyridine tautomerism (76AHCS1, p. 87), especially 2-pyridone (15a)/2-hydroxypyridine (15b), has received more attention from theoreticians than any other example of tautomerism, probably in part because it is a simple model for biologically important molecules such as thymine, cytosine, and uracil (Scheme 8). 

Uracil, thymine, and cytosine have been studied using this technique (89JA2308 and references therein). For uracil and thymine, the dioxo tautomer predominates in the case of cytosine (70), three tautomers were detected, 70a, 70b, and 70c, the last one being the least abundant. The gas-phase tautomeric equilibrium of 2-pyridone 15a and 2-hydroxypyridine 15b has been studied by MW spectroscopy (93JPC46) using both a conventional spectrometer and a jet-cooled millimeter-wave spectrometer. The relative abundances are 3 1 in favor of the hydroxy form 15b, which exists in the Z conformation shown (Scheme 23). 

Gas-phase studies where relevant tautomeric compounds are described are ihore scarce, but include uracil, thymine, and adenine [97CPL(269)39]. In the case of the 2-pyridone/hydroxypyridine equilibrium, the intensity of the OH and NH stretching vibrations was measured for eight temperatures in the range from 428 to 533 K in the gas phase. This allows determination otAH and AS for the equilibrium (92JPC1562). 

The tautomerisation of the purine bases adenine and guanine and of the pyrimidine bases thymine, cytosine, and uracil has important implications in molecular biology, and the occurrence of rare tautomeric forms of these bases has been suggested as a possible cause of spontaneous mutagenesis (Lowdin, 1965 Pullman and Pullman, 1971 Kwiatowski and Pullman, 1975). Three of the most likely tautomers for cytosine are shown in [87]—[89], together with the less likely imino forms [90] and [91] (Scanlan and Hillier,... 

We should note particularly that uracil and thymine are dioxypyrimidines, whereas cytosine is an amino-oxypyrimidine. All three pyrimidines are thus capable of existing in several tautomeric forms (see Section 11.6.2). 

The bases are monocyclic pyrimidines (see Box 11.5) or bicyclic purines (see Section 11.9.1), and all are aromatic. The two purine bases are adenine (A) and guanine (G), and the three pyrimidines are cytosine (C), thymine (T) and uracil (U). Uracil is found only in RNA, and thymine is found only in DNA. The other three bases are common to both DNA and RNA. The heterocyclic bases are capable of existing in more than one tautomeric form (see Sections 11.6.2 and 11.9.1). The forms shown here are found to predominate in nucleic acids. Thus, the oxygen substituents are in keto form, and the nitrogen substituents exist as amino groups. 

Tautomeric structures of adenine, guanine, cytosine, thymine and uracil are—... 

The Mg+ complexes of cytosine, thymine and uracil are the most complex system studied via photodissociation spectroscopy to date . A complication for these systems is that these nucleobases can exist in various tautomeric forms and that complexation of a metal can change the stability order of the tautomers. DFT calculations located four tautomeric Mg(cytosine)+ complexes, and three of these (29, 30, and 31) were suggested to be responsible for the four reactive photofragment ions 32-35 observed at a wavelength of 360 nm (Scheme 4) . Related photofragmentation reactions were observed for the Mg(thymine)+" and Mg(uracil)+" complexes . ... 

The principal tautomeric properties of the fundamental biological pyrimidines—cytosine, uracil, and thymine—are due to the presence in these N-heteroaromatic compounds of electron-donor substituents such as NH2 and OH and of SH in some important analogs. The labile hydrogen may remain attached at the exocyclic 0, N, or S atom or migrate to one of the ring nitrogens, giving rise to three principal types of tautomerism (Scheme 1) ... 

Like cytosine, uracil (or thymine, its 5-methyl derivative) can exist in six tautomeric forms 27-32. A large amount of experimental evidence shows that uracil and thymine have the diketo (dilactam)... 

Wierzchowski et al.325 recorded in aqueous medium the IR specta of the monoanions of thymine and of 1-methyl- and 3-methylthymine. The data demonstrated that the monoanions of thymine consist of an equilibrium mixture of two tautomeric forms 34 and 35 corresponding to the dissociation of the N-l or the N-3 protons, respectively. The fractional content of the thymine monoanion 35 in the mixture of the two monoanions was evaluated from the extinction of the characteristic bands of the anion of thymine and 1-methylthymine to be 0.4. A marked shift in equilibrium of the tautomers was observed on going from a NaCO in D20 solution of thymine to NaOD in 75% dioxan-D20. Calculation of the tautomeric equilibrium showed that in 75% dioxan the fraction of 35 was 0.25, compared to 0.4 in aqueous medium. 

As in the case of cytosine, several NMR and NQR studies were performed in search of the predominating tautomeric structures of uracil and thymine and their nucleotides and nucleosides. Investigation of PMR spectra of these compounds in nonaqueous solvents, such as dimethyl sulfoxide, localized the mobile protons in a number of 5- and 6-substituted uracils.59,61,328 These and similar studies63,85,329,330 indicated that dilactam structure 32 predominates in uracil compounds in aqueous and nonaqueous solutions as well as in the solid state. Proton and N-15 magnetic resonance spectra of several pyrimidines85 confirmed the diketo structure usually ascribed to uracil. 

Overall NMR and NQR spectroscopy data thus indicate that the diketo structure predominates for uracil, thymine, and their nucleosides or nucleotides. These studies have failed to detect other tautomeric forms of these compounds. 

Starting from the comparative study of the ionization constants of uracil itself as well as of its several methylated or ethylated derivatives (representing models of tautomeric forms), it may be seen (Table XVII) that uracil and uridine exist in aqueous solution in the diketo form 32. The pX values are not known for the model tautomers 27, 29, and 30, but these forms have been ruled out on the basis of UV studies. Recently the ionization constants of uracil, thymine, their derivatives and nucleotides were determined over the range 10-50°, and thermodynamic enthalpy, entropy, and free energy changes for protonation and depro-tonation of these compounds have been evaluated.93-95,332... 

As the removal of a proton from thymine results in the establishment of a tautomeric equilibrium between its two monoanionic forms,3425 the emission spectrum of singly ionized thymine may consist of overlapping spectra of both monoanions. In fact, Gill344 has observed some inconsistencies between the absorption and the fluorescence excitation spectra of thymine in 0.01 N NaOH at room temperature. These inconsistencies were of the same kind as those found later by Berens and Wierzchowski,345 who suggested that at room temperature only the thymine monoanion tautomer (34) fluoresced, while at 77°K emissions of both monoanionic species contributed to the observed luminescence spectrum. 

Recent, reports351,352 suggested the existence of uracil and thymine as a mixture of tautomeric forms 28 and 32 in aqueous solutions. 

Daniels352 has shown that the excitation spectra for triplet state formation and fluorescence emission from uracil and thymine in neutral aqueous solution at room temperature were anomalous when compared with the UV absorption spectra of these pyrimidines. These experimental facts have been critically examined with respect to three molecular models, of which the model based on tautomerism of uracil in aqueous solution is, in the opinion of Daniels, the best. The data suggested that the fluorescing tautomer contained an enol group, and the UV data favored the 4-hydroxy structure, i.e., form 28. The second tautomer, from which the triplet originated, was expected to be the predominant diketo form (32). 

Theoretical Quantities0 Characterizing the Tautomeric Stability of Uracils and Thymines Method References Compound Quantity6 (kcal/mole)... 

It should be added that Snyder et al.36i have predicted by means of nonempirical calculations that thymine anion 34 should be more stable than 35 in the gas phase by 21 kcal/mole. It is difficult, however, to compare this figure with tautomeric ratios of the thymine anionic forms in aqueous or in dioxan-water solution. 

Tautomeric equilibrium of guanine and adenine. The keto and amino forms are strongly favored for guanine and adenine, respectively. Comparable tautomeric equilibria exist for thymine, uracil, and cytosine. 

Fidelity in Codon-Anticodon Interaction. Nature. 1976, 263, 289-293. Opposing view Orozco, M., Hernandez, B., Luque, F. J. Tautomerization of 1-Methyl Derivatives of Uracil, Thymine, and 5-Bromouracil. Is Tautomerization the Basis for the Mutagenicity of 5-Bromouridine J. Phys. Chem. B. 1998,102, 5228-5233.)... 

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