Uracil, tautomerism

Uracil reacts with hydrazine to give pyrazol-3(2if)-one (944) and urea N-methyl- and dimethyl-hydrazine behave similarly to give the 2-methyl- and 1,2-dimethyl derivatives. The reactions of hydrazines with uridine and related nucleosides and nucleotides is well studied (67JCS(C)1528). The tautomerism and predominant form of uracil are discussed in Section 2.13.1.8.4. 

The aromaticity of the pyrimidine and purine ring systems and the electron-rich nature of their —OH and —NHg substituents endow them with the capacity to undergo keto-enol tautomeric shifts. That is, pyrimidines and purines exist as tautomeric pairs, as shown in Figure 11.6 for uracil. The keto tautomer is called a lactam, whereas the enol form is a lactim. The lactam form vastly predominates at neutral pH. In other words, pA) values for ring nitrogen atoms 1 and 3 in uracil are greater than 8 (the pAl, value for N-3 is 9.5) (Table 11.1). 

Azauracil and its alkyl derivatives are readily reducible by polarography, in contrast with uracil. This makes it possible to exploit the method analytically. More detailed studies of the polaro-graphic behavior of these substances are in good agreement with the results of spectral studies about the tautomeric form and type of dissociation. ... 

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). 

Estrin, D. A., L. Paglieri, and G. Corongiu. 1994. A Density Functional Study of Tautomerism of Uracil and Cytosine. J. Phys. Chem. 98, 5653. 

Ring-chain tautomerism of the uracils 297 and cytosines 299 (R = H, Me) to the respective pyrimido[6,l-3][l,3]oxa-zines 298 and 300 takes place in CD3OD/DMSO-1S6 in the presence of Et3N or NaOD. Cfe-addition is predominant. 

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,... 

Tautomerism is responsible for genetic mistakes and for the whole concept of genetic evolution. As an example, cytosine in its imino form pairs with adenine and thus acts as a mimic of uracil. Cytosine normally pairs with adenine, but tautomerism leads to a mutation (Scheme 17).1... 

Potentially tautomeric pyrimidines and purines are /V-alkylated under two-phase conditions, using tetra-n-butylammonium bromide or Aliquat as the catalyst [75-77], Alkylation of, for example, uracil, thiamine, and cytosine yield the 1-mono-and 1,3-dialkylated derivatives [77-81]. Theobromine and other xanthines are alkylated at N1 and/or at N3, but adenine is preferentially alkylated at N9 (70-80%), with smaller amounts of the N3-alkylated derivative (20-25%), under the basic two-phase conditions [76]. These observations should be compared with the preferential alkylation at N3 under neutral conditions. The procedure is of importance in the derivatization of nucleic acids and it has been developed for the /V-alkylation of nucleosides and nucleotides using haloalkanes or trialkyl phosphates in the presence of tetra-n-butylammonium fluoride [80], Under analogous conditions, pyrimidine nucleosides are O-acylated [79]. The catalysed alkylation reactions have been extended to the glycosidation of pyrrolo[2,3-r/]pyrimidines, pyrrolo[3,2-c]pyridines, and pyrazolo[3,4-r/]pyrimidines (e.g. Scheme 5.20) [e.g. 82-88] as a route to potentially biologically active azapurine analogues. 

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. 

Reactions of uracil and structurally analogous compounds have been thoroughly studied 49, 50). Uracil (2,4-dihydroxypyrimidine), a component of the nucleic acids, can be classified as a heteroaromatic compound only with reserve, sinee the keto form dominates in the tautomeric equilibrium. 

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

N-Alkylation is promoted by prior conversion of the pyrimidinones into their respective silyl ethers. Besides selectivity in the alkylation reactions, silylation confers solubility on molecules which otherwise may be difficult to dissolve in nonhydroxylic organic solvents. Selective N-3-alkylation of uracils requires initial protection of N-1. The alkylation of tautomeric thiones invariably proceeds to give an A-alkyl derivative any N-, 0-, or C-alkylation is less rapid and can be avoided. 

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 . ... 

FIGURE 8-9 Tautomeric forms of uracil. The lactam form predominates at pH 7.0 the other forms become more prominent as pH decreases. The other free pyrimidines and the free purines also have tautomeric forms, but they are more rarely encountered. 

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)... 

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... 

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