3- Methylcytosine tautomers

For instance Shugar and Fox106 have shown that the spectrum of cytosine resembles that of 1-methylcytosine (form 2), not that of 2-methoxycytosine (form 1). Similarly, Kenner et al.100 have established that lactam-imine forms 6 were unimportant both for 1-methylcytosine (thus also for cytosine itself) and for its aminoacetyl derivatives. Katritzky and Waring60 have extended these studies and in particular showed that tautomers 3 and zwitterionic structures 10 were unimportant in the tautomeric equilibrium in both aqueous and dimethyl sulfoxide solutions. Although these last comparisons were made with only two partially methylated cytosines still capable of tautomerism, the reported conclusions agree with those reached later by Brown and Lyall96 on much wider evidence. 

It is interesting that the dominant form of 3-methylcytosine in aqueous solution has been established102 as form 3 rather than the imine forms 5 or 6. This conclusion agrees with that drawn from pK analysis (cf. the Kt values in Table III) that the concentration of tautomers 6 is smaller than that of tautomers 3. 

Methyladenine in rare tautomer form 1 -Methylcytosine 3 -Methy lcytidine... 

The complexation of the latter with creatinine analog shifts the equilibrium further in favor of 202d (93T7627). IR spectra and X-ray diffraction studies showed only the normal amino-oxo tautomer of cytosine (88JA8319) and 3-methylcytosine hemihy-drate (78AX(B)1730) in the solid state. 

A -Methylation of cytosine stabilizes the amino-oxo tautomer, which is predicted to be the most stable form of 1-methylcytosine in the gas phase independent of the level of calculations. The stabilization of the amino-oxo tautomer of 1-methylcyto-sine on hydration is even more pronounced than that of the parent cytosine, so the population of the imino tautomer in aqueous solution is insignificant (86JST(148)45, 00JST(532)157, 01JPC(A)6575). For 3-methylcytosine, the imino-keto form 203a was predicted to be predominant in the gas phase (86JST(148)45). 

Abs absoiption transitions of cytosine in water experimental data for keto-N3H and imino tautomers correspond to 3-methylcytosine and 3-methylcytidine, respectively, obtained in aqueous solution at pH 11 [279], °ground state dipole moments of keto-N3H, imino and enol tautomers at the HF/6-311G(d,p) level are 8.15, 5.12 and 3.34 Debye, respectively, scaled (scaling factor 0.72) excitation energies, Rydberg contamination. 

A comparison of the lowest singlet mi transition of cytosine tautomers presented in Tables 19 and 20 suggests that, widi respect to the keto-NlH tautomer, the transition in the keto-N3H tautomer is appreciably red-shifted for both the isolated and hydrated forms. While in the case of the enol and imino tautomers, the isolated forms show a blue-shift with respect to the isolated form of the keto-NlH tautomer for hydrated species, the imino form shows a slight blue-shift, and the enol form does not show any shift (Tables 19 and 20). The observed red-shift in the first mt transition of the keto-N3H tautomer is in accordance with the experimental fact that the absorption spectrum of 3-methylcytosine in aqueous media shows a significant red-shift with a peak near 289 nm (4.29 eV) compared to the corresponding transition of cytosine observed near 266 nm (4.66 eV). The observ transitions of 3-methylcytosine near 4.29 and 5.47 eV can be explained in terms of the computed transitions of hydrated forms of the keto-N3H tautomer near 4.25 and 5.68 eV, respectively (Table 20). The computed transitions of the imino form can be compared with the observed transitions of 3-methylcytidine in a water solution. Table 20 shows that the observed transition near 4.64 and 5.59 eV of 3-methylcj4idine can be explained in terms of the computed transitions of the imino form of cytosine within an error of about 0.3 eV. Therefore, it appears that the absorption spectra of aqueous solutions of cytosine would be mainly dominated by the keto-NlH tautomer and contributions fix>m other tautomers will not be significant. 

Before analysis of the interactions of the nucleic acid bases with the clay minerals in the presence of water and cation one needs to understand the individual interactions of NAs with isolated water and with a cation. Such theoretical study was performed for 1 -methylcytosine (MeC) [139]. The study revealed influence of water and cation in the proton transfer for this compound. This leads to the formation of imino-oxo (MeC ) tautomer. Topology of the proton transfer potential surface and thermodynamics of stepwise hydration of MeCNa+ and MeC Na+ complexes is further discussed. The one dimensional potential energy profile for this process followed by the proton transfer with the formation of hydrated MeC Na+ is presented in Fig. 21.2. One-dimensional potential energy profile for amino-imino proton transfer in monohydrated N1-methylcytosine (this represents the situation when tautomerization is promoted by a single water molecule without the influence of Na+ cation) and for the case of pure intramolecular proton transfer (tautomerization is not assisted by any internal interactions) is also included. The most important features of this profile do not depend on the presence or absence of Na+ cation. All the potential energy curves have local minima corresponding to MeC and MeC. However, the significant difference is observed in the relative position of local minima and transition state, which results in a different thermodynamic and kinetic behavior for all presented cases (see Fig. 21.2). 

Another important thermodynamic characteristic is represented by the free energy difference between amino- and imino- tautomers of methylcytosine. These parameters describe a relative stability of tautomers or in other words the relative concentration of tautomers at the equilibrium state. Moreover, this energy difference is very often discussed in regards to the contribution of this proton transition to the... 

The thermodynamic and kinetic parameters of the stepwise hydration of 1-methylcytosine and its imino-oxo tautomer in the presence of the Na" " cation have been investigated [139]. Hydrationof 1-methylcytosineby one water molecule leads to an increase of the concentration of its imino-oxo tautomer in the equilibrium mixture and decrease of the barrier of the tatutomer formation (to 15.6 kcal/mol). If the sodium cation is present the tautomeric form is much less favored and tautomerization barrier increases to 25.2 kcal/mol. The computationally predicted values of the rate constants suggest that the tautomerization of 1-methylcytosine to its imino-oxo form proceeds mainly due to a presence of the hydrated (MeCW) species. Based on the kinetic analysis of the tautomerization process in hydrated MeC in the presence of sodium ions it was concluded that complexes of hydrated MeC with Na+ are unlikely to contribute to the frequency of DNA point mutations caused by the tautomers. This is due to the fact that the interactions with Na" " lead to a decrease of both the rate and the equilibrium constants of the tautomerization reactions in hydrated 1-methylcytosine. 

Frequency shifts of more than 200 cm due to water complexation were computed for the N—H stretching mode [OOJSTl]. In a combined theoretical/ experimental study, Smets et al. found smaller shifts for different H-bonded complexes of the amino-oxo tautomer of 1-methylcytosine with water [96JPC6434]. 

---