9-Substituted adenines, tautomerism

The crystal structures of 9-substituted adenines confirm the 6-amino structure. Specific stacking patterns are found in crystals of purine derivatives which are also observed for nucleosides, mono- and oligonucleotides. For X-ray results on tautomerism see Table 2 (p 309). Other sources of X-ray data are given in Table 6. 

The amino groups are replaced with oxygen. Although here a biochemical reaction, the same can be achieved under acid-catalysed hydrolytic conditions, and resembles the nucleophilic substitution on pyrimidines (see Section 11.6.1). The first-formed hydroxy derivative would then tautomerize to the carbonyl structure. In the case of guanine, the product is xanthine, whereas adenine leads to hypoxanthine. The latter compound is also converted into xanthine by an oxidizing enzyme, xanthine oxidase. This enzyme also oxidizes xanthine at C-8, giving uric acid. 

A number of physicochemical properties which have been investigated for a series of simple derivatives of the different tautomeric forms of adenine, prominent among which are dipole moments and ultraviolet absorption spectra, throw additional light on the problem. Table VIII indicates the results of a theoretical evaluation of the dipole moments for the different tautomeric forms (12-19) of adenine as well as the experimental values of the moments in methyl and benzyl derivatives of these forms with the exception of the derivatives of the N(1)H form for which, unfortunately, no experimental data could be obtained because of lack of sufficiently soluble 1-substituted derivatives. 

There are some additional possibilities for proton tautomerism with adenine, guanine, and cytosine (Fig. 15.5), where one of the protons can move from one ring nitrogen atom to another one. This type of tautomerism is restricted to the free bases and cannot occur in the nucleosides where pyrimidine N(l) and purine N(9) are substituted by the furanose moiety. 

Information on tautomerism, and sites of protonation of purines has been derived from NMR spectral studies. Thus protonation of adenine is first suggested to occur at N-1 with no evidence for protonation of the amino group (65JOC1110) although protonation of the substituted amino group does occur in 6-dimethylamino-3-methylpurine (68CC1002). 

Table 4 presents the proton affinities PA and deprotonation enthalpies DPE of thiouracils calculated at the B3LYP/6-31+G(d,p) computational level. Inspecting this Table, we find that first, the thio substitution of uracil systematically increases its PAs by 3-6 kcal/mol and second, it decreases the DPEs of uracil by 6-13 kcal/mol. As far as the base pair A thioU is considered, it particularly implies a lowering, on the one hand, of the potential well at the Sio atom of thiouracil corresponding to the proton transfer from the N8 atom of adenine to the Sio of thiouracil and, on the other one, a raising of the potential well at the N3 atom of thiouracil involved in the proton transfer from the N3-H bond to the Ni atom of adenine. Therefore, summarizing, the thio substitution of uracil is in a favor to the double proton transfer mechanism of the occurrence of the spontaneous point mutations proposed by Lowdin [19]. Table 4 also includes the PAs of the T2 tautomer of uracil and thiouracils. A comparison with the corresponding PAs of the parental normal nucleobases shows that their tautomerization to the T2 form is accompanied by an increase of the proton affinity by 20-23 kcal/mol. 

The mechanisms by which the nucleobases return to the groimd state are subtly connected to the molecular structure of these bases. For instance, simple tautomerization of adenine into 2-aminopurine results in an increase of excited-state lifetime from 1.1 to 30 ps (Canuel et al. 2005). Methyl-substitution of cytosine or cytidine at Cs position increases the lifetime in water solution by a factor of seven (Malone et al. 2003). Fluoro-substitution at the same site or acetyl-substitution at N4 have even larger effects, increasing the lifetime from Ips to, respectively, 88 and 280 ps (Malone et al. 2003). Double methyl substitution in positions Ni and N3 of thymine increases its lifetime in gas phase from 5 ps (Canuel et al. 2005) to about 150 ps (He et al. 2003). Similar effects were also reported for single and double methyl substitutions in macil (He et al. 2003). 

The N-substitution of a heterocyclic N-donor of purines represents a significant restriction on the tautomeric possibilities associated with the H atom usually linked to N9(purines). Thus, alkylation at N9 on adenine or guanine increases the metal... 

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