Nucleic acid bases aromatic character

As a particular case of the substitution in nucleic acid bases, the insertion/ addition of a benzene ring to the natural bases can be considered (Scheme 30 2006JPCA(110)12249). The analysis of the local aromaticity, expressed by HOMA, NICS, FLU, and PDI indices, revealed notable differences in the aromatic character of the natural and size-expanded bases. Insertion/ addition of the benzene ring reduces aromaticity of six-membered rings in natural bases as well as the aromatic character of the benzene ring. An inverse correlation between the HOMO-LUMO gap and the aromaticity of the fused benzene ring was also found. Therefore, it has been su ested that... 

Free energies of solvation in water and chloroform indicate that in general the nucleic acid bases are better solvated in water than in chloroform, but the results are not extremely different. This suggests that the nucleic acid bases have a dual character they bear a large number of polar groups which favor their hydration, but the aromatic cores are probably better solvated in apolar solvents like chloroform. The theoretical results in Tables 6 and 7 agree well... 

The purines and pyrimidines are relatively stable compounds with considerable aromatic character. Nevertheless, they react with many different reagents and, under some relatively mild conditions, can be completely degraded to smaller molecules. The chemistry of these reactions is complex and is made more so by the fact that a reaction at one site on the ring may enhance the reactivity at other sites. The reactions of nucleic acids are largely the same as those of the individual nucleosides or nucleotides, the rates of reaction are often influenced by the position in the polynucleotide chain and by whether the nucleic acid is single or double stranded. The reactions of nucleosides and nucleotides are best understood in terms of the electronic properties of the various positions in the bases.26 33 Most of the chemical reactions are nucleophilic addition or displacement reactions of types that are discussed in Chapters 12 and 13. 

Theoretically, the purine- and pyrimidine-based nucleic acid constituents and the barbiturates have the potential to occur in several tautomeric forms of the keto/ enol and amino/imino type where the aromatic character of the six-membered pyrimidine ring is fully or, as in the barbiturates, partially retained, as illustrated in Fig. 15.4. In these molecular species, which are all feasible on the basis of organic chemical considerations, the hydrogen-bonding donor/acceptor properties of the functional amino, imino, enol and keto groups vary considerably, being donor in one form and acceptor in the other. 

A nucleic acid gives more than 40 well-defined absorption bands in the IR spectrum (300-4000 cm region). For elucidating the nature of the normal vibrations of a nucleic acid, it is helpful to examine the effects of base composition on the vibrational frequencies, as well as the intensity and anisotropy of the IR absorption. Three of the four natural bases of a DNA (adenine, guanine, and cytosine) have an amino group w hich is considered to be nearly coplanar, because the purine or pyrimidine rings have aromatic character and the C—N bonds have some double-bond character. 

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