Geometric and energetic consequences of prototropy for adenine and its structural models – a review

Abstract

Heterocycles containing one or more amidine moieties {-NH-C(R) ]N-} such as adenine and its building blocks, imidazole, 4-aminopyrimidine, and purine, are excellent examples of tautomeric systems for which changes of position(s) of labile proton(s) cause parallel changes of geometric and energetic parameters for prototropic tautomers. One-electron oxidation has a slight effect on this relationship. The amino-imine conversions within the amidine group(s) are favored. Well delocalized (aromatic) tautomers, containing labile proton(s) at heteroatom(s), are major, minor, or rare forms. Non-aromatic tautomers with a labile proton at the C atom can be considered as very rare isomers. Dramatic changes take place for reduced heterocycles. Electron delocalization is not the main factor that dictates tautomeric preferences. The HOMED/DE relationship seems to be more complex. The enamino-imine conversions predominate and some very rare forms have the lowest energies. This clearly shows the importance of very rare tautomers, often neglected in proton-transfer, electron-transfer, and ion-radical reactions.

DFT studies on the favored and rare tautomers of neutral and redox cytosine

“…This relation has been recently discussed for some simple tautomeric systems [21]. Good linear relationships have been found for the neutral aromatic NH and nonaromatic CH tautomers of imidazole and purine, which have no substituent, and which possess solely the endo functional groups [52,53,[80][81][82][83]. Prototropy is also well related to electron delocalization for the neutral NH and CH tautomers of aminoazines and for the NH-NH and NH-CH tautomers of adenine [52,53,81].…”

Proposal for a chemically consistent way to annotate ions arising from the analysis of reference compounds under ESI conditions: A prerequisite to proper mass spectral database constitution in metabolomics

“…After the desolvation process, proton transfer can occur from an atom of M to another one; this phenomenon is called prototropy . Several distinct protonated canonical forms may be competitively generated for a given compound as long as heteroatoms having electron lone‐pairs, or π‐bonds from unsaturation(s) are present and available in a multifunctional molecular entity (Figure ).…”

“…After the desolvation process, proton transfer can occur from an atom of M to another one; this phenomenon is called prototropy. 26 Several distinct protonated canonical forms may be competitively generated for a given compound as long as heteroatoms having elec- Figure 6). Indeed, the protonation or deprotonation of a zwitterion that can reach a conformation displaying a salt-bridge interaction may lead to the formation of ions whose structure displays three formal charges (see L-lysine, Table 1).…”

How different is pyrimidine as a core component of DNA base from its diazine isomers: A DFT study?

“…In the isomers, each carbon atom only bonds one hydrogen atom, so that the chemical shift of the C-NMR and H-NMR exhibit similar patterns. However, for the C-NMR spectra, the carbons directly bond with nitrogens, that is, C (2) (159.08 ppm) and C (4) (156.92 ppm) of PyM has the largest chemical shift among all the C-NMR of the isomers, followed by the pair of carbons directly connecting to the nitrogens in PyD, C (3) and C (6) at 152.25 ppm, the four equivalent carbons, C (2) , C (3) , C (5) , and C (6) in PyA at 144.93 ppm, then the other pair of carbons, C (4) and C (5) in PyD at 126.66 ppm, and finally C (5) in PyM at 117.93 ppm which does not directly bond with any nitrogens. The C-NMR to its other diazine isomers and hence the chemical environment of the nitrogens in PyM is less strong.…”