The attachment of amino fragment to purine: inner-shell structures and spectra

The impact of the amino fragment (-NH₂) attachment on the inner-shell structures and spectra of unsubstituted purine and the purine ring of adenine are studied. Density functional theory calculations, using the LB94/TZ2P//B3LYP/TZVP model, reveal significant site-dependent electronic structural changes in the inner shell of the species. A condensed Fukui function indicates that all of the N and C sites, except for N₍₁₎ and C₍₅₎, demonstrate significant electrophilic reactivity (f^- > 0.5 in |e|) in the unsubstituted purine. Once the amino fragment binds to the C₍₆₎ position of purine to form adenine, the electrophilic reactivity of these N and C sites is greatly reduced. As expected, the C₍₆₎ position experiences substantial changes in energy and charge transfer, owing to the formation of the C-NH₂ bond in adenine. The present study reveals that the N1s spectra of adenine inherit the N1s spectra of the unsubstituted purine, whereas the C1s spectra experience significant changes although purine and adenine have geometrically similar carbon frames. The findings also indicate that the attachment of the NH₂ fragment to purine exhibits deeply rooted influences to the inner-shell structures of DNA/RNA bases. The present study suggests that some fragment-based methods may not be applicable to spectral analyses in the inner shell.