Structural effects on the stability of some hydrogen-bonded complexes with nucleobases

Abstract

The effect that additional groups flanking the hydrogen bond donor/acceptor arrays have on the association constants (K(a)) of complexes of chloroform-soluble thymine and adenine derivatives has been investigated by NMR shift titration. Constants for thymine and 2,6-diaminoacyl pyridine derivatives, in which the acyl group bears either (CH2)(n)R or some other substituent, vary greatly. The peak value of K(a) = 1130 M-1 occurs for n = 2 and R = phenyl. Computer modeling with CHARMm suggests that this is due to a weak additional stabilization by a C-H-π interaction; in line with this the complex shows small upfield NMR shifts for the terminal methyl groups. Four other receptors were prepared which could, in principle, form hydrogen bonds with all donor/acceptor sites of adenine; NMR titrations, however, showed very low complexation energies, probably due to deviations from the ideal hydrogen bond geometry necessary to form stronger complexes.