The dimethylene-bridged molecular clips having naphthalene sidewalls and bearing either lithium phosphate or lithium methanephosphonate groups in the central benzene-spacer-unit bind various nucleosides and nucleotides in buffered aqueous solution at pH = 7.2. The binding constants (Ka) and the complexation-induced ~1H NMR shifts of the guest signals (△δ_(max)) were determined by NMR titration experiments. The host-guest complexes of the phosphate-substituted clip with caffeine and theophylline (Ka = 31400 or 16800 M~(-1)) are more stable than those with cytidine and uridine (Ka = 5240 or 5390 M~(-1)) and with adenosine and guanosine (Ka = 1470 or 1120 M~(-1)). In the case of the phosphonate-substituted clip 2 the selectivity in the complex formation toward one type of nucleoside is, however, less pronounced. The complexes of the nucleotides such as AMP, GMP, CMP, or UMP with both clips are less stable than the corresponding complexes of the nucleosides. To understand the observed selectivities in the complex formation we discuss attractive and repulsive electrostatic interactions on the basis of electrostatic potential surfaces (EPS) calculated for host and guest molecules by quantum chemical methods and hydrophobic effects which contribute to the complex stability to a large extent. The observed large complexation-induced ~1H NMR shifts (△δ_(max)) of the guest signals provide good evidence that in each complex the nucleobase is encapsulated inside the clip cavity.
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