Goodness of fit in complexes between substrates and ribonuclease mimics: Effects on binding, catalytic rate constants, and regiochemistry

The hydrolysis of 4-tert-butylcatechol cyclic phosphate and of 4-methylcatechol cyclic phosphate catalyzed by alpha-cyclodextrin-6A,6B-bisimidazolide, and by the corresponding derivatives of beta-cyclodextrin (beta CD) and gamma-cyclodextrin (gamma CD), was examined, All three catalysts were able to hydrolyze the substrate derived from 4-methylcatechol, but only the beta CD- and gamma CD-based catalysts could hydrolyze the substrate based on 4-tert-butylcatechol. Saturation kinetics were observed, from which k(cat) and K-m values were derived. The k(cat)'s showed a bell-shaped dependence on pH, indicating a bifunctional mechanism in which one imidazole acted as a base while the other, protonated, acted as an acid catalyst. The strongest binding was observed between the substrate derived from tert-butylcatechol and the beta CD-based catalyst, and this combination also had the highest k(cat), An Arrhenius plot showed that the good fit of the tert-butyl group into the beta CD cavity leads to an entropy advantage for catalysis within the complex, as well as an advantage in the binding. Furthermore, the combination with the best binding and catalytic constant also exhibited the highest regioselectivity in the substrate hydrolysis, being essentially completely selective for one mode of hydrolysis. All these effects reflect the result of a tight fit of the substrate into the catalyst binding cavity, leading to a well-defined reaction geometry.