Altered transition state for the reaction of an RNA model catalyzed by a dinuclear zinc(II) catalyst

The cyclization of 2-(hydroxypropyl)-4-nitrophenyl phosphate (HpPNP) catalyzed by the dinuclear zinc complex of 1,3-bis(1,4,7-triazacyclonon-1-yl)-2- hydroxypropane (1) proceeds by a transition state that is different from that of the uncatalyzed reaction. Kinetic isotope effects (KIEs) measured in the nucleophilic atom and in the leaving group show that the uncatalyzed cyclization has a transition state (TS) with little phosphorus-oxygen bond fission to the leaving group ¹⁸k^lg = 1.0064 ± 0.0009 and ¹⁵k = 1.0002 ± 0.0002) and that nucleophilic bond formation occurs in the rate-determining step (¹⁸k_nuc ) 1.0326 ( 0.0008). In the catalyzed reaction, larger leaving group isotope effects ( ¹⁸k_lg ) 1.0113 ± 0.0005 and ¹⁵k = 1.0015 ± 0.0005) and a smaller nucleophile isotope effect (¹⁸k _nuc = 1.0116 ± 0.0010) indicate a later TS with greater leaving group bond fission and greater nucleophilic bond formation. These observed nucleophile KIEs are the combined effect of the equilibrium effect on deprotonation of the 2′-hydroxyl nucleophile and the KIE on the nucleophilic step. An EIE of 1.0245 for deprotonation of the hydroxyl group of HPpNP was obtained computationally. The different KIEs for the two reactions indicate that the effective catalysis by 1 is accompanied by selection for an altered transition state, presumably arising from the preferential stabilization by the catalyst of charge away from the nucleophile and toward the leaving group. These results demonstrate the potential for a catalyst using biologically relevant metal ions to select for an altered transition state for phosphoryl transfer.