A calix[4]arene with acylguanidine units as an efficient catalyst for phosphodiester bond cleavage in RNA and DNA model compounds

Abstract

A calix[4]arene scaffold, blocked in the cone conformation and decorated at the upper rim with two acylguanidine units, effectively catalyzes the cleavage of phosphodiester bonds of HPNP and BNPP under neutral pH conditions. The catalyst performance is discussed in terms of acceleration over background hydrolysis and effective molarity (EM). The combination of potentiometric acid–base titrations with pH-rate profiles for HPNP and BNPP cleavage in the presence of 2·2HCl additives points to a marked synergic action of an acylguanidine/acylguanidinium catalytic dyad in 2H⁺, via general base–electrophilic bifunctional catalysis. Acceleration factors over background larger than 3 orders of magnitude are obtained. The connection of the guanidine/guanidinium dyad to the calixarene scaffold by means of carbonyl joints has a double advantage: (i) the acidity of the guanidinium moiety is enhanced by the electron-withdrawing carbonyl group and maximum conversion into the catalytically active form 2H⁺ occurs at almost neutral pH, lower than the pH needed for the monoprotonated form 1H⁺ devoid of carbonyl groups; (ii) the EM value for HPNP cleavage with 2H⁺ is definitely higher than that with 1H⁺, suggesting a highly preorganized catalyst that perfectly fits in a strainless ring-shaped transition state in the catalyzed process. DFT calculations also provide useful insights into the reaction mechanisms and transition states.