On the question of stepwise vs. concerted cleavage of RNA models promoted by a synthetic dinuclear Zn(ii) complex in methanol: implementation of a noncleavable phosphonate probe

Abstract

To address the question of concerted versus a stepwise reaction mechanisms for the cyclization of the 2-hydroxypropyl aryl and alkyl RNA models (1a–k) promoted by dinuclear Zn(II) complex (4) at ^s_spH 9.8 and 25 °C, the non-cleavable O-hydroxypropyl phenylphosphonate analogues 6a and 6b were subjected to the catalytic reaction in methanol. These phosphonates did not undergo isomerization in the study, the only observable methanolysis reaction being release of 1,2-propanediol and the formation of O-methyl phenylphosphonate. The observed first order rate constants for methanolysis promoted by 4 are k_obs^6a = (1.47 ± 0.09) × 10⁻⁴ s⁻¹ and k_obs^6b = (2.08 ± 0.09) × 10⁻⁶ s⁻¹, respectively. The rates of methanolysis of a series of O-aryl phenylphosphonates (8a–f) in the presence of increasing [4] were analyzed to provide binding constants, K_b, and the catalytic rate constant, k_cat^max, for the unimolecular decomposition of the 8 : 4 Michaelis complex. A Brønsted plot of the log (k_cat^max) vs.^s_spK_a^phenol (acidity constant of the conjugate acid of the leaving group in methanol) was fitted to a linear regression of log k_cat^max = (−0.80 ± 0.07)^s_spK_a + (10.2 ± 1.0) which includes the datum for 6a. The datum for 6b, which reacts ∼70–fold slower, falls significantly below the linear correlation. The data provide additional evidence consistent with a concerted cyclization of RNA models 1a–k promoted by 4.