Catalytic Role of Vicinal OH in Ester Aminolysis: Proton Shuttle versus Hydrogen Bond Stabilization

Abstract

This computational study provoked by the process of peptide bond formation in the ribosome investigates the influence of the vicinal OH group in monoacylated diols on the elementary acts of ester aminolysis. Two alternative approaches for this influence on ester ammonolysis were considered: stabilization of the transition states by hydrogen bonds and participation of the vicinal hydroxyl in proton transfer (proton shuttle). The activation due to hydrogen bonds of the vicinal hydroxyl via tetragonal transition states was rather modest; the free energy of activation was reduced by only 5.2 kcal/mol compared to the noncatalyzed reaction. The catalytic activation via the proton shuttle mechanism with participation of the vicinal OH in the proton transfer via hexagonal transition states resulted in considerable reduction of the free energy of activation to 33.5 kcal/mol, i.e., 16.0 kcal/mol lower than in the referent process. Accounting for the influence of the environment on the reaction center by a continuum model (for ε from 5 to 80) resulted in further stabilization of the rate-determining transition state by 4-5 kcal/mol. The overall reduction of the reaction barrier by about 16 kcal/mol as compared to the noncatalyzed process corresponds to about 10(9)-fold acceleration of the reaction, in agreement with the experimental estimate for acceleration of this process in the ribosome.

Hierarchical approach to conformational search and selection of computational method in modeling the mechanism of ester ammonolysis

“…As reported elsewhere [52], the analysis of the Gibbs free energy of activation of different transition states resulted in essentially the same conclusion. In order to evaluate the influence of the polarization and diffuse functions in the basis set of hydrogen atoms, we can compare the calculated energies of different stationary points along the reaction paths obtained with 6-31 + G* and 6-31 + + G** basis sets (Table 2).…”

“…This selection of the reagents is not accidental but determined by the presence in the formylethanediol molecule of a vicinal hydroxyl next to the reaction center analogously to the ribose ring in tRNA. As shown in our theoretical investigations of the mechanism for this model reaction (Scheme 1a and b) [17,52], the latter one based on the transition state search reported here, the catalytic role of this vicinal hydroxyl group could be explained by the stabilization of the transition state structures via formation of intramolecular hydrogen bonds (tetragonal transition states in Scheme 1a) or by a direct participation of this vicinal hydroxyl in the proton transfer process (hexagonal transition states in Scheme 1b). Both possible reaction paths are presented in Scheme 1a and b, while the applied notation of the atoms is presented in Scheme 1c on the example of the tetrahedral intermediate I.…”

A two-step chemical mechanism for ribosome-catalysed peptide bond formation

“…Recently, computational methods were used to evaluate concerted proton shuttle mechanisms with and without an additional water molecule, and favored a fully concerted eight-member proton shuttle(similar to transition state A) 10 . Alternatively, other computational studies have indicated a stepwise proton shuttle would be favorable 11,12 . All of these possibilities have been proposed 4,8–13 .…”

“…The 2′-hydroxyl is important for the ribosome reaction, but the pK a of a hydroxyl dictates that if it abstracts the amino proton it must donate its proton elsewhere. This mechanism, termed the “proton shuttle” has been proposed in a variety of forms for the ribosome 8–12 . Alternatively, the 2′-hydroxyl may provide an important transition state hydrogen bond, with another group or a water molecule deprotonating the nucleophile.…”

“…Two computational studies favor the carbonyl oxygen, which would otherwise develop a negative charge 11,12 . This would result in an uncharged tetrahedral intermediate, which would be consistent with the lack of pH dependence of the reaction.…”