Role of Solvent on Nonenzymatic Peptide Bond Formation Mechanisms and Kinetic Isotope Effects

Abstract

Based on the hypothesis that similar mechanisms are involved in the peptide bond formation in aqueous solution and in the ribosome, the aminolysis of esters in aqueous solution has been the subject of numerous studies as the reference reaction for the catalyzed process. The mechanisms proposed in the literature have been explored in the present paper by hybrid QM/MM molecular dynamics simulations. The free energy profiles have been computed with the QM region of the system described at semiempirical AM1 level and by DFT within the M06-2X functional. According to the results, the formation of adduct zwitterion species is a preliminary step required for all possible mechanisms. Then, from different conformers of this species, four different paths were found: three of them taking place through concerted mechanisms of four-, six- and eight-membered ring transition states, and a stepwise mechanism through a neutral intermediate. Comparison of the free energy profiles indicates that the concerted mechanisms would be kinetically favored, with free energy barriers in very good agreement with experimental data. Calculations of kinetic isotope effects, when including the solute interactions with the first solvation shell, show that the 8-membered ring TS renders values in better agreement with available experimental data. Quantitative discrepancies can be attributed to different employed models in experiments and calculations.