Figure 5.

General acid-base catalysis yields equivalent pH dependence for cleavage and ligation. The roles of general acid and base will be exchanged between cleavage and ligation reactions. However, the rates of reaction are proportional to f_A × f_B, which have the same shape for both forward and reverse reactions, although the magnitudes are very different.

A. Simulation of reaction rate as a function of pH for an acid of pK_a = 6 and a base of pK_a = 10.5, corresponding to the proposed mechanism for cleavage. The upper panel plots the fractions of the protonated acid (f_A) and unprotonated base (f_B) in red dotted and green solid lines respectively, with f_A × f_B shown in the lower panel.

B. Simulation of the reaction rate as a function of pH for an acid with pK_a = 10.5 and a base with pK_a = 6 corresponding to the proposed mechanism for ligation, following the presentation in part A. Note that the pH dependence of f_B and the product f_A × f_B are experimentally indistinguishable for the ligation reaction, in contrast to the cleavage reaction shown in A.