Analyzing Kemp's amide cleavage: A model for amidase enzymes

DFT calculations at B3LYP/6-31G (d, p) level for the cleavage reactions in Kemp's mono- and di-acid amides 1-9 (an amidase model) under physiological conditions, indicate that the rate limiting step in the acylolysis process is a proton transfer from the carboxyl group onto the amide carbonyl oxygen. It is proposed that accelerations in rate are mainly due to the distance between the two reactive centers (r) and the attack (hydrogen bond) angle (α). In fact, a linear correlation was found between the activation energy (ΔG‡) and r2 × sin (180 − α). On the other hand, in contrast to previous studies the ground-state pseudoallylic strain effect was found to contribute a little if any to the cleavage rate in Kemp's triacid tertiary amides. In addition, the calculation results suggest a change in the mode and the mechanism of the amide cleavage upon changing the pH of the reaction medium. Thus, peptidase enzymes are extremely reactive around neutral pH while their activities vanish under basic medium.