Ab initio/LD studies of chemical reactions in solution: Reference free-energy surfaces for acylation reactions occurring in serine and cysteine proteases

Abstract

A systematic ab initio study of the reactions of amides with alcohols and thiols in aqueous solution is presented. This study is aimed at providing well-defined reference free-energy surfaces for the corresponding studies of the catalytic power of serine and cysteine protease. The applied methodology consists of the combined ab initio and Langevine dipoles (LD) solvent model, and a systematic calibration using the available experiments. The study of the base-catalyzed and general-base-catalyzed methanolysis of formamide, which serves as a reference reaction of serine protease, indicates that when a water molecule is the base the initial proton transfer is concerted with the RO− nucleophilic attack. However, with histidine as a general base this reaction is a stepwise process with a shallow surface that can allow also for a concerted path. It is also found that the protonation of the nitrogen of the oxyanion leads to breaking of the CN bond. The study of a reference reaction of cysteine protease indicates that the initial proton transfer to the general base occurs before the RS− attack on the amide. The nucleophilic attack may be concerted with the protonation of the amide nitrogen, but a stepwise process where the protonation occurs after the formation of the tetrahedral intermediate is also possible. The CN bond cleavage appears to be the last step of the reaction. The common belief that thiols have greater tendency to add to carbonyl groups than alcohols is revisited. It is found that this is probably true because the reactivity of thiols can involve unassisted proton transfer to the nitrogen or oxygen of the amide concerted with the nucleophilic attack. The possibility that thiolysis of amides in solution circumvents the general-base catalysis mechanism should thus be taken into account in comparing enzymatic reactions to uncatalyzed solution reactions. Having relatively reliable potential surfaces for the reference reactions of serine and cysteine proteases should allow one to calibrate potential surfaces for the corresponding enzymatic reactions. This can be very useful for calibrating empirical valence bond (EVB) potential surfaces or other hybrid quantum mechanical/molecular mechanical (QM/MM) semiempirical potential surfaces. In addition, our results will be useful for ab initio studies that use the EVB surfaces as reference potentials. Furthermore, any attempts to study these enzymatic reactions by quantum mechanical approaches should be validated by examining the corresponding solution reactions and the present study should be helpful in such validation studies. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 77: 44–53, 2000