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

A systematic ab initio study of the reactions of amides with alcohols and t hiols in aqueous solution is presented. This study is aimed at providing we ll-defined reference free-energy surfaces for the corresponding studies of the catalytic power of serine and cysteine protease. The applied methodolog y consists of the combined ab initio and Langevine dipoles (LD) solvent mod el, 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 w hen a water molecule is the base the initial proton transfer is concerted w ith the RO- nucleophilic attack. However, with histidine as a general base this reaction is a stepwise process with a shallow surface that can allow a lso for a concerted path. It is also found that the protonation of the nitr ogen of the oxyanion leads to breaking of the CN bond. The study of a refer ence reaction of cysteine protease indicates that the initial proton transf er to the general base occurs before the RS- attack on the amide. The nucle ophilic 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 appear s to be the last step of the reaction. The common belief that thiols have g reater tendency to add to carbonyl groups than alcohols is revisited. It is found that this is probably true because the reactivity of thiols can invo lve unassisted proton transfer to the nitrogen or oxygen of the amide conce rted with the nucleophilic attack. The possibility that thiolysis of amides in solution circumvents the general-base catalysis mechanism should thus b e taken into account in comparing enzymatic reactions to uncatalyzed soluti on reactions. Having relatively reliable potential surfaces for the referen ce 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) semiempiri cal potential surfaces. In addition, our results will be useful for ab init io studies that use the EVE surfaces as reference potentials. Furthermore, any attempts to study these enzymatic reactions by quantum mechanical appro aches should be validated by examining the corresponding solution reactions and the present study should be helpful in such validation studies. (C) 20 00 John Wiley & Sons, Inc.