Acid-base catalysis kinetic steps

Figure 16.7 Mechanism of aspartyl proteases involving general acid-base catalysis and the formation of a protonated terahedral intermediate. Bottom Proposal by T. J. Rodriguez. T. A. Angeles, and T. D. Meek, Biochemistry 32, 12380 (1993), that the first step is peptide bond isomerization. This accounts for the observed inverse 15N/14N kinetic isotope effect, which implies that bonding with the N atom becomes stiffer in the transition state.

For ethane-1,2-diol the diester C2 is in equilibrium with the reactants, and its decomposition to the reaction products is rate limiting and not subject to acid-base catalysis. When the concentrations employed are such that C2 is present in appreciable concentration, the mixed-order kinetics described in section 1.3.2 are observed. Second-order kinetics (for the overall reaction) can arise in three ways (a) C2 in equilibrium, but its concentration negligible, (b) formation of C2 from Ci rate limiting, and the latter in equilibrium with the reactants but present in very low concentration, and (c) formation of Q rate-limiting. For pinacol in the range pH 2-10 alternative (a) cannot be operative because general acid-base catalysis is observed. The most likely step to be subject to catalysis is the formation of C2 from Cl, i.e. alternative (b), because this is a cyclisation and a base (B) could well facilitate reaction by removal of the C-OH proton, viz. 

The main parts of this scheme were proposed earlier by Theorell and co-workers 119,291) on the basis of inhibitor binding and steady-state kinetic studies. Other suggested mechanisms based on general acid-base catalysis 297), reduction of the enzyme 362), or direct participation of histidine 363) or cysteine 364) in the hydride transfer step are highly unlikely in view of the crystallographic and kinetic results reviewed in this chapter. Contrary to expectations the mechanism described here is in most details very different from that proposed for lactic dehydrogenase 126). 

The meaning of fccat is the easiest to understand. This is the rate constant for the conversion of the substrate to the product within the active site of the catalyst, and is often called the turnover number. Note that it is a unimolecular rate constant, with units of s All the factors that we have examined in this chapter that can impart transition, state stabilization will influence fccat—namely, proximity, acid-base catalysis, electrostatic considerations, covalent catalysis, and the relief of strain. This rate constant is for the chemical" step of catalysis, and it is thus the focus of efforts to interpret transition state binding relative to the substrate binding. Note that the scheme in Eq. 9.48 is for a simple, single-step conversion. As in other kinetic analyses, if multiple chemical steps are involved in converting the substrate to the... 

Stoichiometry (28) is followed under neutral or in alkaline aqueous conditions and (29) in concentrated mineral acids. In acid solution reaction (28) is powerfully inhibited and in the absence of general acids or bases the rate of hydrolysis is a function of pH. At pH >5.0 the reaction is first-order in OH but below this value there is a region where the rate of hydrolysis is largely independent of pH followed by a region where the rate falls as [H30+] increases. The kinetic data at various temperatures both with pure water and buffer solutions, the solvent isotope effect and the rate increase of the 4-chloro derivative ( 2-fold) are compatible with the interpretation of the hydrolysis in terms of two mechanisms. These are a dominant bimolecular reaction between hydroxide ion and acyl cyanide at pH >5.0 and a dominant water reaction at lower pH, the latter susceptible to general base catalysis and inhibition by acids. The data at pH <5.0 can be rationalised by a carbonyl addition intermediate and are compatible with a two-step, but not one-step, cyclic mechanism for hydration. Benzoyl cyanide is more reactive towards water than benzoyl fluoride, but less reactive than benzoyl chloride and anhydride, an unexpected result since HCN has a smaller dissociation constant than HF or RC02H. There are no grounds, however, to suspect that an ionisation mechanism is involved. 

Show that a mechanism involving general base catalysis is indistinguishable kinetically from one involving a specific base-catalyzed step followed by a general acid-catalyzed step. 

A kinetic study in 50% aqueous DMSO has shown that the first step in the three-step mechanism (Scheme 24) proposed for the 5NV reaction between para-substituted (methylthio)benzylidene Meldrum s acids (61) and four aliphatic primary amines is rate determining.101 The evidence supporting this mechanism is that the reactions are second order kinetically and show no base catalysis. A value of /Wc = 0.32 for the reaction with primary amines is smaller than the /9nuc = 0.41 found for the reaction with the less reactive secondary amines, indicating that N-Ca bond formation is more... 

The observation of general base-catalysis in the hydration of the carbonyl group can be explained by one of two kinetically indistinguishable mechanisms. These are (a) one-step general base catalysis represented in formula (18), or (b) specific base-general acid catalysis, (19). 

A study of the kinetics of nitrosation of iV,iV -dimethyl-A"-cyanoguanidine in acid media (Scheme 13) [where the substrate exists as its conjugate acid (130)] has established that the mechanism of the reversible reaction is similar to that found for nitrosation of amides and ureas, rather than amines (for which attack of the nitrosating agent on the free base is usually rate limiting).The reaction, which is subject to general-base catalysis but not influenced by halide ion, involves reversible rate-limiting proton transfer in the final step and exhibits solvent deuterium isotope effects of 1.6 and... 

---