Proton abstraction from carbon acids

Gerlt, J. and A. Gassman, P.G. (1992) Understanding enzyme-catalyzed proton abstraction from carbon acids details of stepwise mechanisms for (5-elimination reactions, J. Am. Chem. Soc. 114, 5928-5934. 

Gerlt JA, Gassman PG. Understanding the rates of certain enzyme-catalyzed reactions-proton abstraction from carbon acids, acyl-transfer reactions, and displacement-reactions of phosphodiesters. Biochemistry 1993 32 11943-11952. 

Gerlt, J. A. and Gassman, P. G. (1993) Understanding the Rates of Certain Enzyme-Catalyzed Reactions Proton Abstraction from Carbon Acids, Acyl-Transfer Reactions, and Displacement Reactions of Phosphodiesters, Biochemistry 32, 1194311952. 

Table 6.1. Examples of the rate accelerations for enzyme-catalyzed proton abstraction from carbon acids.

In summary, insufficient data are available to decide whether enzymes that catalyze proton abstraction from carbon acids either need or are able to reduce the values of G int from those measured for nonenzymatic reactions. But the conclusion is inescapable these enzymes must significantly stabilize the enolate anion intermediate if the observed values of kct and the associated rate acceleration are to be understood. 

As noted previously, the vast majority of enzymes that catalyze proton abstraction from carbon acids must be able to reduce the value of AG° from that used to describe the nonenzymatic reaction. Focusing on reactions that do not involve organic cofactors, stabilization of the enolate anion intermediate is most reasonably accomplished either by hydrogen-bonding or electrostatic interactions with active site components. 

Gerlt, j. a., Gassman, P. G., An Explanation for Rapid Enzyme-Catalyzed Proton Abstraction from Carbon Acids Importance of Late Transition States in Concerted Mechanisms, J. Am. Chem. Soc. 1993, 115, 11552-11568. 

Figure 4. Br0nsted plots and isotope effects, for proton abstraction from carbon acids, from Pohl and Hupe (30). The upper plot shows rate data for oxyanion and thiol anion catalyzed proton abstraction from 4-(4-nitrophenoxy)-2-butanone (o,v )t acetylacetone and ethyl...

Proton abstraction from carbon acids to give carbanions may be catalysed by hydroxamate anions bound to poly(2-ethyl 1-vinylimidazole) quatemized with dodecyl and ethyl bromides. For example, proton removal from benzoin (19) by IV-methylmyristohydroxamate anion is 2.1 x 10 -fold faster in the presence of... 

A quantitative understanding of how enzymes catalyze rapid proton abstraction from weakly acidic carbon acids is necessarily achieved by dissecting the effect of active site structure on the values of AG°, the thermodynamic barrier, and AG int, the intrinsic kinetic barrier for formation of the enolate anion intermediate. The structural strategies by which AG° for formation of the enolate anion is reduced sufficiently such that these can be kinetically competent are now understood. In divalent metal ion-independent reactions, e.g., TIM, KSI, and ECH, the intermediate is stabilized by enhanced hydrogen bonding interactions with weakly acidic hydrogen bond donors in divalent metal-dependent reactions, e.g., MR and enolase, the intermediate is stabilized primarily by enhanced electrostatic interactions with... 

Both mechanisms, acid-catalyzed and base-catalyzed, consist of two proton-transfer steps proton abstraction from carbon and proton transfer to oxygen. The difference between the two is that the sequence of steps is reversed. Proton abstraction from the a carbon is the first step in the base-catalyzed mechanism it is the second step in the acid-catalyzed one. In each mechanism, proton abstraction from the a carbon is rate-determining. 

The debromination of gem-dibromocyclopropanes by dimsyl anion (73) involves removal of a soft halogen by the carbon base. The formation of allenes from the reaction of g cm-dibromocyclopropanes with alkyllithiums (74) must proceed at its early stages by a similar mechanism. Halogen-metal exchange of a e/n-dibromocyclopropanecarboxylic acid (75) is 2.5 times faster than proton abstraction from the acid This is a remarkable demonstration of the HSAB axiom. 

From a study of the decompositions of several rhodium(II) carboxylates, Kitchen and Bear [1111] conclude that in alkanoates (e.g. acetates) the a-carbon—H bond is weakest and that, on reaction, this proton is transferred to an oxygen atom of another carboxylate group. Reduction of the metal ion is followed by decomposition of the a-lactone to CO and an aldehyde which, in turn, can further reduce metal ions and also protonate two carboxyl groups. Thus reaction yields the metal and an acid as products. In aromatic carboxylates (e.g. benzoates), the bond between the carboxyl group and the aromatic ring is the weakest. The phenyl radical formed on rupture of this linkage is capable of proton abstraction from water so that no acid product is given and the solid product is an oxide. 

Proton abstraction from a model carbon acid, hydroxyacetaldehyde, by formate anion has been examined theoretically for the gas phase and for aqueous solution.152 The reaction shows an early transition state, whereas its enzymatic equivalent has a late transition state. Solvation brings the transition state foiward. The factors that contribute to producing the later transition state in enzymes are discussed. 

In the case of amines, protonation that withdraws electron density from the center of reaction lowers the rate of reaction by a factor of 30 (Das and von Sonntag 1986). Besides H-abstraction from carbon [reactions (18) and (21)], the formation of N-centered radical cations is observed [reactions (19)/(22) and (20) for amino acids see, e.g Bonifacic et al. 1998 Hobel and von Sonntag 1998]. Reaction (20) is also an H-abstraction reaction. The ET reaction (19)/(22) may proceed via a (bona-fide, very short-lived) adduct (Chap. 7). 

The alanine racemization catalyzed by alanine racemase is considered to be initiated by the transaldimination (Fig. 8.5).26) In this step, PLP bound to the active-site lysine residue forms the external Schiff base with a substrate alanine (Fig. 8.5, 1). The following a-proton abstraction produces the resonance-stabilized carbanion intermediates (Fig. 8.5, 2). If the reprotonation occurs on the opposite face of the substrate-PLP complex on which the proton-abstraction proceeds, the antipodal aldimine is formed (Fig. 8.5,3). The subsequent hydrolysis of the aldimine complex gives the isomerized alanine and PLP-form racemase. The random return of hydrogen to the carbanion intermediate is the distinguishing feature that differentiates racemization from reactions catalyzed by other pyridoxal enzymes such as transaminases. Transaminases catalyze the transfer of amino group between amino acid and keto acid, and the reaction is initiated by the transaldimination, followed by the a-proton abstraction from the substrate-PLP aldimine to form a resonance-stabilized carbanion. This step is common to racemases and transaminases. However, in the transamination the abstracted proton is then tranferred to C4 carbon of PLP in a highly stereospecific manner The re-protonation occurs on the same face of the PLP-substrate aldimine on which the a-proton is abstracted. With only a few exceptions,27,28) each step of pyridoxal enzymes-catalyzed reaction proceeds on only one side of the planar PLP-substrate complex. However, in the amino acid racemase... 

The one-base mechanism is characterized by the retention of the substrate-derived proton in the product (internal retum).30) With this criterion, reactions catalyzed by a-amino-c-caprolactam racemase,323 amino acid racemase of broad specificity from Pseudomonas striata333 have been considered to proceed through the one-base mechanism. However, such internal returns were not observed in the reactions of alanine racemases from K coli B,33) B. stearothermophilus,263 and S. typhirmaium (DadB and /1/r).263 The internal return should not be observed in the two-base mechanism, because the base catalyzing the protonation to the intermediate probably obtains the proton from the solvent. But the failure of the observation of the internal return can be also explained by the single-base mechanism in which exchange of the proton abstracted from the substrate a-carbon with the solvent is much faster than its transfer to the a-carbanion. Therefore, lack of the internal return does not directly indicate the two-base mechanism of the alanine racemase reaction. 

Through lack of an unambiguous method for direct determination, the acidity constants of carbon acids have, for many years, been estimated from the rate of proton abstraction by means of rate-equilibrium relationships. Thus, Bell (1943) (see also Hibbert, 1977) estimated the acetaldehyde, acetone and acetophenone acidity constants (19.7,20.0 and 19.2, respectively) by assuming that the rate constants for proton abstraction from several mono- and dicarbonyl compounds to a single base (A-) with pAHA = 4.0 obey a Bransted equation in its differential form (47). By taking curvature into account, the... 

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