Alcohol substrate binding

For hydrogenation to take place, the substrate usually needs to bind to the metal complex, although exceptions are known to this rule [25]. Substrate inhibition can occur in a number of ways, for example if more than one molecule of substrate binds to the metal complex. At low concentration this may be a minor species, whereas at high substrate concentration this may be the only species. One example of this is the hydrogenation of allyl alcohol using Wilkinson s catalyst. Here, the rate dependence on the substrate concentration went through a maximum at 1.2 mmol IT1. The authors propose that this is caused by formation of a complex containing two molecules of allyl alcohol (Scheme 44.1) [26],... 

The essential features of the catalytic cycle are summarized in Figure 12.6. After binding of NAD+ the water molecule is displaced from the zinc atom by the incoming alcohol substrate. Deprotonation of the coordinated alcohol yields a zinc alkoxide intermediate, which then undergoes hydride transfer to NAD+ to give the zinc-bound aldehyde and NADH. A water molecule then displaces the aldehyde to regenerate the original catalytic zinc centre, and finally NADH is released to complete the catalytic cycle. 

The proposed mechanism is given in Scheme 15. Initially the dissociation of water, maybe trapped by the molecular sieve, initiates the catalytic cycle. The substrate binds to the palladium followed by intramolecular deprotonation of the alcohol. The alkoxide then reacts by /i-hydride elimination and sets the carbonyl product free. Reductive elimination of HOAc from the hydride species followed by reoxidation of the intermediate with dioxygen reforms the catalytically active species. The structure of 13 could be confirmed by a solid-state structure [90]. A similar system was used in the cyclization reaction of suitable phenols to dihydrobenzofuranes [92]. The mechanism of the aerobic alcohol oxidation with palladium catalyst systems was also studied theoretically [93-96]. 

The latest proposed mechanisms1462 for several zinc-containing metalloenzymes combine elements from both types of mechanism by suggesting that the substrate binds to the enzyme through the C—O group, but that in the process the metal-bound water molecule is not displaced, so that the reaction proceeds via a five-coordinate intermediate. This hybrid mechanism is discussed below in greater detail for alcohol dehydrogenase. 

Both these mechanisms propose that the alcohol substrate combines with the unprotonated form of the enzyme-NAD+ complex. Kvassman and Pettersson have proposed an alternative mechanism in which alcohol binding to the binary complex requires the presence of a neutral... 

In their mechanism, presented as a series of proton equilibria in Scheme 10, the reaction is controlled by three steps (a) ionization of the zinc-bound water, which destabilizes the binary complex to an extent that substrate binding cannot occur (p/ 3, Scheme 10) (b) a stabilizing effect of alcoholate ion formation in the ternary complex. The pH dependence of this step is the result of ionization of the alcohol.1449 (c) The dissociation of the alcohol from the ternary complex. This is similar in rate to the dissociation of aldehydes, which might be expected for a substitution mechanism, both neutral species forming structurally similar ternary complexes. 

The kinetic mechanism is an acyl-enzyme mechanism (Figure 9.7) the substrate binds non-covalently, the serine displaces the alcohol or amine part of the substrate to form an acyl-enzyme, and water then displaces the serine to yield the acid product and free enzyme. 

The substrate binding pocket of horse liver alcohol dehydrogenase comprises residues from both subunits (Fig. 26B) [123]. The active site is shown in Fig. 27, with NAD(H) bound, and p-bromobenzyl alcohol bound in a non-productive binding mode. The hydrophobic residues (from both subunits) that line the substrate binding... 

Fig. 28. The substrate binding pocket of horse liver alcohol dehydrogenase, as in Fig. 27, viewed here into the pocket towards the zinc (not itself shown). Stereo drawing from the work of Brandon and colleagues. 

Fig. 30. Horse liver alcohol dehydrogenase substrate binding pocket, unoccupied. Stereo drawing from the work of Branden and colleagues. 

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