Tetrahedral mechanism substrates

In an alternative mechanism, the substrate molecule is again coordinated to tetrahedral Zn, with the coordinated water molecule now serving as a site for transient proton transfer, thereby generating a penta-coordin ated zinc intermediate. Formation of this intermediate during substrate turnover was supported by time-resolved freeze-quenched X-ray absorption fine spectroscopic analysis of the thermophilic bacterium Thermoanaerobaaer brockii alcohol dehydrogenase (TbADH). These results thus provided further evidence for the dynamic alteration of the Zn from a tetrahedral to a penta-coordinated form with detection of two new penta-coordinated intermediate states these included the water molecule in the zinc coordination sphere during a single catalytic cycle. 

When written in this way it is clear what is happening. The mechanisms of these reactions are probably similar, despite the different p values. The distinction is that in Reaction 10 the substituent X is on the substrate, its usual location but in Reaction 15 the substituent changes have been made on the reagent. Thus, electron-withdrawing substituents on the benzoyl chloride render the carbonyl carbon more positive and more susceptible to nucleophilic attack, whereas electron-donating substituents on the aniline increase the electron density on nitrogen, also facilitating nucleophilic attack. The mechanism may be an addition-elimination via a tetrahedral intermediate ... 

Nucleophilic substitution at a vinylic carbon is difficult (see p. 433), but many examples are known. The most common mechanisms are the tetrahedral mechanism and the closely related addition-elimination mechanism. Both of these mechanisms are impossible at a saturated substrate. The addition-elimination mechanism has... 

Of course, we have seen (p. 430) that SnI reactions at vinylic substrates can be accelerated by a substituents that stabilize that cation, and that reactions by the tetrahedral mechanism can be accelerated by P substituents that stabilize the carbanion. Also, reactions at vinylic substrates can in certain cases proceed by addition-elimination or elimination-addition sequences (pp. 428, 430). 

In contrast to such systems, substrates of the type RCOX are usually much more reactive than the corresponding RCH2X. Of course, the mechanism here is almost always the tetrahedral one. Three reasons can be given for the enhanced reactivity of RCOX (1) The carbonyl carbon has a sizable partial positive charge that makes it very attractive to nucleophiles. (2) In an Sn2 reaction a cr bond must break in the rate-determining step, which requires more energy than the shift of a pair of n electrons, which is what happens in a tetrahedral mechanism. (3) A trigonal carbon offers less steric hindrance to a nucleophile than a tetrahedral carbon. 

Ion 21 can either lose a proton or combine with chloride ion. If it loses a proton, the product is an unsaturated ketone the mechanism is similar to the tetrahedral mechanism of Chapter 10, but with the charges reversed. If it combines with chloride, the product is a 3-halo ketone, which can be isolated, so that the result is addition to the double bond (see 15-45). On the other hand, the p-halo ketone may, under the conditions of the reaction, lose HCl to give the unsaturated ketone, this time by an addition-elimination mechanism. In the case of unsymmetrical alkenes, the attacking ion prefers the position at which there are more hydrogens, following Markovnikov s rule (p. 984). Anhydrides and carboxylic acids (the latter with a proton acid such as anhydrous HF, H2SO4, or polyphosphoric acid as a catalyst) are sometimes used instead of acyl halides. With some substrates and catalysts double-bond migrations are occasionally encountered so that, for example, when 1 -methylcyclohexene was acylated with acetic anhydride and zinc chloride, the major product was 6-acetyl-1-methylcyclohexene. ... 

As with the tetrahedral mechanism at an acyl carbon, nucleophilic catalysis (p. 427) has been demonstrated with an aryl substrate, in certain cases. 

Reactivity factors in additions to carbon-hetero multiple bonds are similar to those for the tetrahedral mechanism of nucleophilic substitution. If A and/or B are electron-donating groups, rates are decreased. Electron-attracting substituents increase rates. This means that aldehydes are more reactive than ketones. Aryl groups are somewhat deactivating compared to alkyl, because of resonance that stabilizes the substrate molecule but is lost on going to the intermediate ... 

This is like the A1 mechanism except that the protonated substrate SH +, instead of reacting alone, reacts with something else in the rate-determining step, a nucleophile or a base, written as Nu in equation (41). A typical example of this very common mechanism is ester hydrolysis, say of the methyl esters in equation (42), where SH+ reacts with two water molecules in the slow step,29 giving the neutral tetrahedral intermediate [5] directly. Reasonably enough, the rate equations obtainable are very similar to those for the A1 mechanism, with the addition of an extra aNu term, see equation (43) ... 

Fig. 2. The generally accepted mechanism for the hydrolysis of peptide substrates by the serine proteases. The precise locations of the protons are still moot their positions here are taken from Steitz and Shullman (1982). I, Michaelis complex II and V, tetrahedral intermediates III and IV, acyl-enzyme VI, product complex.

The structure and mechanism of catalysis of FTase were well defined in the late 1990s from several X-ray crystallography and elegant biochemical studies [24,26-30]. The enzyme is a heterodimer of a and P subunits [31,32]. The P subunit contains binding sites for both the farnesyl pyrophosphate and the CAAX protein substrates. A catalytic zinc (Zn " ) identified in the active site of the P subunit participates in the binding and activation of the CAAX protein substrates [28]. The Zn " is coordinated to the enzyme in a distorted tetrahedral geometry and surrounded by hydrophobic pockets [24,27]. Upon binding of the CAAX peptide, the thiol of the cysteine displaces water and is activated for a nucleophilic attack via thiolate on the C-1 carbon atom of farnesyl pyrophosphate [30]. 

Fig. 33. The promoted-water tetrahedral intermediate (a) in the carboxypeptidase A mechanism is simulated by the binding of the ketomethylene substrate analog BBP (Fig. 32b) as the gm-diol(ate) (b). [Reprinted with permission from Christianson, D. W., Lipscomb, W. N. (1989) Acc. Chem. Res. 22,62-69. Copyright 1989 American Chemical Society.]...

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