Enzyme reaction rate acceleration

We are applying the principles of enzyme mechanism to organometallic catalysis of the reactions of nonpolar and polar molecules for our early work using heterocyclic phosphines, please see ref. 1.(1) Here we report that whereas uncatalyzed alkyne hydration by water has a half-life measured in thousands of years, we have created improved catalysts which reduce the half-life to minutes, even at neutral pH. These data correspond to enzyme-like rate accelerations of >3.4 x 109, which is 12.8 times faster than our previously reported catalyst and 1170 times faster than the best catalyst known in the literature without a heterocyclic phosphine. In some cases, practical hydration can now be conducted at room temperature. Moreover, our improved catalysts favor anti-Markovnikov hydration over traditional Markovnikov hydration in ratios of over 1000 to 1, with aldehyde yields above 99% in many cases. In addition, we find that very active hydration catalysts can be created in situ by adding heterocyclic phosphines to otherwise inactive catalysts. The scope, limitations, and development of these reactions will be described in detail. 

A most significant advance in the alkyne hydration area during the past decade has been the development of Ru(n) catalyst systems that have enabled the anti-Markovnikov hydration of terminal alkynes (entries 6 and 7). These reactions involve the addition of water to the a-carbon of a ruthenium vinylidene complex, followed by reductive elimination of the resulting hydridoruthenium acyl intermediate (path C).392-395 While the use of GpRuGl(dppm) in aqueous dioxane (entry 6)393-396 and an indenylruthenium catalyst in an aqueous medium including surfactants has proved to be effective (entry 7),397 an Ru(n)/P,N-ligand system (entry 8) has recently been reported that displays enzyme-like rate acceleration (>2.4 x 1011) (dppm = bis(diphenylphosphino)methane).398... 

In subsequent studies it has been found that a combination of Lewis-acid and micellar catalysis can lead to huge (in fact, enzyme like) rate acceleration in water. In the absence of Lewis-acid catalysts, micelles tend to inhibit Diels-Alder reactions, largely because of the particular nature of the substrate binding sites at the micelle. This problem can be solved by adding Lewis-acid catalysts that bind effectively at the micellar surface. 

Micellar catalysis, conducted in the absence of Lewis acid tends to inhibit the Diels-Alder reaction, relative to the reaction in water. The reason is that the local reaction medium in the Stern region is less favorable than bulk water. However, by combining Lewis-acid and micellar catalysis, enzyme-hke rate accelerations can be obtained (Table 7.5) in case the Lewis acid acts as the counterion for the miceUe. " ... 

The best way to combine all these parameters is to trace back the catalytic action of enzymes to intramolecularity. It is generally accepted that when van der Waals distances (contact distances) are imposed for definite times upon reactive groups, intramolecular reactions occur then at enzyme-like rates (accelerations of 10 to 10 0 are associated to enzyme-catalysed reactions). On the other hand, according to the Page-Jencks theory [17] the fast rates of intramolecular reaction "are merely an entropic consequence of converting a bimolecular reaction into a unimolecular reaction". 

Supramolecular systems can be considered as new tools of modern physical organic chemistry. The study of catalytic processes using supramolecular model systems aims to explain the observed rate enhancement in terms of structure and mechanism. In some cases, the model systems may even provide a simplified simulation of the action of an enzyme and lead to further understanding of the different mechanism by which enzymes are able to achieve impressive reaction rate accelerations and turnover numbers. 

Molecular models show that during the course of the acylation reaction, the bound substrate is pulled partially out of the cyclodextrin cavity in forming the tetrahedral reaction intermediate. In other words, the model enzyme is not exhibiting the required transition state selectivity. Furthermore, excessively rigid substrates experience difficulty in rotating while bound in order to accommodate the need of the cyclodextrin hydroxyl group to attach perpendicular to the substrate ester plane, and subsequently rotate to become incorporated into the plane of the new ester product (Scheme 12.1). These problems were addressed by examination of substrates, such as p-nitro derivatives in which the ester protrudes further from the cavity, and substrates with more rotational flexibility such as alkyne 12.3. In these refined systems, much more enzyme-like rate accelerations of factors of up to 5 900 000-fold were observed for 12.4, for example. 

Enzymes demonstrate both high specificities and significant reaction rate accelerations. The relative values of enzymic over non-enzymic reactions may be from 10 ° to 10 (orotidine decarboxylase) and the turnover numbers range from one catalytic event per minute to 10 per second (hydration of CO2 to HC03 by carbonic anhydrase). The molecular entities of enzymes cover proteins, ribozymes and catalytic antibodies. 

So the 10 kcal mol drop in activation energy for this reaction is predicted to result in an almost 22,000,000-fold increase in the rate constant - a large reaction rate acceleration. While this number may not be completely correct it does provide an insight into the means by which catalysts, enzymes in particular, can speed up chemical reactions. 

Sometimes, our well-being depends on interfering with an enzyme-mediated rate acceleration. Cholesterol (p. 121) is formed in the body by a lengthy process in which the thioester A is reduced to mevalonic add, which is then converted in a series of reactions into cholesterol. 

Another remarkable characteristic of enzymes is their high catalytic efficiency. Enzyme-catalyzed reactions usually display high reaction rate accelerations from 10 to 10 fold. 

Enzymes are proteins of high molecular weight and possess exceptionally high catalytic properties. These are important to plant and animal life processes. An enzyme, E, is a protein or protein-like substance with catalytic properties. A substrate, S, is the substance that is chemically transformed at an accelerated rate because of the action of the enzyme on it. Most enzymes are normally named in terms of the reactions they catalyze. In practice, a suffice -ase is added to the substrate on which die enzyme acts. Eor example, die enzyme dial catalyzes die decomposition of urea is urease, the enzyme dial acts on uric acid is uricase, and die enzyme present in die micro-organism dial converts glucose to gluconolactone is glucose oxidase. The diree major types of enzyme reaction are ... 

The sensitivity of cellular constituents to environmental extremes places another constraint on the reactions of metabolism. The rate at which cellular reactions proceed is a very important factor in maintenance of the living state. However, the common ways chemists accelerate reactions are not available to cells the temperature cannot be raised, acid or base cannot be added, the pressure cannot be elevated, and concentrations cannot be dramatically increased. Instead, biomolecular catalysts mediate cellular reactions. These catalysts, called enzymes, accelerate the reaction rates many orders of magnitude and, by selecting the substances undergoing reaction, determine the specific reaction taking place. Virtually every metabolic reaction is served by an enzyme whose sole biological purpose is to catalyze its specific reaction (Figure 1.19). 

Enzymes display enormous catalytic power, accelerating reaction rates as much as lO over uncatalyzed levels, which is far greater than any synthetic catalysts can achieve, and enzymes accomplish these astounding feats in dilute aqueous... 

Enzymes are powerful catalysts. Enzyme-catalyzed reactions are typically 10 to times faster than their uncatalyzed counterparts (Table 16.1). (There is even a report of a rate acceleration of >10 for the alkaline phosphatase-catalyzed hydrolysis of methylphosphate )... 

Any or all of these mechanisms may contribute to the net rate acceleration of an enzyme-catalyzed reaction relative to the uncatalyzed reaction. A thorough understanding of any enzyme would require that the net acceleration be accounted for in terms of contributions from one or (usually) more of these mechanisms. Each of these will be discussed in detail in this chapter, but first it is important to appreciate how the formation of the enzyme-substrate (ES) complex makes all these mechanisms possible. 

Some enzyme reactions derive much of their rate acceleration from the formation of covalent bonds between enzyme and substrate. Consider the reaction ... 

The entropic hypothesis seems at first sight to gain strong support from experiments with model compounds of the type listed in Table 9.1. These compounds show a huge rate acceleration when the number of degrees of freedom (i.e., rotation around different bonds) is restricted. Such model compounds have been used repeatedly in attempts to estimate entropic effects in enzyme catalysis. Unfortunately, the information from the available model compounds is not directly transferable to the relevant enzymatic reaction since the observed changes in rate constant reflect interrelated factors (e.g., strain and entropy), which cannot be separated in a unique way by simple experiments. Apparently, model compounds do provide very useful means for verification and calibration of reaction-potential surfaces... 

As discussed in the early sections it seems that there are very few effective ways to stabilize the transition state and electrostatic energy appears to be the most effective one. In fact, it is quite likely that any enzymatic reaction which is characterized by a significant rate acceleration (a large AAgf +p) will involve a complimentarity between the electrostatic potential of the enzyme-active site and the change in charges during the reaction (Ref. 10). This point may be examined by the reader in any system he likes to study. 

Enzymes accelerate reaction rates by lowering the activation barrier AGp. While they may undergo transient modification during the process of catalysis, enzymes emerge unchanged at the completion of the reaction. The presence of an enzyme therefore has no effect on AG for the overall reaction, which is a function solely of the initial and final states of the reactants. Equation (25) shows the relationship between the equilibrium constant for a reaction and the standard free energy change for that reaction ... 

Enzymes are proteins catalyzing all in vivo biological reactions. Enzymatic catalysis can also be utilized for in vitro reactions of not only natural substrates but some unnatural ones. Typical characteristics of enzyme catalysis are high catalytic activity, large rate acceleration of reactions under mild reaction conditions, high selectivities of substrates and reaction modes, and no formation of byproducts, in comparison with those of chemical catalysts. In the field of organic synthetic chemistry, enzymes have been powerful catalysts for stereo- and regioselective reactions to produce useful intermediates and end-products such as medicines and liquid crystals. ... 

The function of enzymes is to accelerate the rates of reaction for specific chemical species. Enzyme catalysis can be understood by viewing the reaction pathway, or catalytic cycle, in terms of a sequential series of specific enzyme-ligand complexes (as illustrated in Figure 1.6), with formation of the enzyme-substrate transition state complex being of paramount importance for both the speed and reactant fidelity that typifies enzyme catalysis. 

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