Catalytically active sites catalytic cycle

The reducing agent itself is in fact always an oxidised hydrocarbon (HCxKDy), such as an alcohol or an aldehyde. The oxidation of HC can follow two routes total oxidation, or mild oxidation to HC%Oy compounds. NO2 has been observed to favor this second route. The design of a three-function catalyst needs thus to address three separate catalytic cycles oxidation of NO to NO2, mild oxidation of HC to HC Op and decomposition-reduction of NO with total oxidation of HC Oy species (and recovery of the free active site). These cycles share no common adsorbed species [49] and are not kinetically coupled, but they must run in a concerted way. 

Ornithine decarboxylase is a pyridoxal dependent enzyme. In its catalytic cycle, it normally converts ornithine (7) to putrisine by decarboxylation. If it starts the process with eflornithine instead, the key imine anion (11) produced by decarboxylation can either alkylate the enzyme directly by displacement of either fluorine atom or it can eject a fluorine atom to produce viny-logue 12 which can alkylate the enzyme by conjugate addidon. In either case, 13 results in which the active site of the enzyme is alkylated and unable to continue processing substrate. The net result is a downturn in the synthesis of cellular polyamine production and a decrease in growth rate. Eflornithine is described as being useful in the treatment of benign prostatic hyperplasia, as an antiprotozoal or an antineoplastic substance [3,4]. 

Figure 2. Mechanism of PDH. The three different subunits of the PDH complex in the mitochondrial matrix (E, pyruvate decarboxylase E2, dihydrolipoamide acyltrans-ferase Ej, dihydrolipoamide dehydrogenase) catalyze the oxidative decarboxylation of pyruvate to acetyl-CoA and CO2. E, decarboxylates pyruvate and transfers the acetyl-group to lipoamide. Lipoamide is linked to the group of a lysine residue to E2 to form a flexible chain which rotates between the active sites of E, E2, and E3. E2 then transfers the acetyl-group from lipoamide to CoASH leaving the lipoamide in the reduced form. This in turn is oxidized by E3, which is an NAD-dependent (low potential) flavoprotein, completing the catalytic cycle. PDH activity is controlled in two ways by product inhibition by NADH and acetyl-CoA formed from pyruvate (or by P-oxidation), and by inactivation by phosphorylation of Ej by a specific ATP-de-pendent protein kinase associated with the complex, or activation by dephosphorylation by a specific phosphoprotein phosphatase. The phosphatase is activated by increases in the concentration of Ca in the matrix. The combination of insulin with its cell surface receptor activates PDH by activating the phosphatase by an unknown mechanism.

The mechanism for the lipase-catalyzed reaction of an acid derivative with a nucleophile (alcohol, amine, or thiol) is known as a serine hydrolase mechanism (Scheme 7.2). The active site of the enzyme is constituted by a catalytic triad (serine, aspartic, and histidine residues). The serine residue accepts the acyl group of the ester, leading to an acyl-enzyme activated intermediate. This acyl-enzyme intermediate reacts with the nucleophile, an amine or ammonia in this case, to yield the final amide product and leading to the free biocatalyst, which can enter again into the catalytic cycle. A histidine residue, activated by an aspartate side chain, is responsible for the proton transference necessary for the catalysis. Another important factor is that the oxyanion hole, formed by different residues, is able to stabilize the negatively charged oxygen present in both the transition state and the tetrahedral intermediate. 

The discovery of a new heterodinuclear active site in [NiFe] hydro-genases opens the way for the proposal of catalytic cycles based on the available spectroscopic data on the different active site redox states, namely EXAFS studies that reveal that the Ni-edge energy upon reduction of the enzyme supports an increase in the charge density of the nickel (191). 

As an introductory example we take one of the key reactions in cleaning automotive exhaust, the catalytic oxidation of CO on the surface of noble metals such as platinum, palladium and rhodium. To describe the process, we will assume that the metal surface consists of active sites, denoted as We define them properly later on. The catalytic reaction cycle begins with the adsorption of CO and O2 on the surface of platinum, whereby the O2 molecule dissociates into two O atoms (X indicates that the atom or molecule is adsorbed on the surface, i.e. bound to the site ) ... 

We can think of a heterogeneous catalyst as a collection of active sites (denoted by ) located at a surface. The total number of sites is constant and equal to N (if there is any chance of confusion with N atoms, we will use the symbol N ). The adsorption of the reactant is formally a reaction with an empty site to give an intermediate I (or more conveniently R if we explicitly want to express that it is the reactant R sitting on an adsorption site). All sites are equivalent and each can be occupied by a single species only. We will use the symbol 6r to indicate the fraction of occupied sites occupied by species R, making N6r the number of occupied sites. Hence, the fraction of unoccupied sites available for reaction will be 1 - 0r The following equations represent the catalytic cycle of Fig. 2.7 ... 

Partial oxidations over complex mixed metal oxides are far from ideal for singlecrystal like studies of catalyst structure and reaction mechanisms, although several detailed (and by no means unreasonable) catalytic cycles have been postulated. Successful catalysts are believed to have surfaces that react selectively vith adsorbed organic reactants at positions where oxygen of only limited reactivity is present. This results in the desired partially oxidized products and a reduced catalytic site, exposing oxygen deficiencies. Such sites are reoxidized by oxygen from the bulk that is supplied by gas-phase O2 activated at remote sites. 

It is most convenient to explain catalysis using an example. We have chosen a hydrogenation catalysed by nickel in the metallic state. According to the schematic of Fig. 3.1 the first step in the actual catalysis is adsorption . It is useful to distinguish physisorption and chemisorption . In the former case weak, physical forces and in the latter case relatively strong, chemical forces play a role. When the molecules adsorb at an active site physisorption or chemisorption can occur. In catalysis often physisorption followed by chemisorption is the start of the catalytic cycle. This can be understood from Fig. 3.2, which illustrates the adsorption of hydrogen on a nickel surface. 

These catalysts are activated by hydrogenation of the cyclooctadiene ligand, which releases cyclooctane and opens two coordination sites at iridium. The mechanism has been probed by computational studies.40 It is suggested that the catalytic cycle involves... 

X-ray diffraction studies on several forms of the enzyme have demonstrated that the active site is composed of a pseudo-tetrahedral zinc center coordinated to three histidine imidazole groups and either a water molecule [(His)3Zn-OH2]2+ (His = histidine), or a hydroxide anion [(His)3Zn-OH] +, depending upon pH (156,157). On the basis of mechanistic studies, a number of details of the catalytic cycle for carbonic anhydrase have been elucidated, as summarized in Scheme 22... 

A dinitrosyl (NO)2 species forms, whose dissociation leads to N2 the remaining adsorbed oxygen species have to be scavenged by the activated reductant, C, HvOz to recover the free active site, permitting the catalytic cycle to turn over (Figure 5.1, function 3) [10]. 

If the two Oads species are not scavenged, then the reaction will stop. This is the case, for instance, of NO decomposition on Cu/ZSM-5 [25], Adsorbed oxygen species have to be scavenged either by an activated form of the initial HC reductant, such as QH O , (alcohol, aldehyde, etc.) or by the initial HC if their total oxidation is simultaneous with NO decomposition-reduction to N2. These oxygenates and/or HC suffer a total oxidation to C0/C02 and H20, regenerating the active site this is the principle of catalysis. Once the active site is recovered, the reaction continues to turn over. This is the catalytic cycle . 

Figure 2-9. Reaction scheme for the complete catalytic cycle in glutathione peroxidase (left). Numbers represent calculated reaction barriers using the active-site model. The detailed potential energy diagram for the first elementary reaction, (E-SeH) + H2O2 - (E-SeOH) + H2O, calculated using both the active-site (dashed line) and ONIOM model (grey line) is shown to the right (Adapted from Prabhakar et al. [28, 65], Reprinted with permission. Copyright 2005, 2006 American Chemical Society.)...

As an illustration, we briefly discuss the SCC-DFTB/MM simulations of carbonic anhydrase II (CAII), which is a zinc-enzyme that catalyzes the interconversion of CO2 and HCO [86], The rate-limiting step of the catalytic cycle is a proton transfer between a zinc-bound water/hydroxide and the neutral/protonated His64 residue close to the protein/solvent interface. Since this proton transfer spans at least 8-10 A depending on the orientation of the His 64 sidechain ( in vs. out , both observed in the X-ray study [87]), the transfer is believed to be mediated by the water molecules in the active site (see Figure 7-1). To carry out meaningful simulations for the proton transfer in CAII, therefore, it is crucial to be able to describe the water structure in the active site and the sidechain flexibility of His 64 in a satisfactory manner. 

It is concluded that the occupation of the step and kink sites plays a crucial role in the promotion of the Pt catalyst. The cyclic voltammetry results can be used to explain the conversion trends observed in Figure 2. For unpromoted 5%Pt/C the Pt step and kink sites are unoccupied and available for adsorption of reactant and oxidant species. During reaction these sites facilitate premature catalyst deactivation due to poisoning by strongly adsorbed by-products (5) and (or) the formation of a surface oxide layer (6). The 5%Pt,0.5%Bi/C catalyst has a portion of these Pt step and kink sites occupied and the result is a partial reduction in the catalyst deactivation and a consequent increase in alcohol conversion. As the Bi level is increased to lwt.% almost all of the Pt step and kink sites are occupied and the result is a catalyst with high activity. As more Bi is introduced onto the catalyst surface a bulk Bi phase is formed. Since the catalyst activity is maintained it is speculated that the bulk Bi phase is not involved in the catalytic cycle. 

It is well known that Rh(I) complexes can catalyze the carbonylation of methanol. A heterogenized catalyst was prepared by ion exchange of zeolite X or Y with Rh cations.126 The same catalytic cycle takes place in zeolites and in solution because the activation energy is nearly the same. The specific activity in zeolites, however, is less by an order of magnitude, suggesting that the Rh sites in the zeolite are not uniformly accessible. The oxidation of camphene was performed over zeolites exchanged with different metals (Mn, Co, Cu, Ni, and Zn).127 Cu-loaded zeolites have attracted considerable attention because of their unique properties applied in catalytic redox reactions.128-130 Four different Cu sites with defined coordinations have been found.131 It was found that the zeolitic media affects strongly the catalytic activity of the Cd2+ ion sites in Cd zeolites used to catalyze the hydration of acetylene.132... 

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