The Active Site

In the following sections, a brief account of the state of knowledge for each one of these important points will be presented. 

The characterization of HDS catalysts has been the sub ject of a large number of papers, and virtually all the surface techniques and analytical tools available today, as well as powerful theoretical methods, have been extensively employed in order to tackle this exceedingly complicated problem [see e.g. ref. 15]. Tlie mass of information thus obtained has been interpreted in terms of several different models that have been evolving over the years into a rather sophisticated and well founded picture however, in spite of all the data available and of over seven decades of industrial practice, the exact nature and the structure of the catalytically active HDS sites of standard catalyst formulations continue to be the subject of controversy and frequent speculation. A great deal of the published work in this area has been devoted to the study of unpromoted catalysts in both calcined and sulfided forms, and this has resulted in the clarification of several important aspects nevertheless, for the sake of brevity, our description will concentrate essentially on the promoted Co-Mo catalysts in their sulfided forms, which are the ones most frequently used for practical purposes. Many excellent reviews widely cover the various theories and models which have been put forward for HDS active sites (see e.g. refs. 14, 15, and references therein) and thus there is no need to repeat that information at length here. 

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The site specificity of reaction can also be a state-dependent site specificity, that is, molecules incident in different quantum states react more readily at different sites. This has recently been demonstrated by Kroes and co-workers for the Fl2/Cu(100) system [66]. Additionally, we can find reactivity dominated by certain sites, while inelastic collisions leading to changes in the rotational or vibrational states of the scattering molecules occur primarily at other sites. This spatial separation of the active site according to the change of state occurring (dissociation, vibrational excitation etc) is a very surface specific phenomenon. 

First, it is possible to excite a chromophore corresponding to the active site, and detennine which modes interact with it. Second, by using UV excitation, the amino acids with phenyl rings (tryptophan and tyrosine, and a small contribution from phenylalanine) can be selectively excited [4], The frequency shifts in the resonance Raman spectrum associated with them provide infomiation on their enviromnent. 

Catalysis in a single fluid phase (liquid, gas or supercritical fluid) is called homogeneous catalysis because the phase in which it occurs is relatively unifonn or homogeneous. The catalyst may be molecular or ionic. Catalysis at an interface (usually a solid surface) is called heterogeneous catalysis, an implication of this tenn is that more than one phase is present in the reactor, and the reactants are usually concentrated in a fluid phase in contact with the catalyst, e.g., a gas in contact with a solid. Most catalysts used in the largest teclmological processes are solids. The tenn catalytic site (or active site) describes the groups on the surface to which reactants bond for catalysis to occur the identities of the catalytic sites are often unknown because most solid surfaces are nonunifonn in stmcture and composition and difficult to characterize well, and the active sites often constitute a small minority of the surface sites. 

An alternative to elucidating the active sites on a surface is to synthesize them. For example, a new catalyst for metathesis of alkanes. 

Zambelli T, Wintterlin J and ErtI G 1996 Identification of the active sites of a surface-catalyzed reaction Soienoe 273 1688-90... 

Jedrzejas, M. J., Singh, S. Brouillette, W. J. Air, G. M. Luo, M. A. 1995. Strategy for theoretical binding constant, Ki calculation for neuraminidase aromatic inhibitors, designed on the basis of the active site structure of influenza virus neuraminidase. Proteins Struct. Funct. Genet. 23 (1995) 264-277... 

Klapper, I., Hagstrom, R., Fine, R., Sharp, K., Honig, B. Focusing of electric fields in the active site of cu,zn superoxide dismutase. Proteins Struct. Pune. Genet. 1 (1986) 47-79. 

R. C. Wade, M. E. Davis, B. A. Luty, J. D. Madura, and J. A. McCammon. Gating of the active site of triose phosphate isomerase Brownian dynamics simulations of flexible peptide loops in the enzyme. Biophys. J., 64 9-15, 1993. 

For many applications, especially studies on enzyme reaction mechanisms, we do not need to treat the entire system quantum mechanically. It is often sufficient to treat the center of interest (e.g., the active site and the reacting molecules) quantum mechanically. The rest of the molecule can be treated using classical molecular mechanics (MM see Section 7.2). The quantum mechanical technique can be ab-initio, DFT or semi-empirical. Many such techniques have been proposed and have been reviewed and classified by Thiel and co-workers [50] Two effects of the MM environment must be incorporated into the quantum mechanical system. 

Example Yon can monitor improper torsion angles to determine wh ich side of a substrate m olecn le faces the active site of a protein. Select three atoms on the substrate molecule and a fourth in the active site. These atom s define an improper torsion angle. Save th is selection as a named selection. Then observe a plot of this improper torsion angle (in the Molecular Dynam ics Results dialog... 

Fig. 10.12 Sequence alignment of trypsin, chymotrypsin and thrombin (bovine). The active sites histidine, aspartic acid and serine are highlighted.

Noble M E M, R K Wierenga, A-M Lambeir, F R Opperdoes, W H Thunnissen, K H Kalk, H Groendijk and W G J Hoi 1991. The Adaptability of the Active Site of Trypanosomal Triosephosphate Isomerase as Observed in the Crystal Structures of Three Different Complexes. Proteins Structure, Function and Genetics 10 50-69. 

Molecular volumes are usually computed by a nonquantum mechanical method, which integrates the area inside a van der Waals or Connolly surface of some sort. Alternatively, molecular volume can be determined by choosing an isosurface of the electron density and determining the volume inside of that surface. Thus, one could find the isosurface that contains a certain percentage of the electron density. These properties are important due to their relationship to certain applications, such as determining whether a molecule will fit in the active site of an enzyme, predicting liquid densities, and determining the cavity size for solvation calculations. 

Molecular simulation techniques can be used to predict how a compound will interact with a particular active site of a biological molecule. This is still not trivial because the molecular orientation must be considered along with whether the active site shifts geometry as it approaches. 

Once the molecules are aligned, a molecular field is computed on a grid of points in space around the molecule. This field must provide a description of how each molecule will tend to bind in the active site. Field descriptors typically consist of a sum of one or more spatial properties, such as steric factors, van der Waals parameters, or the electrostatic potential. The choice of grid points will also affect the quality of the final results. 

FIGURE 27 19 Proposed mechanism of hydrolysis of a peptide catalyzed by carboxypeptidase A The peptide is bound at the active site by an ionic bond between its C terminal ammo acid and the positively charged side chain of arginine 145 Coordination of Zn to oxygen makes the carbon of the carbonyl group more positive and increases the rate of nucleophilic attack by water... 

Living systems contain thousands of different enzymes As we have seen all are structurally quite complex and no sweeping generalizations can be made to include all aspects of enzymic catalysis The case of carboxypeptidase A illustrates one mode of enzyme action the bringing together of reactants and catalytically active functions at the active site... 

Metallocene (Section 14 14) A transition metal complex that bears a cyclopentadienyl ligand Metalloenzyme (Section 27 20) An enzyme in which a metal ion at the active site contributes in a chemically significant way to the catalytic activity... 

Figure 11.39 summarizes the reactions taking place in this amperometric sensor. FAD is the oxidized form of flavin adenine nucleotide (the active site of the enzyme glucose oxidase), and FAD1T2 is the active site s reduced form. Note that O2 serves as a mediator, carrying electrons to the electrode. Other mediators, such as Fe(CN)6 , can be used in place of O2. 

The addition polymerization of a vinyl monomer CH2=CHX involves three distinctly different steps. First, the reactive center must be initiated by a suitable reaction to produce a free radical or an anion or cation reaction site. Next, this reactive entity adds consecutive monomer units to propagate the polymer chain. Finally, the active site is capped off, terminating the polymer formation. If one assumes that the polymer produced is truly a high molecular weight substance, the lack of uniformity at the two ends of the chain—arising in one case from the initiation, and in the other from the termination-can be neglected. Accordingly, the overall reaction can be written... 

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