Active Site Models Experimental Considerations

Typically, the full amino acid is replaced by a simplified ligand which only models the metal-ligand interaction. For example, histidine is replaced by 

Coordination of the active site metal by water molecules and substrates is obviously much more variable and the X-ray structure may be of little assistance. In order to determine experimentally the orientation of the substrate, a crystal would need to be grown with the substrate bound. Notwithstanding the problems of obtaining X-ray quality crystals in the first place, by its very nature, the enzyme will attempt to convert the substrate to product and capturing a bound state may not be possible. However, many reactions require an additional reactant—say a molecule of O2—and thus the substrate-bound form may remain stable under anaerobic conditions. The structure of catechol dioxygenase with substrate bound has been determined in this way [36]. 

Extended X-ray absorption fine structure (EXAFS) spectroscopy is a powerful complementary technique since single crystals are not required. EXAFS gives element-specific information and has a higher resolution than single crystal diffraction albeit restricted to a range of a few Angstroms from the 

Another issue about active site models concerns the possible roles played by groups not directly attached to the metal centre(s), and which therefore may not figure in the model built for the calculations, but which are nevertheless crucial to the activity of the enzyme. Obviously, there is a big problem if these roles are not recognised. However, in cases where, say, site directed mutagenesis experiments have revealed a critical role for some group or groups, the modeller needs to give serious consideration to how to in- 

Having collected the available experimental data one tries to construct what looks like a reasonable model. Small ligands such as water or dioxygen can obviously be fully treated but many of the other ligands will have to be truncated [41]. For amino-acid side chains, there is usually an obvious choice. For example, histidine can be replaced by imidazole, methionine by dimethyl sulfide, tyrosine by phenol, cysteine by methylthiol and so on. 

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The SCR catalyst is considerably more complex than, for example, the metal catalysts we discussed earlier. Also, it is very difficult to perform surface science studies on these oxide surfaces. The nature of the active sites in the SCR catalyst has been probed by temperature-programmed desorption of NO and NH3 and by in situ infrared studies. This has led to a set of kinetic parameters (Tab. 10.7) that can describe NO conversion and NH3 slip (Fig. 10.16). The model gives a good fit to the experimental data over a wide range, is based on the physical reality of the SCR catalyst and its interactions with the reacting gases and is, therefore, preferable to a simple power rate law in which catalysis happens in a black box . Nevertheless, several questions remain unanswered, such as what are the elementary steps and what do the active site looks like on the atomic scale ... 

Models for human and pig COMT are easy to build using the experimental structure of the rat COMT, due to the high degree of homology between the rat, human, and pig COMT enzymes (Figure 4). The active sites are especially well conserved—the few differences in the active-site residues are collected in Table 2. The kinetic data show that the Km values of common substrates for rat and human COMT are very similar. Pig COMT shows, however, a considerably higher Km value for catechol [46]. The same difference is apparent for inhibitors represented by the K values in Table 1. 

Amorphous aluminosilicates represent a wide variety of systems with surfaces whose states are strongly dependent on the biography of a system. The very specificity of the amorphous structures and the more limited possibility of application of physical methods to their study results in much poorer knowledge about the structures of the amorphous aluminosilicate surfaces than in the case of crystalline systems. This makes quantum-chemical treatment considerably more qualitative in this case. Cluster models of active sites appear here mainly a priori and experimentally independent and provide, to some extent, an additional way of studying such systems. 

There is a considerable difference between the number of active sites as determined from the limiting number of spins 7 X 1014/sq. meter, and from the saturation composition. This can be partly explained by the magnitude of the experimental errors involved. Some prohibiting mechanism may exist which has not been taken into account in the model. Thus, use of a site for cation formation may render inactive a certain number of neighboring sites. 

Some aspects related to catalysts characteristic and behaviour will be treated such as determination of metal surface area and dispersion, spillover effect and synterisation. A detailed description of the available techniques will follow, taking in consideration some aspects of the gas-solid interactions mechanisms (associative/dissociative adsorption, acid-base interactions, etc.). Every technique will be treated starting from a general description of the related sample pretreatment, due to the fundamental importance of this step prior to catalysts characterisation. The analytical theories will be described in relation to static and dynamic chemisorption, thermal programmed desorption and reduction/oxidation reactions. Part of the paper will be dedicated to the presentation of the experimental aspects of chemisorption, desorption and surface reaction techniques, and the relevant calculation models to evaluate metal surface area and dispersion, energy distribution of active sites, activation energy and heat of adsorption. 

The computational studies on surface chemistry of Co catalysts have offered significant supports to the investigation of FTS on Co catalysts. However, the work is far from decent. As the experimental studies indicated, surface reconstruction and phase transition were certain to take place under practical FTS conditions. The theoretical studies about surface reconstruction and phase transition of Co catalysts, however, are fairly rare. In addition, cluster models were less studied in the previous theoretical work compared to slab models. However, practical catalytic reactions do not always happen as proposed in ideal plane models, nor the active sites distribute homogeneously on the surface. The investigation on cluster models is acting a crucial role in the study of heterogeneous catalysis. Accordingly, more considerations on surface reconstruction, phase transition, and cluster models should be taken into account in future work. 

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