Active sites, physicochemical

In short, the space within the active site and the orientation of the substrate are both important determinants for the positional specificity of plant LOXs and are modified by additional factors such as substrate concentration, the physicochemical state of the substrate, pH, or temperature (Lopez-Nicolas and others 2000). However, it should be stressed that for other LOXs regiospecificity may be determined in a more complex manner. 

Fig. 5.5 Putative interactions of the cocrystallized selective Cox2 ligand SC-558 with its active site, assuming a neutral sulfonamide group - the state used to assign pharmacophore feature flags by the used software. Dotted lines stand for hydrogen bonds, the other residues being responsible for hydrophobic contacts. From a physicochemical point of view, an ionized SO2 NH involved in a salt bridge with Arg 513 and hydrogen bonding to the other tautomer of His 90 would make more sense.

In starting a residue analysis in foods, the choice of proper vials for sample preparation is very important. Available vials are made of either glass or polymeric materials such as polyethylene, polypropylene, or polytetrafluoroethylene. The choice of the proper material depends strongly on the physicochemical properties of the analyte. For a number of compounds that have the tendency to irreversible adsorption onto glass surfaces, the polymer-based vials are obviously the best choice. However, the surface of the polymer-based vials may contain phthalates or plasticizers that can dissolve in certain solvents and may interfere with the identification of analytes. When using dichloromethane, for example, phthalates may be the reason for the appearance of a series of unexpected peaks in the mass spectra of the samples. Plasticizers, on the other hand, fluoresce and may interfere with the detection of fluorescence analytes. Thus, for handling of troublesome analytes, use of vials made of polytetrafluoroethylene is recommended. This material does not contain any plasticizers or organic acids, can withstand temperatures up to 500 K, and lacks active sites that could adsorb polar compounds on its surface. 

The basic question of mimetic catalysis is the determination of physicochemical properties of enzymes to be simulated in the synthesized biomimic in accordance with the reaction modeled. Firstly, let us try to answer one of the key questions that arise in biomimic construction how important is it to reach the enzymatic specificity in the synthesis of their analogs To put it another way, should the dynamic (tertiary) structure of the enzyme responsible for the selectivity control mechanism be simulated by active site protection from competitive admixtures This feature of the enzymes distinguishes them from usual catalysts. 

Let us discuss the questions outlined in more detail using the example of conjugated substrate oxidation with hydrogen peroxide. Hydrogen peroxide concentration in the reaction mixture is reduced in the course of the reaction, followed by the change of the key active sites (H02 and OH radical) and, correspondingly, the physicochemical situation is changed not for the benefit of selective transformation of the raw material. 

Physicochemical methods, i.e. adsorption of probe molecules followed by varied analytical techniques (gravimetry, chromatography, calorimetry, spectroscopic techniques, etc.) are currently used for estimating more precisely the concentration of the potential active sites.[34 36] However, very few methods are well adapted for this purpose most of the methods employed for the characterization of the acidity of solid catalysts lead to values of the total concentrations of the acid sites (Brpnsted + Lewis) and to relative data on their strength, whereas few of them discriminate between Lewis and Brpnsted acid sites. It is however the case for base adsorption (often pyridine) followed by IR spectroscopy, from which the concentrations of Brpnsted and Lewis sites can be estimated from the absorbance of IR bands specific for adsorbed molecules on Brpnsted or Lewis sites. 

---