Substrate, accessible surface area

Fig. 5.5 Relationship between Gibbs free energy and accessible surface area of the substrates. Substrate amino acids are indicated as one-letter code. Boxed numbers show the slope of the straight line (cal/mol-A2).

Cellulosic substrates contain pores or voids of different sizes [10,12,13]. Pore structure determines the internal accessible surface area of a cellulose substrate and thus affects its accessibility or reactivity. 

The cellulase complex diffuses through the pore system to the microfibrils, attacks the cellulose chains and hydrolyses each chain to the end. The diflerences in the efficacy of cellulases on various fibres are dependent on number of factors such as the amounts of non-cellulosic wood pulp-derived matter, the degree ol polymerisation, the type and degree of crystallinity, and the type and number of chemical substitutions to the cellulose [27-30]. Key features for the cellulose substrate are crystallinity, accessible surface area and pore dimensions [31 ]. Variation of any of these factors, e.g., structural changes of cellulose substrate by pre-treatments, will influence the course of the entire degradation process [32, 33]. 

Shin and Kim [39] used the accessible surface area of essential amino acid residues of the amine pyruvate aminotransferase and various amino donors and acceptors to explore the active site structure. Their results suggested a model consisting of two pockets, one large and the other small. The size difference between the binding pockets and the strong repulsion for a carboxylate in the small pocket were key determinants of the substrate specificity and stereoselectivity. 

The factors so far examined have ignored the contribution of the solvent entropy to the thermodynamic balance of association. If water molecules that surround the enzyme and substrate are released upon binding this may make a favourable contribution to the free energy of binding if the water molecules released are less restricted in the bulk solvent. The hydrophobic energy of enzyme-substrate complexes is proportional to the loss of accessible surface area that occurs upon binding. 

For an atom in the enzyme or the substrate to interact with the solvent it must be able to form Van der Waals contact with water molecules. The accessible surface area of an atom is defined as the area on the surface of a sphere, radius R on each point of which the centre of a solvent molecule can be placed in contact with the atom without penetrating any other atoms of the molecule (Fig. 12). R is the sum of the Van der Waals radii of the atom and solvent molecule [27]. There is a linear relationship between the solubility of hydrocarbons and the surface area of the cavity they form in water [28]. It has been estimated that the hydrophobicity of residues in proteins is 100 J/mole/A of accessible surface area [29]. The surface tension of water is 72 dynes/cm so to form a free surface area of water of 1 A costs 435 J/mole/A. The implication is that the free energy of cavity formation in water to receive the hydrophobic group is offset by favourable interactions (dispersion forces) between the solute and water. 

From the above results on CALB activity as a function of particle size for polystyrene and PMMA resins, we believe %-surface area occupied by CALB is a critical factor that can be used to improve immobilized CALB activity. Increased %-accessible surface area will increase the probability of collisions between substrates and CALB. As %-accessible surface area for CALB increased for PMMA resins a corresponding increase in polyester synthesis reaction rates was observed (see above). CALB immobilized on styrenic particles of variable size showed little differences in both %-accessible surface area and polyester synthesis catalyst activity. The potential benefit of decreasing bead particle size is to decrease diffusion constraints that lead to productive collisions between enzyme and substrate. However, for polystyrene resins, as particle size decreased, the percent of resin area in which reactions can occur does not change. In contrast, decreasing PMMA particle size dramatically... 

In our glycine 76 study (Okoniewska et al., 2000), this position was substituted with alanine, valine, and serine. These amino acids differ in their van der Waals volumes, accessible surface areas, polarities, and allowable energy levels on Ramachandran plots for individual amino acids. Rate constants for the activation process were calculated for the mutants and the wild-type enzymes at pH 1.1, 2.0, and 3.0. Samples were taken at different activation times, quenched, and the amount of pepsin formed was determined with synthetic substrate I. Activation rate constants presented in Table 15.5 corresponded to first-order reaction constants. All the mutants activated at rates slower than those for the wild-type, regardless of amino acid size and polarity. At all pH conditions, the activation reactions were slowest for valine and serine mutants, which had comparable reaction rates. The alanine mutant activated more slowly than did the wild-type but was faster than the other two mutants. 

In most cases, BBSs malce use of biofilms attached to the electrodes to achieve the bioelectrocatalysis. Thus, the electrode plays a dual role, as substrate for biofilm formation as well as suitable surface for electron exchange with the cells or terminal electron shuttles. Consequently, its microbially accessible surface area -... 

We showed that these mesoporous silica materials, with variable pore sizes and susceptible surface areas for functionalization, can be utilized as good separation devices and immobilization for biomolecules, where the ones are sequestered and released depending on their size and charge, within the channels. Mesoporous silica with large-pore-size stmctures, are best suited for this purpose, since more molecules can be immobilized and the large porosity of the materials provide better access for the substrates to the immobilized molecules. The mechanism of bimolecular adsorption in the mesopore channels was suggested to be ionic interaction. On the first stage on the way of creation of chemical sensors on the basis of functionalized mesoporous silica materials for selective determination of herbicide in an environment was conducted research of sorption activity number of such materials in relation to 2,4-D. 

It is often found that the ratio R (measured, for instance, by gas adsorption methods) of actual metal surface area accessible to the gas phase, to the geometric film area, exceeds unity. This arises from nonplanarity of the outermost film surface both on an atomic and a more macroscopic scale, and from porosity of the film due to gaps between the crystals. These gags are typically up to about 20 A wide. However, for film thicknesses >500 A, this gap structure is never such as completely to isolate metal crystals one from the other, and almost all of the substrate is, in fact, covered by metal. In practice, catalytic work mostly uses thick films in the thickness range 500-2000 A, and it is easily shown (7) that intercrystal gaps in these films will not influence catalytic reaction kinetics provided the half-life of the reaction exceeds about 10-20 sec, which will usually be the case. 

Many silane coupling agents can be applied to substrates by volatilization in an enclosed chamber under heat or vacuum. In this approach, the substrate is placed within the chamber in a fashion to allow for vapor phase molecules to access all areas that are to be derivatized. This method is commonly used for silanizing glass slides or substrates that are difficult to suspend in a silane solution. Slides are often placed in racks within the chamber and all surfaces get modified... 

Specific, surface confined reactions not only directly involve catalysis but also the built-up of sdf-assembled multilayers (see Fig. 9.1 (3)) with co-functionalities for more complex (bio-) catalytic systems such as proteins or the directed deposition of active metals. Furthermore, SAM on flat substrates can be used for the study and development of e.g. catalytic systems, but are not useful for large scale applications because they have very limited specific surface. Here, nanoparticle systems covered with 3D-SAMs are the ideal solution of combining the advantages of high surface area, defined surface composition and accessibility of proximal active catalytic centers. 

Despite the high specific surface areas, the amount of accessible catalyst remains low due to the limited thickness of the porous catalytic layer dictated by considerations such as the adhesion to the substrate. The susceptibility of the fine channels to blockage with solid impurities or deposits formed in the reaction, together with the problems of integrating connections with the external macroenvironments and ensuring uniform gas distribution between the individual channels, a prerequisite for numbering up, represent further questions that have to be resolved for the industrial application of microreactors to become practicable. 

The study of both heterogeneous catalysts and enzymes is dominated by the concept of the active site. Specifically, in enzymes the active site is known to represent only a small portion of the large protein molecule that is the enzyme [6], The active site may lie at or near the surface, but it may also be buried in an active site groove or crevice that limits access of all but the desired substrate. Clearly, the total surface area of the protein is significantly larger than that of the active site. 

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