Competency 5.1 Chemical Thermodynamics

This considerable enhancement in redox properties may however remain chemically hidden. Several causes may converge to mask these properties. First of all electron transfer is an intermolecular act of reactivity even when thermodynamically feasible it may have to compete with very rapid intramolecular acts of deactivation (fluorescence, phosphorescence, internal conversion)99. The rate of electron transfer is given by the Rehm-Weller equation96,100... 

The understanding of the SSP process is based on the mechanism of polyester synthesis. Polycondensation in the molten (melt) state (MPPC) is a chemical equilibrium reaction governed by classical kinetic and thermodynamic parameters. Rapid removal of volatile side products as well as the influence of temperature, time and catalysts are of essential importance. In the later stages of polycondensation, the increase in the degree of polymerization (DP) is restricted by the diffusion of volatile reaction products. Additionally, competing reactions such as inter- and intramolecular esterification and transesterification put a limit to the DP (Figure 5.1). 

It is rare that a catalyst can be chosen for a reaction such that it is entirely specific or unique in its behaviour. More often than not products additional to the main desired product are generated concomitantly. The ratio of the specific chemical rate constant of a desired reaction to that for an undesired reaction is termed the kinetic selectivity factor (which we shall designate by 5) and is of central importance in catalysis. Its magnitude is determined by the relative rates at which adsorption, surface reaction and desorption occur in the overall process and, for consecutive reactions, whether or not the intermediate product forms a localised or mobile adsorbed complex with the surface. In the case of two parallel competing catalytic reactions a second factor, the thermodynamic factor, is also of importance. This latter factor depends exponentially on the difference in free energy changes associated with the adsorption-desorption equilibria of the two competing reactants. The thermodynamic factor also influences the course of a consecutive reaction where it is enhanced by the ability of the intermediate product to desorb rapidly and also the reluctance of the catalyst to re-adsorb the intermediate product after it has vacated the surface. 

This reaction is not a simple one. There are a number of intermediate chlorosilanes generated by competing reactions (10). The process is sensitive both to the thermodynamics and kinetics of the chemical reactions, and to the fluid mechanics (qv) of the gas flow in the reactor. The overall procedure involves purging the reactor with hydrogen gas, raising the temperature of the reactor, cleaning the wafers with a brief HC1 etch, and replacing the HQ with the silicon source gas. A complete process cycle can take up to an hour. 

Several studies since then have supported this suggestion, and now it is widely accepted that conformational change/structural perturbation is a prerequisite for amyloid formation. Structural perturbation involves destabilization of the native state, thus forming nonnative states or partially unfolded intermediates (kinetic or thermodynamic intermediates), which are prone to aggregation. Mild to harsh conditions such as low pH, exposure to elevated temperatures, exposure to hydrophobic surfaces and partial denaturation using urea and guanidinium chloride are used to achieve nonnative states. Stabilizers of intermediate states such as trimethylamine N-oxide (TMAO) are also used for amyloidogenesis. However, natively unfolded proteins, such as a-synuclein, tau protein and yeast prion, require some structural stabilization for the formation of partially folded intermediates that are competent for fibril formation. Conditions for partial structural consolidation include low pH, presence of sodium dodecyl sulfate (SDS), temperature or chemical chaperones. 

From the above it can be seen that the hydrolytic behavior of N2F2 is quite different from those of the other binary nitrogen fluorides discussed earlier. Difluorodiazine is strongly endothermic (12) and thermodynamically unstable (11) this makes it necessary to consider not only direct chemical attack by water but also the thermal decomposition to the elements. The reactivity of d -N2F2 toward glass (2) presents an additional question of possible competing reactions with the container walls. 

However, details of this process including the mode of urea binding, the protonation state of individual surround protein residues, and the exact identity of the nucleophile are still under debate. Cyanate also was proposed as a possible intermediate in the urease mechanism (33). Recent quantum chemical calculations and molecular dynamics simulations indicated that hydrolytic and ehmination mechanisms might indeed compete, and that both are viable reaction channels for urease (34—37). Finally, an important issue is Why does urease require nickel as the metal of choice, whereas most other metallohydrolases use zinc While it was speculated that, inter alia, the relatively rigid and stable coordination environment around the Ni(II) ions as opposed to the higher kinetic lability and lower thermodynamic stability of Zn(II) complexes might play a role (31), this fundamental question has not yet been answered. 

Categories that cause problems for this definition of chemical substance include (1) enantiomers (species containing equal amounts of two optical isomers, like I- and d-tartaric acid) (2) azeotropic mixtures (3) dissociative compounds in equilibrium (4) certain types of mixed crystals or other polymorphic compounds (e.g,d- and /-camphoroxime) (5) synthetic polymers (6) many biochemical compounds (7) systems that are not in "pure" thermodynamic equilibrium and (8) isotopes. In each case, pragmatic decisions have to be made, as the notion of pure substance cannot be essen-tialized. There are no competing definitions of "pure substance" that can avoid the need for "inspired adhoccery" to deal with difficult cases. 

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