Chemical reference reaction

Source From R. A. Alberty, Arch. Biochem. Biophys. 389, 94 109 (2001). Copyright Academic Press. Note The apparent equilibrium constants for these reactions do not depend on ionic strength because the equilibrium constants for the chemical reference reactions and acid dissociation do not depend on ionic strength. 

This result is reasonable because the chemical reference reaction shows that 2 hydrogen ions are bound. This is affected in the neighborhood of pH 6.2 by the binding of a hydrogen ion by bicarbonate and malate. As pH 9 is approached, the dissociation of the hydrogen ion from bicarbonate begins to have an effect. 

Citrate is a key intermediate of the tricarboxylic acid (TCA) cycle, also known as the Krebs cycle, in the central metabolism of cells. (The set of reactions of the TCA cycle will be considered in some detail in Chapter 6.) One reaction in the cycle is the combination of oxaloacetate (OAA) and the acetyl group from acetyl coenzyme A (ACCOA), in the presence of H2O, to form citrate (CIT), thiol coenzyme A (COASH), and hydrogen ion (H+). The chemical reference reaction for this aldol condensation-hydrolysis reaction catalyzed by citrate synthase is ... 

The standard Gibbs free energy for the chemical reference reaction for pyruvate dehydrogenase is computed... 

It is evident that very different types of bonds are split. It is important to remember that these apparent equilibrium constants at 298.15 K and ionic strength 0.25 M are a consequence of the equilibrium constants of chemical reference reactions and p/fs of reactants. Any attempt to interpret these K values has to take into account these two different types of effects. The next two sections explore these effects in the hydrolysis of phosphate compounds. 

It is also possible to choose a chemical reference reaction that involves selected solute species ... 

There are significant differences in the control experiments that are possible in each of these systems. Before the quantifier bio- can be applied, the possibility of abiotic alteration of the substrate during incubation must be eliminated or taken into consideration. Only the first design lends itself readily to this control. For experiments using cell suspensions, the obvious controls are incubation of the substrate in the absence of cells or using autoclaved cultures. Care should be exercised in the interpretation of the results, however, since some reactions may apparently be catalyzed by cell components in purely chemical reactions. The question may then legitimately be raised whether or not these are biochemically mediated. Two examples are given as illustration of apparently chemically mediated reactions, which have been referred to in Chapter 1 ... 

A baseline potential pulse followed each current pulse in order to strip extracted ions from the membrane phase and, therefore, regenerated the membrane, making it ready for the next measurement pulse. This made sure that the potentials are sampled at discrete times within a pulse that correspond to a 6m that is reproducible from pulse to pulse. This made it possible to yield a reproducible sensor on the basis of a chemically irreversible reaction. It was shown that the duration of the stripping period has to be at least ten times longer than the current pulse [53], Moreover the value of the baseline (stripping) potential must be equal to the equilibrium open-circuit potential of the membrane electrode, as demonstrated in [52], This open-circuit potential can be measured prior to the experiment with respect to the reference electrode. 

As such, their energetics should be better described by quantum chemical models which are simple enough for routine application than the energetics of hydrogenation in the absence of a reference reaction (see discussion earlier in this chapter). 

Until this point, we have focused on cases in which we could neglect chemical bond formation between the sorbate and materials in the solid phase. However, at least two kinds of surface reactions are known to be important for sorption of some chemicals (referred to as chemisorption). Simply, some organic substances can form covalent bonds with the NOM in a sediment or soil (see Fig. 9.2) other organic sor-bates are able to serve as ligands of metals on the surfaces of inorganic solids (Fig. 11.le). We discuss these processes below. 

Table 9.1 Chemical modification reactions referred to in this text ... 

Most commonly, correlations are made to chemical constants that are defined by the effect of substituents on a reference reaction. They are usually designated o and are applied to QSARs in the form of Hammett s equation or its various extensions. Alternatively, a descriptor can be a property of a substrate molecule that is available, is readily measurable, and/or can be calculated by independent means, such as octanol/water partition coefficients. Despite their numerous successful applications in QSAR studies, experimentally determined o constants also have some disadvantages. They are available only for a limited set of substituents and are not of very good quality for uncommon functional groups. As an alternative, the use of quantum-chemical parameters may be a solution. 

Chemical oxidation reactions and radical-induced hydrophobic-to-hydrophilic aging processes tend to increase the water solubility of OAs and, therefore, are thought to enhance the activity of atmospheric OAs as cloud condensation nuclei (CCN). As discussed by Gysel et al. (2004), at 75-90% of relative humidity (RH) the inorganic fraction dominates the water uptake (59-80%). Nevertheless, under the same conditions of RH, between 20% and 40% of total particulate water is associated with water-soluble organic matter. More data concerning the multiphase aerosol and cloud processes, as well as the chemical reactivity of carbonaceous aerosol components, have been compiled in the reviews of Jacobson et al. (2000), Kanakidou et al. (2005), and Poschl (2005) (and references therein). 

This set of chemical reactions is not unique for example, the reference reaction can be written with H2P04. Additional reactions are involved if Mg2 + or other cations are bound reversibly by these species. The conservation matrix for this... 

Many reactions that fit the definition of an organic chemical redox reaction (Section 17.1) have already been presented in Chapters 1-16. The presentation of these reactions in various other places—without alluding at all to their redox character—was done because they follow mechanisms that were discussed in detail in the respective chapters or because these reactions showed chemical analogies to reactions discussed there. Tables 17.3 and 17.4 provide cross-references to all oxidations and reductions discussed thus far. 

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