Dead-end species

Figure 26 Proposed mechanism of nitrite reduction to NO by cdj. (A B) reductive activation of resting (inactive enzyme) and tyrosine displacement (not shown) (B C) nitrite binding (C D) protonation of nitrite complex (D E) cleavage of N-0 bond and elimination of H2O (E F) intramolecular iron oxidation (valence isomerization) (F G H C and F G I C) redox reactions involving heme c and heme cl nitrosyl complex followed by rapid dissociation of NO ( ) enzyme gets trapped in a "dead end" species in the absence of reducing substrate or nitrite. Adapted with permission from Ref (21). Copyright 2014 American Chemical Society.

Different mechanisms can occur according to intermediates which are on the pathway between N and D, or which are dead-end species. Mechanism V describes the process when intermediates are on the pathway from N to D ... 

With four-state mechanisms, diagnostic equations have also been obtained. For example, when X and X2 are dead-end species (mechanism VII), a relation between experimental parameters must be expected such that... 

In cytochrome c dead-end species were observed (mechanism VI). These abortive intermediates were interpreted as incorrectly folded states (Ikai and Tanford, 1971, 1973) of the polypeptide chain that cannot progress by direct folding to the native state, but must necessarily unfold to the state D (completely unfolded polypeptide chain) before refolding. Probably different incorrectly folded states could be formed from an unfolded polypeptide chain, and folding is the result of a kinetic competition between the correct kinetic pathway(s) which drive(s) the protein to the native form and the incorrect pathways which lead to incorrectly folded species. The occurrence of abortive intermediates was also reported for j8-lactoglobulin (Tanford, 1972) where both and X2 intermediates were found on a dead-end pathway. In mechanisms III, VI, and VII, it was assumed that the intermediates are never populated at equilibrium outside the transition zone. 

A well-understood catalytic cycle is tliat of the Wilkinson alkene hydrogenation (figure C2.7.2) [2]. Like most catalytic cycles, tliat shown in figure C2.7.2 is complex, involving intennediate species in tire cycle (inside tire dashed line) and otlier species outside tire cycle and in dead-end patlis. Knowledge of all but a small number of catalytic cycles is only fragmentary because of tire complexity and because, if tire catalyst is active, tire cycle turns over rapidly and tire concentrations of tire intennediates are minute thus, tliese intennediates are often not even... 

It is important to note, however, that beyond a = 1/2 by no means all of the material will be combined into infinite molecules. For example, in spite of the favorable probability of branching, a chain selected at random may be terminated at both ends by unreacted functional groups. Or it may possess a branch at only one end, and both of the succeeding two chains may lead to unreacted dead ends. These and other finite species will coexist with infinite networks as long as l/2[Pg.353]

The isomerization barrier of 15.0-20.0 kcal mol-1 (AG ) can be considered to be large enough to allow isolation and characterization of bis(q3-<2 /),A- nms-dodecatrienediyl-Nin stereoisomers of 7b41 as reactive intermediates in the stoichiometric cyclotrimerization process. Furthermore, the trans orientation of the two allylic groups gives rise to an insurmountable barrier for reductive elimination for these cases, which prevents these species from readily leaving the thermodynamic sink via a facile reductive elimination. The isolated intermediates clearly constitute dead-end... 

One key feature of the model is that the [Fe2(0H)S03]3+ species is a dead-end intermediate with respect to the overall redox process. The actual redox reaction consists of only two steps ... 

Rubber appears to be a metabolic dead-end because there have been no findings of enzymes capable of breaking down the rubber in latex. The exact termination reaction of the rubber polymerization is not known. Different end-groups have been detected by NMR in rubber purified from a range of species, indicating that molecule dephosphorylation and release may involve esterification, cyclization, or hydrolysis [262]. 

Exceptions exist to this tendency for ready incorporation of the initial transformation products of xenobiotic compounds into a common pathway. First, occasionally a product is formed which is unreactive in subsequent steps in a particular microorganism. Such partially degraded compounds have been referred to as dead-end metabolites (Knackmuss, 1981). An example of this is the 5-chloro-2-hydroxy-muconic acid semialdehyde produced by the meta cleavage of 4-chlorocatechol by a particular pseudomonad species ... 

The structural homogeneity of the alkaloids from Pauridiantha can also be connected to a glucolysis step occurring at a late stage of the biosynthetic evolution. As a consequence, glucoalkaloids are abundant in most Pauridiantha species, but their structure remains primitive, e.g., they are close to that of strictosidine, the first of the alkaloids formed in vivo. This biosynthetic dead end can... 

No examples of consumption of adult representatives of rapa whelk by fishes or other hydrobionts are known only its planktonic larvae may be consumed by planktivorous fishes. Rapa whelk is an active predator that consumes valuable representatives of benthos. It inserts significant changes into the structure of bottom biocoenoses and often is the dominating species of the bottom communities being itself an ecological dead-end. Therefore, its commercial extraction is extremely important for reducing the pressure on bivalve mollusks. 

The effect of a "dead-end" side reaction such as that to the tetracarbonyl acyl will be examined in detail in Section 8.7. Suffice it for now to say that accumulation of cobalt in the form of this inactive species reduces the rate, which, nevertheless, still remains given by an equation of the form of eqn 6.12. 

In natural systems, the value of the pH is strongly influenced by the carbonate equilibria reactions. The 063 species of these reactions will pair with a cation, thus guiding the equilibrium reactions into a dead end by forming a precipitate. For example, the complete carbonate equilibria reactions are as follows ... 

Let us digress for a moment from our discussion of the saturation pH in order to find the dead end cation for the carbonate system equilibria. Several of these cations can possibly pair with the carbonate. The pairing will be governed by the value of the solubility product constant, A small value of the means that only small values of the concentration of the constituent species are needed to form a product equal to the This, in turn, means that solids with smaller will easily form the solids. Thus, of all the possible cations that can pair with the carbonate, the one with the smallest K, value is the one that can form a dead end for the carbonate equilibria reactions. Mg forms MgCOs with a K,p of 10. Ca forms CaCOs with a K,p of 4.8(10 ). Table 11.3 shows other carbonate solids with the respective solubility product constants. 

Proton condition—A condition of balance between species that contain the proton and counteracting species that do not contain the proton at a particular end point such as the dead end. 

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