Activated complexes, energy levels structure

The use of the symbol E in 5.1 for the environment had a double objective. It stands there for general environments, and it also stands for the enzyme considered as a very specific environment to the chemical interconversion step [102, 172], In the theory discussed above catalysis is produced if the energy levels of the quantum precursor and successor states are shifted below the energy value corresponding to the same species in a reference surrounding medium. Both the catalytic environment E and the substrates S are molded into complementary surface states to form the complex between the active precursor complex Si and the enzyme structure adapted to it E-Si. In enzyme catalyzed reactions the special productive binding has been confussed with the possible mechanisms to attain it lock-key represents a static view while the induced fit concept... 

Actual catalysis is a chemical phenomenon, since the intimate mechanisms of catalytic transformations are determined by chemical interaction of reagents with the catalyst, atomic structure, and the energy of formed intermediate active complexes [5], It obviously is the world of molecular chemistry of the interface phenomena, kinetics, and mechanisms of catalytic transformations at a molecular level. 

Potential energy surfaces or profiles are descriptions of reactions at the molecular level. In practice, experimental observations are usually of the behaviour of very large numbers of molecules in solid, liquid, gas or solution phases. The link between molecular descriptions and macroscopic measurements is provided by transition state theory, whose premise is that activated complexes which form from reactants are in equilibrium with the reactants, both in quantity and in distribution of internal energies, so that the conventional relationships of thermodynamics can be applied to the hypothetical assembly of transition structures. 

For some reactions, especially those involving large molecules, it might be difficult to determine the precise structure and energy levels of the activated complex. In such cases, it can be useful to phrase the transition-state theory result for the rate constant in thermodynamic terms. It does not bring any new information but an alternative way of interpreting the result. This formulation leads to an expression where the preexponential factor is related to an entropy of activation that, at least qualitatively, can be related to the structure of the activated complex. We will encounter the thermodynamic formulation again in Chapter 10, in connection with chemical reactions in solution, where this formulation is particularly useful. 

DeVault and Chance assumed that the energy levels of cytochrome and chlorophyll were properly matched to begin with, perhaps as a result of extensive natural selection on the structures of both molecules thus, no prior rearrangement of donor and recipient molecules is necessary. Bennett and Jones made explicit allowance for this prior adjustment of energy levels in cytochrome c and a, by assuming that the initial c/a complex may have to undergo an activation step to match energy levels before electron transfer can occur ... 

Fig. 18. Experimental d orbital energy level diagram for resting metapyrocatechase, its substrate complex, and the enzyme-substrate-azide ternary system (top). The spectroscopically effective structural mechanism derived from this energy diagram for the Fe(II) active site in metapyrocatechase is also shown (bottom).

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