Free energy profiles standard states

Figure 30(a) concerns the EE mechanism for the reaction O + 2 e = R. The solid curve represents the standard free energy profile pertaining to the standard potential E° of the redox couple O/R. In this case, the energy levels of the initial and the final state are equal by definition. Well... 

Attention is devoted to the dependence of electrochemical reactivity upon the thermodynamic driving force. If the free-energy profiles for the precursor and successor states (Fig. lA, 12.3.7.2) can be represented as identically shaped parabolas, then the (intrinsic) cathodic-transfer coefficient, a, as defined by Eq. (1) in 12.3.7.2, will depend upon the standard cathodic overpotential —(E — E°) according to - ... 

Construction of the free energy profile (Figure 6.7) for the whole reaction required a choice of thermodynamic standard state, since bimolecular and unimolecular rate constants were being compared. This was taken as 40 pM, the physiological concentration of the triose phosphates. 

Figure 7.9. Free energy profile obtained from global analysis of racemization progress curves at pH 8.9. Standard state is 5 mM alanine.

Suppose also that the standard free energy profiles along the reaction coordinate have the parabolic shapes shown in Figure 3.3.2. The upper frame of that figure depicts the full path from reactants to products, while the lower frame is an enlargement of the region near the transition state. It is not important for this discussion that we know the shapes of these profiles in detail. 

Fio. 10. Gibbs free energy profiles for the formation of tyrosyl adenylate and pyrophosphate, as defined in Eq. (2), by wild-type (energy levels in dashed lines) and mutant (energy levels in solid lines) tyrosyl-tRNA synthetases, using standard states of 1 W for tyrosine, ATP, and pyrophosphate. [Reprinted with permission from Ref. (25/).]... 

The energetics of an enzyme-catalyzed reaction is usually discussed in terms of a free energy profile this is a diagram showing the relative free energy levels of all enzyme-reactant complexes and the transition states for conversion between them, at some chosen set of standard conditions (Lumry, 1959,1995). 

The problems with constmction of free energy profiles for enzyme-catalyzed reactions is the choice of standard states (Cleland Northrop, 1999). The standard states are, in general, unit concentrations, using whatever unit is being used to evaluate rate constants. For this reason, the concentration terms are usually omitted from thermodynamic equations (Purich Allison, 2000). 

As outlined above, temperature analysis may be successfully performed if the unimolecular and bimolecular rate constants are known if the rate constants are known, and if we choose a standard state, a free energy profile can be drawn. Thus, the above thermodynamic analysis for a monosubstrate reaction shows that the meaningful application of a k/T) against /T plots requires that the individual uni- and bimolecular microscopic rate constants be separated. 

Gj is the classical standard-state free energy of reactants at temperature T. The free energy of activation profile is given as... 

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