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The term "quasithermodynamic," rather than simply "thermodynamic," is appropriate because the activated complex is a mathematical construct rather than a stable or metastable entity. The transition "state" corresponds to an ensemble of systems that has all degrees of freedom of the entire system except one, the reaction coordinate, which is fixed. Protein motions and dynamic effects are included in Eq. 1a, even though the language is quasithermodynamic. Readers should not be confused by the fact that some workers [e.g., (106)] use the word "dynamics" to refer to deviations of the transmission coefficient from unity; in this article, dynamics is used in the more general sense of atomic and molecular motions.
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Focusing on NACs has the practical advantage that their probability of occurring can sometimes be estimated by molecular dynamics simulations with a molecular mechanics force field and may not require a quantum mechanical calculation [but see (63, 130)]. However, there is an inherent difficulty in attempting to draw conclusions from NACs in that there does not seem to be a way of uniquely determining the NAC (e.g., unlike the transition state, it is not a stationary point on the surface, nor does it satisfy a variational criterion). As mentioned in the description of chorismate mutase catalysis (63, 64), an essential conformational change of the substrate is induced by the enzyme as a contribution to lowering the activation free energy. This shows that the phenomenon emphasized in the NAC concept can be very important in some cases. However, the conclusion in (65) that almost the entire barrier lowering Is due to the conformational, change is in disagreement with other analyses (60, 64). For another example, Shurki et al. (67) designed a simulation to evaluate the free energy effect of restricting the reactant conformational space for haloalkane dehalogenase and found a contribution of only 1 to 2 kcal/mol, relative to the full 7 kcal catalytic barrier lowering. The transition-state approach is general enough to include conformational-effects when they are important, and it provides a unified framework that is also valid when conformational effects are negligible.
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We thank A. S. Mildvan, G. A. Petsko, and R. L. Schowen for helpful comments on the manuscript. M.K. and D.G.T. thank A. Kuppermann for many discussions concerning reaction rate theory; the idea of doing this review first arose in a discussion at his 75th birthday symposium in which both of us participated. One of the authors (M.K.) thanks D. Case for illuminating discussions of reaction rate theory, which took place about 30 years ago. This work was supported in part by grants from the NSF and NIH. M.G.-V. thanks the Fulbright Commission and the Government of Catalonia for a scholarship.
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