Conformational rearrangements

The basic chemical description of rare events can be written in terms of a set of phenomenological equations of motion for the time dependence of the populations of the reactant and product species [6-9]. Suppose that we are interested in the dynamics of a conformational rearrangement in a small peptide. The concentration of reactant states at time t is N-n(t), and the concentration of product states is N-pU). We assume that we can define the reactants and products as distinct macrostates that are separated by a transition state dividing surface. The transition state surface is typically the location of a significant energy barrier (see Fig. 1). 

With simple crowns, complex formation may involve various degrees of inclusion of the guest into the cavity of the crown and a conformational rearrangement of the crown is almost always necessary for strong complexation to occur. This will normally involve a redirection of the donor electron pairs on complex formation so that their final orientations optimize a particular host-guest interaction. 

Shchori et al. (1971, 1973) have pointed to the remarkable similarity ( a = 12.6 + 0.7 kcal mol-1) of the activation energies for decomplexation of dibenzo-18-crown-6 [11] and substituted derivatives (Table 20). They too were of the opinion that the activation energy for decomplexation reflects the energy required for a conformational rearrangement. The fact that different crown ethers give different a values can also be explained by this model. 

At ordinary pressure all the ionizable groups have their specific pK values and are present in ionized states according to these values. When pressure increases, we can expect all pK values to change, whereby the overall ionized state of the protein is changed. The whole hydration sheet may also be changed around the protein and conformational rearrangements may occur. This fact indicates that the volume of a protein may be very pressure-dependent. 

The speed of the reduction by the solution radical generated in the pulse radiolysis experiment is also consistent with this proposal conformational rearrangements are highly unlikely on the microsecond time scale. 

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