A Complication Cooperative Effects

The interaction patterns described in the last paragraph are convenient means for a step-wise and additive understanding of molecular recognition processes within supramolecular assemblies. A simple interpretation of cooperative effects would merely consider the action of various attractive interactions at the same time. However, thinking within additive individual contacts silently assumes that the interaction strength is not modulated by the presence of other contacts or even other atoms, which are not involved in such contacts. Thus, the central difficulty, which is associated with the problem that the interactions within a supramolecular assembly cannot be decomposed into single contacts with individual interaction energies, is to account for these cooperative effects. 

The question now arises how all the above-mentioned phenomenologically classified interactions can be quantified. Of course, theory can yield unambiguous results if the additive decomposition of the overall interaction pattern into individual contributions is a suitable approximation in a certain case. It is, however, clear from the outset that many-body effects make a decomposition difficult, although this may be circumvented by a direct reference to the electronic wave function, which automatically adjusts to a given nuclear configuration, i.e. to a given arrangement of atoms. In Ref. [214], for example, an attempt is made to monitor the cooperative action of electrostatics in crown ether hydration via maps of the electrostatic potential. 

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The HREs and RXR-heterodimers are usually composed of two identical or nearly identical copies of the hexamer sequence AGGTCA in direct repeat. The apparently simple structure of the HREs leads to the question of how the receptors of this class can distinguish between the various HREs. Studies with artificial HRE constructs, as well as of naturally occurring HREs, indicate a complicated cooperative effect between HRE structure on the one hand and homo- or heterodimer formation of the receptors on the other hand. 

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