Dimerization
of cyclodextrin (CD) molecules is an elementary step
in the construction of CD-based nanostructured materials. Cooperative
binding of CD cavities to guest molecules facilitates the dimerization
process and, consequently, the overall stability and assembly of CD
nanostructures. In the present study, all three dimerization modes
(head-to-head, head-to-tail, and tail-to-tail) of β-CD molecules
and their binding to three isoflavone drug analogues (puerarin, daidzin,
and daidzein) were investigated in explicit water surrounding using
molecular dynamics simulations. Total and individual contributions
from the binding partners and solvent environment to the thermodynamics
of these binding reactions are quantified in detail using free energy
calculations. Cooperative drug binding to two CD cavities gives an
enhanced binding strength for daidzin and daidzein, whereas for puerarin
no obvious enhancement is observed. Head-to-head dimerization yields
the most stable complexes for inclusion of the tested isoflavones
(templates) and may be a promising building block for construction
of template-stabilized CD nanostructures. Compared to the case of
CD monomers, the desolvation of CD dimers and entropy changes upon
complexation prove to be influential factors of cooperative binding.
Our results shed light on key points of the design of CD-based supramolecular
assemblies. We also show that structure-based calculation of binding
thermodynamics can quantify stabilization caused by cooperative effects
in building blocks of nanostructured materials.