Formation of the various types of daisy chains constructed by modified cyclodextrin depending on the bond angle of the modified part linked to α-cyclodextrin

Inclusion complexes (daisy chains) have been widely used in supramolecular chemistry and molecular machines. To develop new molecular machines, it is important to control the inclusion complex structures constructed using modified cyclodextrins (mCDs). To investigate the influence of the bond angle of the modified part linked to the CD on the inclusion complex structures, coarse-grained Brownian dynamics (BD) simulations were conducted. During the simulations, we observed the various types of inclusion complex structures (acyclic, cyclic, branched acyclic, and branched cyclic daisy chains). For the modified part linked to the outer direction of the CD, daisy chains of various sizes were constructed. However, for the modified part linked to the inner direction of the CD, cyclic dimers ([c2] daisy chain) were mainly constructed. To elucidate the formation difference in the daisy chain structures, depending on the bond angle of the modified part linked to the CD, the free energies of the [c2] daisy chain structures were estimated using the histogram reweighting method. It was observed that the formation of the various types of daisy chain structures was determined by the stability of the [c2] daisy chain.