Structural Analysis and Inclusion Mechanism of Native and Permethylated α-Cyclodextrin-Based Rotaxanes Containing Alkylene Axles.

Native α-cyclodextrin- (α-CD) and permethylated α-CD (PMeCD)-based rotaxanes with various short alkylene chains as axles can be synthesized through a urea end-capping method. Native α-CD tends to form [3]- or [5]pseudorotaxanes and not [2]- or [4]pseudorotaxanes, which indicates that the coupled CDs act as a single fragment. End-capping reactions of the pseudorotaxanes with C18 and C24 axle lengths do not occur because the axle termini are covered by the densely stacked CDs. The number of PMeCDs on the pseudorotaxane is flexible and mainly depends on the axle length. Peracetylated α-CD (PAcCD)-based rotaxanes are synthesized through O-acetylation of the α-CD-based rotaxanes without any decomposition of the rotaxanated structures. The structures of PMeCD-based [3]- and [4]rotaxanes, and the molecular dynamics calculations on [3]pseudorotaxanes, indicate that the tail face of PMeCDs is regularly directed toward the axle termini. On the basis of the results obtained, it can be concluded that the directions and numbers of CDs in rotaxanes containing short alkylene chains depend on 1) the interactions between CDs, 2) the length of the alkylene axle, and 3) the interactions between the axle end and tail face of the CD.