Molecular dynamics conformational search for the factors that determine conformation of modified cyclodextrins

Modified cyclodextrins (modified CDs), which have an appending moiety, form various conformations depending on its moiety. In this study we examined the factors that determine the conformation of modified CDs with p-dimethylaminobenzoyl and p-nitrobenzoyl moiety as a pendant (DMAB-β-CD and NB-β-CD, respectively) using computational chemistry. The structures and potential energies were calculated using molecular dynamics conformational search, and the relationship between conformation and energy calculated from force field was investigated. These calculations suggested that the conformation of the modified CDs is dominated by the opposing influences of the van der Waals energy, which favors locating the appending moiety inside the CD cavity, and the angle related to the bending energy, which favors the moiety outside the cavity.