Simulation of inclusion complex formation and molecular recognition of cyclodextrin

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I developed coarse grained models of cyclodextrin and polymer chain to investigate the inclusion complex process. By carrying out Brownian dynamics simulation using the models, the formation of the inclusion complex was reproduced, and the mechanism of pseudopolyrotaxane formation was revealed. Moreover, I observed two kinds of motions-oscillating motion and shifting motion, after the formation of pseudopolyrotaxane. These two kinds of motions result in random walk of cyclodextrin along polymer chain. I also reproduced the chain length recognition observed in formation of inclusion complex. My simulation results indicated that the difference in the inclusion time between the cyclodextrins and the polymer chains controls chain length recognition.