TUD Organische ChemieImmelGraphicsMolArch+Animationsα-Cyclodextrin in SolutionView or Print (this frame only)View or Print (this frame only)

a-Cyclodextrin in Aqueous Solution

S. Immel, unpublished results.

A 596.95 ps CHARMM[1] molecular dynamics simulation of a-cyclodextrin in aqueous solution (609 water molecules were included in the simulation) was used to analyze the solution properties of this compound. a-Cyclodextrin is a torus shaped carbohydrate molecule composed out of six a(1→4)-linked glucose residues. The shape of this molecule allows for the formation of inclusion complexes with small hydrophobic organic compounds. In aqueous solution the cavity is filled with water, and the process of releasing these encapsulated water molecules into the bulk water phase is of fundamental importance for the formation of inclusion complexes. This movie shows the partial trajectory (approx. 120 ps) of one individual water molecule and the process of its diffusion through the central cavity of the host molecule; snapshot geometries and frames were taken every 0.2 ps from the molecular dynamics simulation. Note the (blue colored) water molecule entering the cavity from the 2-OH and 3-OH side of the cyclodextrin torus (top), and leaving the cavity on the opposite side (bottom) carrying the 6-CH2OH groups. The reverse process was also observed during this simulation. The picture on the left side shows the entire pathway of water diffusion as a blue track.

Water trajectory Alpha-CD water trajectory
   Cyclodextrin formula


(a) B. R. Brooks, R. E.Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comp. Chem. 1983, 4, 187-217. - (b) CHARMM - Chemistry at HARvard Macromolecular Mechanics, 1996; http://yuri.harvard.edu/.

© Copyright PD Dr. S. Immel