TUD Organische ChemieImmelGraphicsMolArch+AnimationsFlexibility of α-CyclodextrinView or Print (this frame only)View or Print (this frame only)

Flexibility of 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S. Immel, unpublished results.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 hydration and dynamic properties of this compound. a-Cyclodextrin is a torus shaped carbohydrate molecule composed out of six a(1→4)-linked glucose residues, carrying the secondary 2-OH and 3-OH groups on one side of the macrocycle. The opposite ring perimeter is made up by the primary 6-CH2OH groups. The dynamics trajectory allows the computation of the anisotropic thermal ellipsoids which display the flexibility and motions of individual molecular fragments (a total of 11939 different molecular structures were analyzed). The animation displays the cyclodextrin torus with the ellipsoids superimposed, the model is rotated in steps of 5 degrees around the vertical axis.

Alpha-CD anisotropic thermal ellipsoids
   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