Large-ring cyclodextrins. A molecular dynamics study of the conformational dynamics and energetics of CD10, CD14 and CD26

Abstract

Molecular dynamics simulations in water were performed on the three largest large-ring cyclodextrins (LR-CD) for which X-ray data is available - CD10, CD14 and CD26. The Glycam-04 force field in AMBER and explicit water molecules (TIP3P) were used in the 20.0 ns simulations. Small variations about the starting conformation of CD10 were detected. Different structural motifs were monitored for CD14 that may represent chiral species of particular interest for exploring supramolecular and chiral molecular recognition effects: broadly opened macroring, that resembles the initial geometry of CD10 but in larger scale, a big circular loop with a small helical turn, deformed figure eight conformation, and a symmetrically squeezed open form ("a dumbbell"). The final geometry of CD14 is free of additional strain introduced by band-flips. The preferred conformation of CD26 contains a small helix and an extended helical portion that transforms also to an arc and a loop. Two modifications of the equilibration step of the simulation protocol were tested. ©ARKAT USA, Inc.