Molecular Dynamics of Large-Ring Cyclodextrins: Principal Component Analysis of the Conformational Interconversions

Abstract

Trajectories obtained from molecular dynamics (MD) simulations of some large-ring cyclodextrins (LR-CDs) were analyzed by a statistical method, principal component analysis (PCA), thus enabling the monitoring of the dominant PCA modes for concerted motions of the macroring atoms in a lower-dimensions subspace. Earlier analyses of macrorings' conformational deformations based on examination of snapshots extracted from the MD simulation trajectories were further supported on more quantitative grounds. The first 10 lowest-indexed modes describe more than 90% of the total atomic motion in all cases, with more than 50% of the contribution coming from the two highest-eigenvalue principal components. Representative average geometries of the cyclodextrin macroring were also obtained.