10.1021/jp805446w.s001
Martin G. Gotsev
Martin G.
Gotsev
Petko M. Ivanov
Petko M.
Ivanov
Molecular Dynamics of Large-Ring Cyclodextrins: Principal Component Analysis of the Conformational Interconversions
American Chemical Society
2009
Molecular Dynamics
PCA modes
Principal Component Analysis
component analysis
macroring atoms
MD simulation trajectories
Conformational InterconversionsTrajectories
cyclodextrin macroring
2009-04-30 00:00:00
Journal contribution
https://acs.figshare.com/articles/journal_contribution/Molecular_Dynamics_of_Large_Ring_Cyclodextrins_Principal_Component_Analysis_of_the_Conformational_Interconversions/2860474
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.