Related Experiment Video
Updated: May 30, 2026

Spatial Separation of Molecular Conformers and Clusters
Published on: January 9, 2014
Computational studies on the conformations of some large-ring cyclodextrins (CDn, n = 20, 21, 22, 23)
1Laboratory of Physical Organic and Computational Chemistry, Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Sofia, Bulgaria. ivanov@bas.bg
Abstract:
Computational studies were carried out on the conformations of large-ring cyclodextrins with degree of polymerization from 20 to 23. Principal component analysis (PCA) was applied for postprocessing of trajectories from conformational search, based on 100.0 ns molecular dynamics simulations. The dominant PCA modes for concerted motions of the macroring atoms were monitored in a lower-dimensions subspace. The first six lowest indexed principal components contribute more than 90% of the total atomic motions in all cases, with about 70% (CD21) to 83% (CD22) contribution coming from the three highest-eigenvalue principal components. Representative average geometries of the cyclodextrin macrorings were also obtained for the whole simulation and for the ten 10.0 ns time intervals of the simulation. We concluded that resemblance exists of the representative conformations of these four cyclodextrins with the circularized three-turn single helical structure proposed for CD21 from small-angle X-ray scattering, as well as with the representative conformations of CD26.
More Related Videos
Related Concept Videos
Stereoisomerism of Cyclic Compounds
Conformations of Cyclohexane
The chair form is the most stable and derives its name from its resemblance to the “easy chair.” In the chair conformation, two carbon atoms are arranged out-of-plane — one above and one below, minimizing the torsional strain. In the chair form, the bond angle is very close to the ideal tetrahedral value,...
Conformations of Cycloalkanes
Stability of Substituted Cyclohexanes
The two chair conformations of cyclohexanes undergo rapid interconversion at room temperature. Both forms have identical energies and stabilities, each comprising equal amounts of the equilibrium mixture. Replacing a hydrogen atom with a functional group makes the two conformations energetically non-equivalent.
For example, in...
Chair Conformation of Cyclohexane
The hydrogen atoms linked to carbons are arranged in two different axial and equatorial orientations to achieve this staggered...
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

