Different Conformational Properties and Frequencies of Periodic Motion in the Beta- and Gamma-Cyclodextrin

Cyclodextrins (CDs) are cyclic oligosaccharides with application in different fields. These systems can encapsulate hydrophobic molecules and allow their solubilization in water. CDs and CD complexes can self-associate forming aggregate or micelle-like structures. Theoretical studies based on molecular mechanics (MM) and molecular dynamics (MD) simulations are demonstrated to be a useful tool for understanding the conformational properties, the stability, their host–guest inclusion complexes in the solid state or in aqueous solution in a good agreement with experimental data. The aim of this work is to compare at atomistic level the conformational properties, the flexibility of the native β- and γ-CD. The β-CD shows very slightly deviation from C7 symmetry, and its glycosidic oxygens are on a flat plane, while in the γ-CD they are in different arrangement on a curved plane. From the variation of the distance between opposite glycosidic oxygens in these CDs, the frequencies of motion due to periodic motions are calculated during MD run. These frequencies indicate faster periodic motion for the β-CD and slower for the γ-CD having larger dimension and less symmetrical structure. MD simulations are an interesting tool for investigating the flexibility of these systems, their possible periodic motion, and their frequencies of motion.