Structure and internal motion of solvated beta-cyclodextrine: a molecular dynamics study

A 5 ns molecular dynamics simulation was performed on a system constituting 5 12 water molecules and one beta-cyclodextrin molecule in a cubic cell with a 26 Angstrom length. The internal motion of the solute molecule was investigated and compared with reports from Molecular Mechanics, Neutron Scattering and Molecular Dynamics. The beta-cyclodextrin structure is markedly distorted with the majority of the primary hydroxyl groups pointing towards the inner cavity. The structure and dynamics of the water molecules in the first solvation shells were also investigated, An average number of 25 water molecules compose the inner shell forming a network of hydrogen bonds with the cyclodextrin hydroxyl groups.