Molecular Simulation On The Complexation Of Cyclodextrin

Cyclodextrins (CDs) have a hydrophilic outer surface and a hydrophobic inner core, conducive for the formation of inclusion complexes through the binding of the small molecules into their core. This property has attracted increasing attention in pharmaceutical science, chiral recognition and supramolecular assembly field. Because of the limit in experimental conditions and methods, many unknown or unclear problems exist in the study of CD complexes. However, the three-dimension structure and the stability of the complex structure can be predicted directly, and the driving force responsible for the complexation can be obtained using molecular simulation methods. In this dissertation, the complexes of CDs with different guests were studied using molecular mechanics and molecular dynamics methods, and the main contents include:1. Several basic aspects about CDs, such as the structure properties, the investigation methods and the applications in several important fields, were introduced. Molecular mechanics (MM) methods, molecular dynamics (MD) methods, and their applications in cyclodextrin study were summarized as an emphasis.2. The chiral recognition of the selected nine pairs of aromatic chiral compounds by native β-CD was studied using a flexible docking algorithm FDOCK. Two main inclusion orientations of the chiral molecule were taken into account. A quantitative empirical free energy relationship model was employed to predict the complex stability constants and the preferred binding modes. The results showed that the calculated complex stability constants are in good agreement with the experimental data. In chiral recognition, although the preferred orientation is determined, the other one may contribute to the stability constants. Furthermore, analyzing each energy term of the complex structure, it can be obtained that the dominant forces holding the host-guest complexes together are the van der Waals forces. Investigating average interaction energy difference between the enantiomers,...