Molecular dynamics simulations and theoretical calculations of cyclodextrin-polydatin inclusion complexes

Abstract In our previous work, the PD/γ-cyclodextrin complex was discovered to have higher calculated Kc and Gibbs free energy (ΔG0) values by the phase-solubility diagram method, and molecular dynamics (MD) simulations were carried out to investigate the structure and dynamics of the 1:1 inclusion complexes formed by β- and γ-cyclodextrins (CD) with PD in water. The simulation results indicated that γ-CD provides the most stable inclusion complex of among all PD-CD complexes in this study. Similar to the MD results, the thermodynamics of the selected inclusion complex structure was calculated by semi-empirical (PM3) and DFT (B3LYP/6-31G) methods. The statistical thermodynamics calculations also suggested that orientation b (including in CD's cavity from the wide side) of the PD/γ-CD inclusion complex is a favourable binding mode and in good agreement with the experimental and MD data. Most importantly, the simulation results of present study are in good agreement with the experimental data.