Puerarin and daidzin,two major isoflavonoids of Radix puerariae,are widely reed in traditional Chinese medicine and are difficult to separate from each other because of the similarity of the molecular structure,as shown in Figure 1.They have been successfully isolated from an extract of R.puerariae by adsorption chromatography on a [β-cyclodextrin ligand coupled to Superose 12 pg with the mobile phase of acetic acid [1].Host-guest supramolecular inclusions between β-cyclodextrin and the two compounds have been investigated by molecular dynamics simulation,considering HAc/water solvent molecules.Computational results revealed that in the complex systems the conformation of β-cyclodextrin in HAc/water solvents was more stable than that in water.Acetic acid could weaken host-guest interactions by interacting with the host,guest,and water molecules,respectively.Furthermore,intra-and intermolecular hydrogen bonds have also been analyzed and used for the explanation of separating puerarin from daidzin.