n-Octylamine modified poly(glycidyl methacrylate-co-ethylene glycol dimethacrylate) (poly(GMA-co-EGDMA)) monoliths were prepared for the rapid screening and determination of puerarin content of a crude extract Radix puerariae. The mixed-mode retention mechanisms for puerarin and its analogues on n-octylamine modified monoliths were investigated using a variety of solvent systems, chromatographic evaluation and molecular dynamics (MDs) modeling. The equilibrated conformations between crosslinked polymers and target molecules were obtained from MD modeling. Both the polymer skeleton and functional groups played important roles in the recognition process. The cross-linker formed a structural network skeleton, in which recognition cavities were formed surrounded by functional groups. The polymer network structures provided good interaction access for isoflavones. The active groups recognized isoflavones by both intermolecular hydrogen bonding and hydrophobic interaction. The interaction energies and retention factors between polymers and target molecules were also evaluated and compared. A higher value of interaction energy corresponded to a higher value of retention factor. The potential of using modeling technology for predicting the chromatographic performances of target molecules was explored. (C) 2009 Elsevier Ltd. All rights reserved.