Objective To investigate interactions differences between L-tryptophan (L-Trp), D-tryptophan (D-Trp) enantiomers and polydopamine (PDA), and elucidate the chiral recognition mechanism in molecular imprinting.Method Computational molecular simulation was used for studing the molecularly imprinted pre-polymerization system with tryptophan as template and PDA as functional monomer. Firstly, conformational searching was used to obtain the potential stable structure of PDA tetramer. Then, molecular docking was employed to identify the interaction between Trp enantiomers and PDA. Finally, Quantum-chemical calculation was used to reveal the reason for the binding difference between the enantiomers and PDA from the perspective of electronic structure.Result Hydrogen bonding played a predominate role in the binding between Trp and PDA. The hydrogen bonding force between L-Trp and PDA was stronger than that between D-Trp and PDA. On the other hand, the frontier orbital Energy gap of L-Trp-PDA complex was bigger than that of D-Trp-PDA complex, and the former complex had tighter binding as well as stronger weak interaction.Conclusion Molecular simulation method is easy and rapid to operate, and it’s suitable for studing the chiral recognition mechanism in molecular imprinting.