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Abstract Herein, we reported the adsorption and desorption of Pb(II) on l -lysine modified montmorillonite (L-Mt) with molecular dynamics simulation. l -lysine (Lys) modified montmorillonite (L-Mt) was prepared, characterized by various analytical techniques, and the simulation studies were performed to evaluate the interlayer structure and interaction properties of l -lysine and L-Mt. The results of X-ray powder diffraction (XRD) and Fourier transform infrared (FTIR) spectrum suggested that Lys+ was intercalated into the interlayer of Na-montmorillonite (Na Mt) successfully. The batch adsorption experiments were implemented to study the adsorption capacity of Pb(II) on L-Mt in water. The maximum adsorption capacity of Pb(II) on the L-Mt (up to 43.3 mmol/100 g) were considerably higher than that on Na Mt (up to 15.3 mmol/100 g), at room temperature. The adsorption isotherms of both, L-Mt and Na Mt can fit the Langmuir isotherm. The adsorption experiments showed that Pb(II) removal efficiency of L-Mt is better than Na Mt in acidic solution. The simulation results revealed the micro-mechanism of Lys+ inserted into the interlayer gallery of Na Mt. It can be deduced that lysine interacted with montmorillonite surface mainly through the protonated side-chain amino group rather than through the protonated main-chain amino group or deprotonated carboxyl group. These consequences are expected to elucidate the adsorption mechanisms occurring at the water/clay minerals interface at atom level, providing significant insight into the adsorption and retention of Pb(II) on L-Mt composite, and lead to relevant engineering applications while treating heavy metals of wastewater. Graphical abstract Unlabelled Image Highlights • l -lysine modified montmorillonite (L-Mt) has higher adsorption capacity for Pb(II) than Na Mt. Their maximum adsorption capacity is 43.3 mmol/100 g and 15.3 mmol/100 g, respectively. • L-Mt is more efficient on the retention of Pb(II) than Na Mt. When pH 3.0, the desorption ratio of Pb(II) is 16.08% and 58.31%, respectively. • The microstructure and interaction between lysine and Na Mt has been revealed by molecular dynamic simulation. [ABSTRACT FROM AUTHOR]