Alginate oligosaccharides (AOS) with low polymerization have gained considerable attention due to their unique physiological activities. However, the lack of understanding regarding the mechanism of action for resin selection and optimization of separation processes has impeded their precise chromatographic separation and large-scale production. Here, the adsorption–desorption characteristics of AOS on the resins with varying solid phase composition, including backbones, functional groups, crosslinking degrees, and counterions resin structures, were analyzed using simulations and experiments. The simulation results revealed that the structural differences of AOS are characterized by their electrostatic potential and lowest unoccupied molecular orbital energy level. Based on molecular simulations, we predicted that the basic anion resin with a styrene backbone would be suitable for AOS separation. Subsequently, we constructed SM-7Cl resin based on the simulation results and performed static adsorption experiments to verify the prediction. SM-7Cl resin demonstrated noteworthy adsorption–desorption performance for AOS, with an adsorption capacity of 471.2 mg/g and a desorption rate of 89.45%. The fitting adsorption isotherm was consistent with the Freundlich model, indicating that the adsorption proceeded spontaneously. The equilibrium times for AOS adsorption on the gel-type resin and the macroporous resin, which both followed a pseudo-second-order kinetic model, were 30 min and 60 min, respectively. This study provides optimized chromatographic media and separation processing that can be implemented for the amplification of chromatographic separation in AOS production.
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