To reduce the environmental pollution caused by organic solvents and improve the extraction efficiency, a green and high-effective natural deep eutectic solvent (NADES) was screened out and prepared for the extraction of flavonoids from Fructus aurantii based on the COMOS-RS and experimental verification. The results showed the results of theoretical screening and experimental verification were consistent, and Ch-Lea was the best extraction solvent, which further proved the COMOS-RS was an efficient tool for the solvent screening. Then, the extraction conditions were investigated. The optimum extraction conditions were as follows: molar ratio (1:2), water content (30%), solid–liquid ratio (1/60 g/g) and extraction time (15 min), yet the extraction temperature and power did not significantly affect the extraction yield. Under the optimal extraction condition, the extraction yield of flavonoids was 122.68 mg/g. Compared with the traditional extraction solvents (methanol and ethanol), Ch-Lea has a higher extraction yield. And the green assessment was conducted based on Eco-Scale methodology, which results indicated the Ch-Lea was more environmentally friendly than methanol and ethanol. Meanwhile, the Ch-Lea has good reusability, and the extraction yields from four reuses were 122.68 mg/g, 125.13 mg/g, 122.56 mg/g and 105.63 mg/g, respectively. Moreover, the extraction mechanism was delved into using molecular dynamics (MD) simulation and reduced density gradient (RDG) analysis. The hydrogen bond interaction, particularly the O-H bonds, between Ch-Lea and the naringin molecule emerged as the primary force driving the extraction process. In summary, Ch-Lea is a green, economical, and highly effective solvent, making it a promising candidate for flavonoid extraction from Fructus aurantii. Its potential as an alternative to traditional extraction solvents further underscores its value.
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