Cell wall disturbance is an important step in the downstream process of improving the efficiency of lipid extraction from microalgae. Surfactants have been proven to be efficient alternatives to organic solvents in the extraction process. In this study, an effective approach involving deep eutectic solvent (DES) (choline chloride and carboxylic acids) treatment supplemented with surfactants has been developed to disrupt the cell walls of microalgae and increase the extraction of lipids suitable for biodiesel production. A combination of polar and non-polar solvents (ethyl acetate and n-butanol) was used for the lipid extraction process. Microalgae biomass pretreated with choline chloride malonic acid supplemented with the surfactant hexadecyl trimethylammonium chloride (HTAC) showed the best results, improving lipid extraction by 12.365%. Further elucidation of the detailed mechanism behind the cell disruption of the microalga wall by DES was achieved using density functional theory (DFT) methods. The DFT calculations revealed that hydrogen bonds between the chloride ion of the DES and hydrogen bond donor (HBD) molecules are key factors dominating the destruction of the cell wall structure of Chlorella pyrenoidosa. The optimization of lipid extraction was performed through a single-factor experiment, which included the effects of different variables (time, temperature, dosage of surfactant, and ratio of n-butanol to ethyl acetate). An extraction period of 60 min at 80 °C with a surfactant concentration of 0.5% at a 1:2 ratio of n-butanol to ethyl acetate was found to produce the maximum lipid yield (16.97%). Transesterification reactions were used to obtain fatty acid methyl esters from the optimized extracted lipids. Thus, it was determined that C16:0 (20.04%), C18:2 (29.95%), and C18:3 (21.21%) were the most prevalent fatty acids. The potential for producing biodiesel from C. pyrenoidosa was validated by the high yields of C18 fatty acid methyl esters, and the properties of biodiesel are within the European and US standards.
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