The non-edible Sapindus mukurossi oil, containing more than 80% unsaturated fatty acids, has potential applications in plastics manufacturing. In this research, a green and economically attractive chemo-enzymatic production of epoxidized fatty acids was performed in the presence of lipase Candida sp. 99–125 and H2O2 in different systems. The obtained experimental results demonstrated that the solvent-free and n-hexane systems yielded superior results compared to other organic solvent systems. A molecular dynamic simulation further proved the influence of different solvents on the structure of lipase. Maximization of the key parameters including enzyme loading, reaction time, molar ratio of H2O2 to the number of double bonds in the substrate, agitation speed, H2O2 addition frequency, and temperature were performed in a solvent-free system. The oxirane value reached 4.61% in 8h under a gradient temperature profile (first incubated at 30°C for 6h, then increased to 35°C and maintained for another 2h) with continuous addition of H2O2. The total molar amount of H2O2 added was equal to the number of CC bonds in the substrate (expressed in moles).
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