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Complex formulations such as emulsions are widely used for enhancing the solubility and delivery of functional ingredients. Many experiments have been reported to evaluate how functional chemical compounds partition between phases of complex structures of micelles and emulsions. A great challenge is to predict these thermodynamic properties of wide chemicals. Here we explore a multi-scale approach for in-silico prediction of the partition coefficient in two steps: At first a molecular dynamic simulation (MD’s) is performed to determine the micelle and emulsion structure of the simulated system. In the second stage the predicted micellar and emulsion structure file is processed in COSMOtherm to determine the Gibbs free energy profile and so the partition coefficient of the whole structure of the aggregate. We report initial progress in predicting the micelle-water partition of a wide chemical space in a model SDS micelle system. The predicted partition coefficient is then compared to published experimental data in order to evaluate the accuracy and reliability of the methodology. Further work will be carried for real-world emulsion systems to achieve a good agreement between calculated and experimental data.