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This thesis consists of three parts; in the first part, parameter sets of the Non-Random Two-Liquid (NRTL) model for five challenging binary liquid-liquid equilibria (LLE) relevant to the cluster of excellence Tailor-Made Fuels from Biomass (TMFB) are generated by means of the AVT.SVT in-house tool BOARPET (Bilevel Optimization Algorithm for Rigorous and Robust Parameter Estimation in Thermodynamics). In the 2nd part, the risks that may result from the aforementioned violation of thermodynamic criteria for process simulation are assessed, by means of several unit operation models in Aspen Plus, as well as flash simulations, formulated and solved in GAMS. The respective parameter sets are selected from the first part, either because these are found to result in violation of thermodynamics, or due to the particular shape of the implied Gibbs free energy curve with respect to composition. In the 3rd part, stoichiometric and non-stoichiometric formulations from literature for the simulation of combined diffusive and chemical equilibrium are compared using local and global solvers through GAMS, for the case study SBA/DSBE/water. The publication is made within the framework of a scientific cooperation at the Vilnius University of Technology/Lithuania.