Our experiments on desulfurization of liquid fuels reveals suitability of novel type I deep eutectic solvents (DES) as potential solvents for thiophenic compounds. While the results are intriguing, molecular interactions leading to the solubility remains unclear. We herein, perform Molecular Dynamics (MD) simulations on tetrabutylphosphonium bromide/ferric chloride (TBP.Br-Fe.Cl3), a DES which showed higher affinity to thiophenic compounds. Simulations on the DES itself shows a preference of chloride ion by TBP over the bromide ion, forming a TBP.Cl.Br complex structure, which possibly explains the freezing point depression associated with formation of the DES. MD analysis of the DES in the presence of thiophene and dibenzothiophene (DBT) shows strong interactions between sulphur-based central ring of these compounds with the TBP ion. Further work need to be done on optimizing these results for possible extraction of sulfur- based solutes from liquid fuels.