Sulfonic acid based and imidazolium-based ionic liquids were studied in this thesis. A classical force field for sulfonic acid was developed in OPLS-AA and CHARMM format. The structure and dynamics of alyl sulfonic acid was examined to validated the force field, including density, heat of vaporization and transport properties. The radial distribution function produced from the force field was also compared with the results of ab inito molecular dynamics. Next, the dissolution of ZnO (1010) surface in a sulfonic acid based ionic liquid was studied using ab initio approaches. Possible pathways of the initial dissolution process are explored. Energies of proton transfer from ionic liquids to ZnO (1010) surfaces are calucated. The solvation of zinc ion is also discussed. For imidazolium-based ionic liquids, its heterogeneous dynamics was invastigated with the help of four point correlation function. In addition, we also proposed a new “mobile” self four point correlation function to better describe the collective motions. A comparison between imidazolium-based ionic liquids, choline acetate and acetonitrile was presented. The effects of the side chain length of imidazolium-based ionic liquids were also discussed in detail. In the end, the interactions between the anions and the hydrogens on the imidazolium ring were examined with the calculation of their vibrational spectroscopy. The results of classical force field and DFT calculations were compared.