To quantify the biomolecular interactions of protein functional groups with biocompatible ionic liquids (ILs), transfer free energies (Delta G'(tr)) of model compounds from water to aqueous ILs solutions have been determined from the solubility measurements, as a function of ILs concentration at T = 298.15 K under atmospheric pressure. The aqueous systems investigated contain amino acids of zwitterionic glycine peptides: glycine (Gly), diglycine (Gly(2)), and cyclic glycylglycine (c(GG)) with ILs of diethylammonium acetate ([Et(2)NH][CH(3)COO], DEAA), triethylammonium acetate ([Et(3)NH][CH(3)COO], TEAA), and trimethylammonium acetate ([Me(3)NH][CH(3)COO], TMAA). It was found that the solubility of model compounds in aqueous IL solutions decreases with increasing IL concentration (salting-out effect). We observed positive values of Delta G'(tr) for Gly, Gly(2), and c(GG) from water to ILs, indicating that the interactions between ILs and protein surface are unfavourable, which leads to stabilization of the native structure of amino acids. Moreover, our experimental data is used to determine transfer free energies (Delta G'(tr)) of the peptide backbone unit (-CH(2)C=ONH-) from water to IL solutions. These results explicitly elucidate that all alkyl ammonium ILs acted as stabilizers for tested model compounds through the exclusion of ILs from surface of model compounds and also reflect the effect of alkyl chain on the stability of protein model compounds. To obtain the mechanism events of the ILs role in enhancing the stability of the model compounds structure, we further studied the UV-vis spectrum analysis. (C) 2011 Elsevier Ltd. All rights reserved.