The interaction mechanisms between the cation and anion in 1-ethyl-3-methyl-imidazolium cysteine ionic liquids [Emim][Cys] were investigated at the B3LYP/6-311＋G(d,p) level. Seven isomers of [Emim][Cys] were optimized, and their vibrational frequencies were calculated to verify the stationary structures. The optimized structures, energies and natural population analysis (NPA) were presented and analyzed in terms of their possible correlation with the interaction energies and the H-bond separations. Theoretical results indicate that the [Emim]＋ and [Cys]－ can form considerably strong H-bond interactions, which is mainly attributed to the interaction between the lone pairs of carbonyl O atom in [Cys]－ and the antibonding orbital of C—H in [Emim]＋, lp(O)®s*(C—H). For the most stable isomer [Emim][Cys]_S1, the carbonyl O atoms of [Cys]－ would prefer to interact with the C(2)—H of the imidazolium ring and the C—H of the methyl group of [Emim]＋, and interaction energy is －387.66 kJ/mol with BSSE correction. The H-bond chemical nature of [Emim][Cys] was investigated by atoms in molecules (AIM) and natural bond orbital (NBO) analyses.

Key words: amino acid ionic liquid, [Emim][Cys], H-bond, natural population analysis (NPA), natural bond orbital (NBO), atoms in molecules (AIM), IR spectra