Biodegradable ionic liquids (bio-ILs) have attracted intensive attention due to toxicological and ecological reasons. It is critically important to understand the structural properties of bio-ILs at the molecular level. In this work, the interactions between four biodegradable naphthenate ionic liquids were investigated by density functional theory. The results indicate that multiple hydrogen bonds (H-bonds) are the major intermolecular structural feature between the cation and anion. These H-bonds were analyzed by natural bond orbital (NBO), quantum theory of atoms in molecules (AIM) and reduced density gradient (RDG) function. The influence of anionic structure on the interaction energy was studied. Based on the canonical orbital analysis, it is found that the sigma-type orbital overlap and the partial charges transfer between the anion and cation, finally, result in the decrease of the energy and rationalize the location of the anion. Additionally, linear relationships between second-order interaction energies and the increment of electron density, as well as the interaction energies and the sum of the electron density at bond critical points for all studied [Ch][NA] ion pairs were found. (C) 2013 Elsevier B.V. All rights reserved.