Abstract Molecular interactions between 1-Ethyl-3-methylimidazolium cation ([Emim]) and hydrophobic amino acids anions (AA) viz ., glycine [Gly], alanine [Ala], valine [Val], leucine [Leu], and isoleucine [Ile] have been studied employing the M05–2X based Density Functional Theory (DFT). It has been shown that the emergent hierarchy in the binding energy, viz. , [Emim]-[Ile] ∼ [Emim]-[Leu] > [Emim]-[Val] > [Emim]-[Ala] > [Emim]-[Gly]; is attributable both to the number of hydrogen bonds and to the CH---π interactions. Molecular electrostatic potential (MESP) serves as a tool for building of [Emim] x [AA] y ( x , y = 1, 2) molecular aggregates. Molecular Electron Density (MED) topographic investigations further revealed an interesting correlation between the electron density at the bond critical point of the hydrogen bond from the acidic proton and the ion-pair binding energies. Normal coordinate-analysis brings forth that the [Emim][AA] ion-pair binding accompanied by the frequency up-shift (blue-shift) of the NH stretching relative to the isolated AA anion; with the largest shift of 54 cm − 1 occurring for [Emim][Leu]. On the other hand, frequency shifts ranging from 49 cm −1 in [Leu] to 34 cm −1 in [Ile], in the opposite direction have been noticed for the C O stretching mode. The direction of frequency shifts of characteristic C O, N H and C H vibrations are justified using the ‘Quantum Theory of Atoms in Molecules’ approach in conjunction with Natural-Bond-Orbital analysis. Frontier orbital analysis and hardness parameters together validate the trends in the binding strengths of ion-pairs as well as in aggregates underlying amino acid based ILs.