The use of β-cyclodextrin(β-CD) as a drug delivery vehicle with amino acid based ionic liquid(AAIL)substituent into eukaryotic cells is well documented and thus increases the bioavailability of diverse therapeutics. Therefore, we have preferred β-CD in our work to stabilize AAILs, which can further be separated in a controlled fashion. AAILs, namely proline nitrate PN and β-CD are presented as model system for its diverse importance in the biotechnological field, electro dialysis separation and drug delivery. In this work, experimental measurements are correlated with Quantum chemical methodology theoretically.2D-correlational experiments, however, show signature of binding of PN with the β-CD. These fascinating results were elucidated with the assist of Molecular docking simulation studies. Confirmations from antimicrobial study are in good agreement with the experiments. Connection developed here, is that the new AAILs based inclusion complex with negligible toxicity would act as a potential carrier. Results reported here are encouraging for practical applications of the AAILs in combination with β-CD. © 2019 Elsevier B.V.