The (R)-(6-Methoxyquinolin-4-yl)[(1S,2S,4S,5R)-5-vinylquinuclidin-2-yl]methanol (quinine)-tetraphenylborate complex was synthesized by reacting sodium tetraphenyl borate with quinine in deionized water at room temperature through an ion-pair reaction (green chemistry) at room temperature. The solid complex was characterized by several physicochemical methods. The formation of ion-pair complex between bio-active molecules and/or organic molecules is crucial to comprehending the relationships between bioactive molecules and receptor interactions. The complex under study was examined for antimicrobial activity. All theoretical calculations were carried out in vacuum and water using the B3LYP level 6–311G(d,p) levels of theory. The theoretical computation allowed for the prediction and visualization of ionic interactions, which explained the complex’s stability. The results of energy optimization showed that the Q-TPB complex is stable with a negative complexation energy. The obtained geometries showed that the boron (B⁻) and nitrogen (N⁺) in piperidine of the two molecules tetraphenylborate and quinine are close to each other, which makes it possible for ions to interact. The modest energy gap between HOMO and LUMO showed that the compound was stable. The computation of the electron transitions of the two models by density functional theory (TD-DFT) in the solvent at the theoretical level B3LYP/6–311G(d,p) allowed for the detection of three UV/visible absorption bands for both models and the discovery of a charge transfer between the host and the guest. The UV absorption, infrared, and H NMR are comparable with the experimental part.