Understanding the role of non-covalent interactions that dictate and fine-tune the direction of self-assembly of functional molecules is crucial for developing stimuli responsive materials. Herein, we systematically designed and synthesized viologen derivatives with hydrophobic dodecyl chains and alkyl carboxylic acid functionalities. The complementary electronic and electrostatic counterpart of viologens was chosen as pyranine. Viologens comprising of a hydrophobic dodecyl chain on one terminal and hydrogen bonding alkyl carboxylic acid on the other (V1andV2) underwent aggregation to a varying extent upon interaction with pyranine. The length of the alkyl carboxylic acid had a greater impact on the nature and morphology of the aggregates. Control molecules (V3andV4) in which 4,4′-bipyridine was symmetrically quaternized with alkyl carboxylic acids did not aggregate upon interaction with pyranine. The delicate balance existing between the hydrophobicity of the dodecyl chains and the intermolecular hydrogen bonding interaction between the alkyl carboxylic acid groups inV1orV2of the corresponding charge transfer (CT) complexes was instrumental in driving the aggregation. The CT aggregates of [V1-Pyr] and [V2-Pyr] exhibited excellent stability in water which disaggregated at physiological pH. We emphasize on the importance of synergy between hydrophobic and hydrogen bonding interactions in reinforcing each other to drive the supramolecular aggregation of the CT complexes. Such pH dependent CT aggregates are of importance as scaffolds in pH controlled drug release. In the present study, the CT aggregates were evaluated for adenosine nucleotide recognition in water; [V1-Pyr] and [V2-Pyr] exhibited selective response towards adenosine monophosphateviadeprotonation induced dissolution of aggregates in water leading to emission enhancement. © The Royal Society of Chemistry 2020.