Abstract <p>Results are considered from quantum chemical modeling of intermolecular interaction between hydrophobic amino acids (phenylalanine and tryptophan) and the aromatic element of a sorbent matrix to which the main contribution is made by π–π interaction. It is established that parallel and T-shaped arrangement of aromatic structures of the amino acids and sorbent relative to one another are obtained for both amino acids. A T-variant arrangement is also obtained for tryptophan, with the heteroatom of the amino acid radical oriented toward the ring of the sorbent matrix. Results are examined from quantum-chemical modeling the formation of the second layer of sorption in the sorbent due to π–π interaction, and the energy and geometric characteristics of the specified systems are analyzed.</p>