In the present study three soft matter – hard matter systems consisting of different nanomaterials and organic molecules were studied using the steered molecular dynamics approach in order to reveal regularities in the formation of organic-inorganic hybrids and the stability of multimolecular complexes, as well as to analyze the energy aspects of adhesion between bio-molecules and layered ceramics. The combined process free energy estimation (COPFEE) procedure was used for quantitative and qualitative assessment of the considered heterogeneous systems. Interaction of anionic and cationic amino acids with the surface of a [Mg4Al2(OH)122+ 2Cl–] layered double hydroxide (LDH) nanosheet was considered. In both cases, strong adhesion was observed despite the opposite signs of electric charge. The free energy of the aspartic amino acid anion, which has two deprotonated carboxylic groups, was determined to be –45 kJ/mol for adsorption on the LDH surface. For the cationic arginine, with only one carboxylic group and a positive net charge, the energy of adsorption was –26 kJ/mol, which is twice higher than that of chloride anion adsorption on the same cationic nanosheet. This fact clearly demonstrates the capability of “soft matter” species to adjust themselves and fit into the surface, minimizing energy of the system. The adsorption of protonated histamine, having no carboxylic groups, on a boehmite nanosheet is also energetically favorable, but the depth of free energy well is quite small at 3.6 kJ/mol. In the adsorbed state the protonated amino-group of histamine plays the role of proton donor, while the hydroxyl oxygens of the layered hydroxide have the role of proton acceptor, which is unusual. The obtained results represent a small step towards further understanding of the adhesion effects within the hard matter – soft matter contact zone.