Multilevel Quantum Chemistry Approach to the Development of a Database of the SAM-Ligand-Metal Ion-Protein Interactions

An ab-initio approach towards building a database of immobilized ligands targeting proteins is presented. Iminodiacetic chelators, precursors of self-assembled monolayers, attached to the gold surface and complexing three divalent metal ions (Cu(II), Zn(II), Ni(II)) is investigated. The strength of the protein–ligand interaction is estimated. Ten models of the iminodiacetic acid metal complex with different degree of complexity were constructed, each focusing on different structural features of the system. The calculations have been performed using the quantum mechanical density functional theory method. The results show that reduction of the complexity of the model by removing the gold surface, the neighboring alkyl chains and the presence of the solvent does not have much impact on the iminodiacetic acid—aminoacid affinity. The interaction between the chelator and the aminoacid represented by imidazole moiety of histidine are also almost unaffected by the length of the alkyl chain. The results indicate that advanced quantum mechanical methods and relatively small model systems can be used to adequately describe the self-assembled monolayer-ligand-metal ion-protein interactions and to create a comprehensive database of ligands for the monolayers.