Interaction of amino acids and DNA nucleobases with copper: a comparative theoretical study

In nanotechnology, amino acids (AAs) and polypeptides serve as biomolecular templates for the synthesis of copper nanoclusters (NCs) and nanoparticles, directing their size, stability, and structural geometry. To elucidate the underlying binding motifs, we performed density functional theory (DFT) calculations on all 20 proteinogenic amino acids complexed with copper, systematically analyzing their coordination preferences, electronic interactions and topology. Our computations of Cu⁺-AA binding energies (G_b) are in agreement with previous mass-spectrometry data. DFT calculations identified deprotonated amino acids (AAs) as the predominant sites for copper (Cu₂, Cu₈ and Cu₂₀) nucleation. Among neutral AAs, arginine, histidine, and tryptophan exhibited the strongest interactions. Moreover, we compared the binding energy of copper, silver and gold with AAs/DNA nucleobases, which led us to a conclusion that Cu atoms possess higher mobility in biopolymer matrices than Au, but lesser mobility than silver. Moreover, several hydrated ion models have been regarded. We suppose, our results are of significant importance for the studies of copper nanostructures and copper-containing proteins.