Binding of silver ion (Ag ⁺ ) and two atomic neutral silver cluster (Ag ₂ ) with a set of amino acids has been studied using Density Functional Theory (DFT) and ab initio MP2 method. We show that binding energy with Ag ₂ is higher for deprotonated anionic amino acids. Cysteine, aspartic acid, and tyrosine with deprotonated side chain exhibit the highest binding energy (G _bind ) values among all the amino acids: − 30.1 kcal mol ⁻¹ , − 30.7 kcal mol ⁻¹ , and − 30.9 kcal mol ⁻¹ , respectively. Binding energies of deprotonated cysteine, glutamic acid, tyrosine, and aspartic acid with silver ion Ag ⁺ are reported here for the first time. Natural bond orbital (NBO) analysis has also been performed to calculate charge transfer, natural populations, occupancies, and Wiberg bond indices of the amino acid–Ag ₂ complexes. Atoms-in-molecules (AIM) theory was used to establish the nature of interactions. It was shown that, in most cases, the bonds between amino acid and Ag ₂ cluster are partially electrostatic and partially covalent.