Understanding the nature of interaction between metal nanoparticles and biomolecules such as amino acids is important in the development and design of biosensors. In this paper, binding of M₃ clusters (M = Au, Ag and Cu) with neutral and anionic forms of histidine amino acid was studied using density functional theory (DFT-B3LYP). It was found that the interaction of histidine with M₃ clusters is governed by two major bonding factors: (a) the anchoring N–M and O–M bonds and (b) the nonconventional N–HM and O–HM hydrogen bonds. The nature of these chemical bonds has been investigated based on quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analyses. In the next step, the effects of Au, Ag and Cu metal clusters on the gas-phase acidity of weak organic acid (histidine) have been explored. The acidity of isolated histidine was compared with the acidity of its Au₃–, Ag₃– and Cu₃–complexed species. Results indicate that upon complexation with M₃ clusters (at 298 K), the gas-phase acidity (GPA) of histidine varies from 339.5 to 312.3, 315.0, and 313.7 kcal mol⁻¹ for Au₃–, Ag₃– and Cu₃–His complexes, respectively (i.e., its dissociation becomes much less endothermic). These values indicate that a weak organic acid can be converted to a super acid when it is complexed with metal clusters. Also, in order to investigate the acidity value of the imidazole moiety in histidine, histidine methyl ester (His-OMe) was selected. Similarly, the acidity of this compound was compared with the acidity of their Au₃, Ag₃ and Cu₃-complexed species. After complexation with M₃ clusters at 298 K, the gas-phase acidity (GPA) of His-OMe varies from 333.0 to 280.0, 304.2 and 291.5 kcal mol⁻¹, respectively. Moreover, pK_a values were determined in water for isolated and complexed species of His and His-OMe. The resulting pK_a values were found to decrease upon complexation with M₃ clusters.