Interaction of biogenic impurities with the Ni (1 1 1) catalyst surface was studied to understand their important role in inhibiting catalysis. Non-bonding interactions of amino acids (Alanine (Ala), Cysteine (Cys), Methionine (Met), Tryptophan (Trp), Histidine (His), Lysine (Lys), Glutamic acid (Glu) and Threonine (Thr)) in aqueous environment were examined using classical molecular dynamics (MD) simulations. The potential of mean force (PMF) profiles of amino acids revealed qualitative differences, resulting into altered orientation and the choice of preferential interacting site with the metal surface. The side chains of all the amino acids were observed to align parallel to the metal surface. Amino acids containing sulfur (Met and Cys) and heterocyclic nitrogen (Trp, His) were observed to interact favorably with the Ni surface. Most of the preferential interacting sites were observed to be in direct contact with the surface except Lys which interacted with the backbone nitrogen oriented away from the surface. The strength of non-bonded interactions varied from −13 to −71 kJ/mol with Ala as the weakest and Trp as the strongest interacting amino acids. The interaction energies scaled linearly with the solvent accessible surface area of the amino acids. Density functional theory (DFT) calculations were utilized to understand the bonding interactions of sulfur (S) containing amino acids (Met and Cys) and the irreversible catalyst deactivation caused by them. DFT calculations showed strong binding for both Cys (−123 kJ/mol) and Met (−115 kJ/mol), undergoing dissociation to form atomic S on the Ni (1 1 1) surface with an intrinsic activation barrier of 32 kJ/mol and 133 kJ/mol, respectively, for the C–S bond cleavage. However, the mechanistic routes for dissociation followed by the two amino acids were a bit different. While in Cys, the C-H activation was followed by C–S cleavage, in Met, C–S bond was activated first to form S-CH3 species on the catalyst surface. In contrast to Met at higher coverage, Cys was observed to decompose to elemental S on the surface. The mechanistic insights thus obtained lead to an explorative theoretical framework for the design of a bimetallic catalyst, which may be used in an integrated bio and chemo-catalytic process with reduced chances of deactivation. The Ni-Au alloy surface showed lower binding energies for both Met (−88 kJ/mol) and S (−132 kJ/mol), as compared to pure Ni surface, indicating promising prospects for the activity of such an alloy catalyst. © 2017 Elsevier Inc.