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Distinct Differences in Peptide Adsorption on Palladium and Gold: Introducing a Polarizable Model for Pd(111) C

Hughes, Zak E., Walsh, Tiffany R.
Journal of physical chemistry 2018 v.122 no.34 pp. 19625-19638
Gibbs free energy, adsorption, amino acids, density functional theory, gold, molecular dynamics, nanomaterials, palladium, peptides, silver, simulation models, solutes, solvents, tempering
Materials-binding peptides offer promising routes to the production of tailored Pd nanomaterials in aqueous media, enabling the optimization of catalytic properties. However, the atomic-scale details needed to make these advances are relatively scarce and challenging to obtain. Molecular simulations can provide key insights into the structure of peptides adsorbed at the aqueous Pd interface, provided that the force field can appropriately capture the relevant biointerface interactions. Here, we introduce and apply a new polarizable force field, PdP-CHARMM, for the simulation of biomolecule–Pd binding under aqueous conditions. PdP-CHARMM was parametrized with density functional theory (DFT) calculations using a process compatible with similar polarizable force fields created for Ag and Au surfaces, ultimately enabling a direct comparison of peptide-binding modes across these metal substrates. As part of our process for developing PdP-CHARMM, we provide an extensive study of the performance of 10 different dispersion-inclusive DFT functionals in recovering biomolecule–Pd(111) binding. We use the functional with best all-round performance to create PdP-CHARMM. We then employ PdP-CHARMM and metadynamics simulations to estimate the adsorption free energy for a range of amino acids at the aqueous Pd(111) interface. Our findings suggest that only His and Met favor direct contact with the Pd substrate, which we attribute to a remarkably robust interfacial solvation layering. Replica exchange with solute tempering molecular dynamics simulations of two experimentally identified Pd-binding peptides also indicates surface contact to be chiefly mediated by His and Met residues at aqueous Pd(111). Adsorption of these two peptides was also predicted for the Au(111) interface, revealing distinct differences in both the solvation structure and modes of peptide adsorption at the Au and Pd interfaces. We propose that this sharp contrast in peptide binding is largely due to the differences in interfacial solvent structuring.