Exploring the intermolecular interaction of serine and threonine dipeptides with gold nanoclusters and nanoparticles of different shapes and sizes by quantum mechanics and molecular simulations

Abstract

The aim of this work is to study the interaction between gold nanoclusters (AuNCs) and two cyclic dipeptides, serine cyclic dipeptide [c(SS)] and threonine cyclic dipeptide [c(TT)] in both gas and water phases by density functional theory (DFT). These two dipeptides have been chosen to elucidate the contribution of their residues and side chains on the AuNC−protein interactions. The binding energies and intermolecular interaction of gold nanoclusters Aun (n = 2, 4 and 6), with c(SS) and c(TT) were calculated. Natural bond orbital (NBO) analysis and atoms in molecules (AIM) theory were used to study the interaction type. We have found that the interaction involved the formation of a polar covalent bond, unconventional Au ….H–N/O hydrogen bond, and an electrostatic Au ….H–C interaction. The interaction of c(SS) or its residue/sidechain with gold nanoclusters was greater than that in case of c(TT) in both gas and water phases. The binding energy of Aun−cyclic dipeptide complexes was found to be size-dependent in the following order: Au4> Au2> Au6. The interactions of c(SS) and c(TT), as well as glycine cyclic dipeptide c(GG), with gold nanoparticles (AuNPs) with different shapes (sphere, simple box, cylinder, and cone) and sizes (3 nm, 5 nm, and 7 nm) were investigated in gas phase using Monte Carlo simulation. The stability of spherical (3 nm) AuNPs− cyclic dipeptide complexes in water were studied using molecular dynamics simulations. The results provided significant information and easy to understand on the interactions among peptide residues, side chains and gold nanoparticles.