Molecular dynamics simulations on the effect of size and shape on the interactions between negative Au(SR), Au(SR) and Au(SR) nanoparticles in physiological saline.

Molecular dynamics simulations employing all-atom force fields have become a reliable way to study binding interactions quantitatively for a wide range of systems. In this work, we employ two recently developed methods for the calculation of dissociation constants between gold nanoparticles (AuNPs) of different sizes in a near-physiological environment through the potential of mean force (PMF) formalism: the method of geometrical restraints developed by Woo et al. and formalized by Gumbart et al. and the method of hybrid Steered Molecular Dynamics (hSMD). Obtaining identical results (within the margin of error) from both approaches on the negatively charged Au(SR) NP, functionalized by the negatively charged 4-mercapto-benzoate (pMBA) ligand, we draw parallels between their energetic and entropic interactions. By applying the hSMD method on Au(SR) and Au(SR), both of them near-spherical in shape and functionalized by pMBA, we study the effects of size and shape on the binding interactions. Au binds weakly with = 13 as a result of two opposing effects: its large surface curvature hindering the formation of salt bridges, and its large ligand density on preferential orientations favoring their formation. On the other hand, Au binds more strongly with = 30 and Au binds the strongest with = 3.2.