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The surface properties of biologically active nanoparticles (NPs) are often dictated by synthetic ligands that are grafted to the NP core to form a protecting monolayer. Ligand selection is thus critical in determining NP surface properties and corresponding interactions at the nano-bio interface, which are relevant to numerous applications including drug delivery and biosensing. However, chemically specific structure–property relationships for rationally selecting ligands to achieve desired biointeractions are largely lacking. In this Focus Article, we review the challenges associated with relating ligand chemical properties to monolayer-protected NP surface properties due to the interplay of ligand–ligand, ligand–solvent, and ligand–biomolecule interactions that are difficult to anticipate. In particular, we highlight unexpected spatially varying properties that emerge even for uniformly functionalized NPs due to the fluctuations of ligands at the nanoscale. We further review the capability of physics-based molecular simulations to reveal these unexpected behaviors, providing powerful computational methods to predict NP properties. Finally, we discuss the opportunity for such simulations to be combined with machine-learning methods to guide the computational design of monolayer-protected NPs prior to synthesis. 

We utilize coarse-grained molecular dynamics simulations and enhanced sampling methods to reveal the effect of ligand branching on the thermodynamics of nanoparticle adsorption to lipid bilayers. 

The interactions of ligand-functionalized nanoparticles with the cell membrane affect cellular uptake, cytotoxicity, and related behaviors, but relating these interactions to ligand properties remains challenging. In this work, we perform coarse-grained molecular dynamics simulations to study how the adsorption of ligand-functionalized cationic gold nanoparticles (NPs) to a single-component lipid bilayer (as a model cell membrane) is influenced by ligand end group lipophilicity. A set of 2-nm diameter NPs, each coated with a monolayer of organic ligands that differ only in their end groups, was simulated to mimic NPs recently studied experimentally. Metadynamics calculations were performed to determine key features of the free energy landscape for adsorption as a function of the distance of the NP from the bilayer and the number of NP-lipid contacts. These simulations revealed that NP adsorption is thermodynamically favorable for all NPs due to the extraction of lipids from the bilayer and into the NP monolayer. To resolve ligand-dependent differences in adsorption behavior, string method calculations were performed to compute minimum free energy pathways for adsorption. These calculations revealed a surprising non-monotonic dependence of the free energy barrier for adsorption on ligand end group lipophilicity. Large free energy barriers are predicted for the least lipophilic end groups because favorable NP-lipid contacts are initiated only through the unfavorable protrusion of lipid tail groups out of the bilayer. The smallest free energy barriers are predicted for end groups of intermediate lipophilicity which promote NP-lipid contacts by intercalating within the bilayer. Unexpectedly, large free energy barriers are also predicted for the most lipophilic end groups which remain sequestered within the ligand monolayer rather than intercalating within the bilayer. These trends are broadly in agreement with past experimental measurements and reveal how subtle variations in ligand lipophilicity dictate adsorption mechanisms and associated kinetics by influencing the interplay of lipid-ligand interactions.