Molecular Features for Probing Small Amphiphilic Molecules with Self-Assembled Monolayer-Protected Nanoparticles

Abstract

The sensing of small molecules poses the challenge of developing devices able to discriminate between compounds that may be structurally very similar. Here, attention has been paid to the use of self-assembled monolayer (SAM)-protected gold nanoparticles since they enable a modular approach to tune single-molecule affinity and selectivity simply by changing functional moieties (i.e., covering ligands), along with multivalent molecular recognition. To date, the discovery of monolayers suitable for a specific molecular target has relied on trial-and-error approaches, with ligand chemistry being the main criterion used to modulate selectivity and sensitivity. By using molecular dynamics, we showcase that either individual molecular characteristics and/or collective features such as ligand flexibility, monolayer organization, ligand local ordering, and interfacial solvent properties can also be exploited conveniently. The knowledge of the molecular mechanisms that drive the recognition of small molecules on SAM-covered nanoparticles will critically expand our ability to manipulate and control such supramolecular systems.

Spotting Local Environments in Self-Assembled Monolayer-Protected Gold Nanoparticles

“…Homoligand SAMs were modeled purely at atomic level. The full computational procedure for constructing the CG and AA SAM-functionalized NPs follows our previous works ,,,, and is described in detail in the Supporting Information. AA nanoparticle models in explicit water were then extracted from equilibrated MD trajectories and used for subsequent MD and SOAP-GMM analysis.…”

“…Thus, we wondered if a general way to identify specific local settings in SAMs could exist. Molecular dynamics (MD) and coarse-grained simulations have been instrumental in retrieving information difficult to infer from experiments and in explaining the behavior of SAM-AuNPs at molecular and nanoscale with good reliability. − Over recent years, the increasingly large amounts of data produced by these calculations have also been used by algorithms to extrapolate molecular patterns and predict (meta)­stable configurations or structural motifs in complex matter. − …”