Atomic Insights into the Evolution of Three-Dimensional Molecular Junctions in Plasmonic Core-Shell Nanoparticles

The plasmonic molecular junctions are of wide interest for the studies of physics, chemistry, and materials science. For the three-dimensional (3D) molecular junctions inside plasmonic core-shell nanoparticles, the junction morphology plays a vital role in optical properties and related applications. However, the atomic insights into the structural evolutions of interior 3D molecular junctions are still lacking. This work investigated the formation of 3D molecular junctions in gap-enhanced Raman tags experimentally and theoretically. With monolayered or double-layered molecules embedded, either symmetric or asymmetric 3D junctions can be tailored in experiments. By studying the interactions between gold atoms and thiolated molecules using molecular dynamics simulation, we revealed that the junction morphology was determined by the embedded molecular layers. Asymmetric nanogaps were formed due to different molecular orientations, packing, and ring stacking structures. We further designed a multinucleation strategy to obtain symmetric and uniform junctions with multilayered molecules. This work offers a general framework for the simulations of complex junction systems, brings new insights into the morphology evolution of 3D plasmonic junctions, and facilitates the developments of molecular-based plasmonic nanodevices.