Abstract: Hierarchical organization of gold nanorods was previously obtained on a substrate, allowing precise control over the morphology of the assemblies and macroscale spatial arrangement. Herein, a thorough description of these gold nanorod assemblies and their orientation within supercrystals is presented together with a sol?gel technique to protect the supercrystals with mesoporous silica films. The internal organization of the nanorods in the supercrystals was characterized by combining focused ion beam ablation and scanning electron microscopy. A mesoporous silica layer is grown both over the supercrystals and between the individual lamellae of gold nanorods inside the structure. This not only prevented the detachment of the supercrystal from the substrate in water, but also allowed small molecule analytes to infiltrate the structure. These nanocomposite substrates show superior Raman enhancement in comparison with gold supercrystals without silica owing to improved accessibility of the plasmonic hot spots to analytes. The patterned supercrystal arrays with enhanced optical and mechanical properties obtained in this work show potential for the practical implementation of nanostructured devices in spatially resolved ultradetection of biomarkers and other analytes.

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