Single-Molecule Mapping of DFT Molecular Energetics and Binding Dynamics of a Multifunctional Molecule Using Whispering Gallery Mode Sensors

Elucidating molecular interactions at nanostructured interfaces is foundational to breakthroughs in catalysis, sensing, and environmental science, yet reconciling theoretical predictions with experimental evidence remains challenging, especially for small, multifunctional molecules with pH-dependent binding behaviour. Here, we present a sensing platform that integrates whispering-gallery mode (WGM) microresonators with gold nanorods (AuNRs) to enable real-time, label-free detection of molecular interactions at single molecule sensitivity. Using glyphosate (GLY) as a model system, we investigate its dynamic binding to AuNRs across a pH gradient. By bridging WGM sensing with density functional theory (DFT) calculations, we resolve the pH-dependent binding kinetics and thermodynamics of GLY on AuNRs, identifying the ionic states and specific conditions regulating its interaction. Our DFT framework, rigorously validated against experimental resonance shifts and surface-enhanced Raman spectroscopy (SERS) data, quantifies interaction energies and reveals the competition between GLY’s and buffer molecules for Au surface sites. Our results demonstrate strong agreement between computational predictions and experimental observations, validating the molecular-level mechanisms of GLY–AuNR interactions. This study highlights the potential of optoplasmonic sensing for probing interfacial molecular interactions with single-molecule sensitivity, providing a robust platform for validating theoretical models. The findings have broad implications for the rational design of nanoparticle-based sensing technologies in environmental monitoring, biomedical diagnostics, and surface chemistry, offering a powerful tool for investigating molecular recognition and binding dynamics at functionalized nanostructures.