Achieving Molecular Recognition of Structural Analogues in Surface‐Enhanced Raman Spectroscopy: Inducing Charge and Geometry Complementarity to Mimic Molecular Docking

Molecular recognition of complex isomeric biomolecules remains challenging in surface‐enhanced Raman scattering (SERS) spectroscopy due to their small Raman cross‐sections and/or poor surface affinities. To date, the use of molecular probes has achieved excellent molecular sensitivities but still suffers from poor spectral specificity. Here, we induce “charge and geometry complementarity” between probe and analyte as a key strategy to achieve high spectral specificity for effective SERS molecular recognition of structural analogues. We employ 4‐mercaptopyridine (MPY) as the probe, and chondroitin sulfate (CS) disaccharides with isomeric sulfation patterns as our proof‐of‐concept study. Our experimental and in silico studies reveal that “charge and geometry complementarity” between MPY's binding pocket and the CS sulfation patterns drives the formation of site‐specific, multidentate interactions at the respective CS isomerism sites, which “locks” each CS in its analogue‐specific complex geometry, akin to molecular docking events. Leveraging the resultant spectral fingerprints, we achieve > 97 % classification accuracy for 4 CSs and 5 potential structural interferences, as well as attain multiplex CS quantification with < 3 % prediction error. These insights could enable practical SERS differentiation of biologically important isomers to meet the burgeoning demand for fast‐responding applications across various fields such as biodiagnostics, food and environmental surveillance.