Small-Molecule-Mediated Molecular Recognition Controls Tryptophan Self-Assembly and Programs Tunable Emission

Engineering fluorescence from natural biomolecules without covalent modification offers a sustainable route to functional optical materials, yet biomolecule-based optical materials remain relatively unexplored, and the molecular principles governing their emergent photophysics remain poorly understood. Here, we demonstrate that small-molecule-directed self-assembly can redirect tryptophan (Trp) from uncontrolled fibrillar aggregation toward well-defined supramolecular architectures while tuning its intrinsic fluorescence through distinct molecular- and solvent-mediated pathways. Co-assembly with l-ascorbic acid (Asc, pH ∼ 3) suppresses the native Trp emission (∼350 nm) and generates a band at 470 nm (λex = 380 nm), showing a remarkable 120 nm red-shift, with a fluorescence quantum yield (ϕ) of 0.13. This process produces spherical assemblies (∼12.5 μm) through first-order kinetics, driven by π–π stacking, hydrogen bonding, and CH−π interactions. These stable assemblies exhibit reversible pH-responsive emission and reduced cytotoxicity compared to conventional dyes. In contrast, hydrazine (Hyd, pH 10) accelerates assembly formation by ∼2.5-fold, yielding larger spheres (∼18 μm) with emission centered at 430 nm (λex = 345 nm), exhibiting a 40 nm blue shift relative to Trp-Asc assemblies. Molecular dynamics simulations reveal distinct molecular mechanisms: Asc directly associates with Trp, whereas Hyd preferentially reorganizes the surrounding water network, indicating a predominantly solvent-controlled pathway for reorganization and association. Metadynamics further reveals that Hyd reshapes the Trp–Trp association landscape, favoring a specific geometry over tighter packing. Thus, small-molecule-mediated control over molecular recognition, solvation, and intermolecular organization can redirect uncontrolled biomolecular aggregation into defined supramolecular architectures while programming emergent fluorescence, establishing a noncovalent strategy for engineering supramolecular fluorophores from native biomolecules.