Flavin mononucleotide (FMN, 1) provides a dynamic conformational probe for studying the covalent cross-linking of dopants into silica. Excitation of FMN 1 leads to photodecomposition only when the side chain is in an appropriate geometry to allow a six-membered ring transition state. Our investigations indicate that the rate of photodecomposition dramatically changes in the sol-gel through the course of the gelation and aging process. Rapid changes in the decomposition rate were observed in the sol very early in the gelation process, indicating that the hydroxyl groups of 1 become covalently fixed within the silicate matrix and that silicate structure is formed around this site very early in the sol-gel process.