The hydrolysis and condensation of a silylated derivative of ureidopyrimidinone led to nanostructured hybrid silica, such as that depicted, as clearly shown by powder XRD studies. The nanostructuring was directly related to molecular recognition through hydrogen bonding. By combining FTIR, solution and solid-state NMR spectroscopic data, the transcription of the hydrogen-bonding networks from the precursor to the final product was clearly evidenced.