A series of molecular dynamics (MD) simulations of different pregelification mixtures representing intermediate stages of the sol gel process were set up to gain insight into the molecular imprinting process in xerogels, namely, to assess the template gel affinity and template self-aggregation. The physical plausibility of the parametrization was checked, confirming the reliability of the simulations. The simulated mixtures differed in the water/methanol ratio (1:3, 5:3, and 5:1) and in the absence/presence of an organic functional group (phenylaminopropyl-) in the silicate species. The simulation results, expressed mainly by the radial distribution functions and respective coordination numbers, showed that the affinity of the template molecule, damascenone (a hydrophobic species), for the gel backbone would not be attained without the tested functional group, phenylaminopropyl-. The affinity, related to the capability to trap the template within the gel network, was derived mostly from the hydrophobic interaction. It was also inferred from MD simulations that lower water contents (methanol-richer mixtures) would facilitate a better dispersion of both the functional group and the template within the final gel, therefore favoring the imprinting process. From the experimental counterparts of the simulated mixtures, a series of imprinted and nonimprinted xerogels were obtained. There was only one xerogel exhibiting the imprinting effect, namely, the one containing the organic group obtained at the lower water/methanol ratio (1:3), in agreement with predictions from the MD simulations. Such congruence demonstrates the ability of MD simulations to provide information regarding the fine aspects of molecular interactions in pregelification mixtures for imprinting.