In this paper we have applied the molecular dynamics simulations in order to analyse the role of the structure directing tetrapropylammonium ions in the aggregation process that leads to silicalite formation. We address the specific question of how the interactions between silica precursor species and tetrapropylammonium ions/water evolve during the formation of the larger aggregates, that show initial micropore formation from more elementary building blocks. We have followed the dynamics and changes in the position of the tetrapropylammonium ions into the formation of TPA-Si22 complexes. Moreover, the analysis based on the geometries of the systems being studied as well as the radial distribution function allowed us to predict the location of the TPA cations in fully formed nanoslabs. An interesting result is reported that the template cannot be accommodated any more in the newly formed cavities, but is pushed out of the channel like cavities to positions where in a later stage channel cross sections can be formed. © 2009 the Owner Societies.