We present an extension of the simple-cubic lattice model developed by Jorge et al. [ J. Am. Chem. Soc. 2005, 127, 14388] of nanoparticle growth in the clear solution synthesis of silicalite-1 (MFI). We have implemented the model on a body-center cubic (bcc) lattice with second-neighbor repulsions, to generate a four-coordinate network that mimics the tetrahedral structure of silica. With this low-coordination lattice model we observe that the nanoparticles are metastable, possessing a core−shell structure with mostly silica in the core and templates forming a shell. Nanoparticle size is found to increase with temperature and decrease with solution pH, in qualitative agreement with results from experiment and the previous lattice model study. The low-coordination model makes it possible to model porosity in the silica core of nanoparticles. We use this feature to investigate the extent of template penetration into the silica core, a level of nuance missing in experimental data on the core−shell model. We find that template penetration is rare for bulky templates. We discuss the implications of this result for understanding the role of these nanoparticles in the growth of MFI, especially in light of recent experiments on the long-time behavior of nanoparticle suspensions.