The reaction ensemble Monte Carlo method was used to model the self-assembly and structure of silica nanoparticles found in the initial stages of the clear-solution synthesis of the silicalite-1 zeolite. Such nanoparticles, which comprise both silica and organic structure-directing agents (OSDAs), are believed to play a crucial role in the formation of silica nanoporous materials, yet very limited atomic-level structural information is available for these nanoparticles. We have modeled silica monomers as flexible tetrahedra with spring constants fitted in previous work to silica bulk moduli and OSDAs as spheres attracted to anionic silica monomers. We have studied one-step and two-step formation mechanisms, the latter involving the initial association of silica species and OSDAs driven by physical solution forces, followed by silica condensation/hydrolysis reactions simulated with reaction ensemble Monte Carlo. The two-step process with preassociation was found to be crucial for generating nearly spherical nanoparticles; otherwise, without preassociation they exhibited jagged, ramified structures. The two-step nanoparticles were found to exhibit a core-shell structure with mostly silica in the core surrounded by a diffuse shell of OSDAs, in agreement with SANS and SAXS data. The Qn distribution, quantifying silicon atoms bound to n bridging oxygens, found in the simulated nanoparticles is in broad agreement with 29Si solid-state NMR data on smaller, 2 nm nanoparticle populations. Ring-size distributions from the simulated nanoparticles show that five-membered rings are prevalent when considering OSDA/silica mole fractions (∼0.2) that lead to silicalite-1, in agreement with a previous IR and modeling study. Nanoparticles simulated with higher OSDA concentrations show ring-size distributions shifted to smaller rings, with three-membered silica rings dominating at an OSDA/silica mole fraction of 0.8. Our simulations show no evidence of long-range silicalite-1 order in these nanoparticles.