The influence of the ligands H, CH₃, OH, and F on the preferred geometric structure of passivated silicon nanoclusters was investigated by ab initio density functional calculations. Si₁₀L₁₆ has enough ligands to allow the silicon core to form the bulk Si like structure often anticipated to be present in silicon nanoparticles. Our calculations confirm that H and CH₃ ligands do favor being uniformly spread over the Si core to form the expected passivated nanoparticle structures. However, we find the more electronegative F or OH ligands to more strongly favor forming SiL₃ groups thereby causing the bulk Si like analog to be appreciably higher in energy. Similar structural trends were also found when comparing the relative energies of L₂SiSiL₂ against LSiSiL₃ with the same series of ligands L. The calculations suggest that to theoretically understand the properties, such as the bright photoluminescence, of passivated Si nanoclusters is going to require a model which takes into account the appropriate structural features of the particle.