Phthalonitrile compounds with Si bridges were recently suggested for producing thermosetting polymer composites with reduced Tg and thus expanded processing range. The detailed experimental investigation of this class of phthalonitriles is still difficult due to development time and costs limitations and the need to take into account the structural changes during the crosslinking. In this paper, we try to overcome these limitations using computer simulations. We performed full-atomistic molecular dynamics simulations of various phthalonitrile compounds to understand the influence of molecular structure on the bulk glass temperature Tg. Two molecular properties affect Tg of the resulting bulk compound: the size of the residue and the length of the Si bridge. The larger residues lead to higher Tgs, while compounds with longer Si bridges have lower Tgs. We have also studied relaxation mechanisms involved in the classification of the samples. Two different factors influence the relaxation mechanisms: energetic, which is provided by the rigidity of molecules, and entropic, connected with the available volume of the conformational space of the monomer.