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Phtalonitrile-based matrixes are thermostable resins used for durable reinforcement materials. The resins are typically produced by two-stage curing of phthalonitrile monomers in presence of initiator. During the first low temperature stage (~200 °C), nitrile groups transform into inter-monomer bonds between isoindoline groups, which is the typical polymerization path. The second curing stage is aimed to reach higher conversion rate and produced at elevated temperatures (300 – 350 °C), at which triazine can be formed by three monomers. Effectively, triazine is a triple link between monomers, making the topology of the polymer network even more complex. The effect of triazine crosslinks in the structure and physical properties of the material is important but unclear up to now. We have developed a multiscale simulations scheme of phthalonitrile thermosetting resins. The scheme contains a set of consecutive phases from dissipative particle dynamics (DPD) level to molecular dynamics. On the first step, we simulate two-stage curing process with DPD technique. Next, a reverse mapping procedure is used to convert coarse-grained structures onto atomistic ones. A Monte Carlo refinement procedure with soft repulsive potentials and molecular dynamics (MD) relaxation in used to avoid the short cycle spearing. The prepared material samples are used for the following MD simulations to estimate thermophysical and mechanical properties of the material. In this report, we present and discuss unusual thermophysical and mechanical properties for the phthalonitrile matrixes obtained with using different comonomers and polymerization protocols. MD analysis indicates that triazine formation prevents the matrix from Tg grow at low conversion degrees. Topological analysis indicates that triazine formation leads to less interconnected matrices with larger cycles, which are less mechanically strong. This counterintuitive behaviour contrasts strongly with common effects induced by high functionality crosslinkers, and originates from the details of the chemical reaction taken into account in the simulation scheme.