We employed the "partially reacted substructure (PRS)" method to enhance the material properties of the diglycidyl ether of bisphenol A (DGEBA) epoxy thermosets. This method involves first partially curing DGEBA with a small amount of poly(oxypropylene)diamine (POPDA) and then adding DGEBA and diethyltoluenediamine (DETDA) to continue to a fully cured sample. PRS-induced DGEBA-DETDA/POPDA 2:1 epoxy-amine stoichiometric samples have consistently higher Tg's and glassy state densities than samples created using one-step cure of a blend of DGEBA with both DETDA and POPDA. PRS-induced samples were found to be twice as tough as non-PRS samples. Because the compositions are identical, differences observed must arise from differences in the network isomers formed by the two curing protocols and the resulting differences in packing and intermolecular interactions. Molecular dynamics (MD) simulations were carried out to better understand these phenomena. The density and glass transition temperature in the simulations are in quantitative agreement with the experimental results. One reason for this Tg increase in PRS-induced samples may be related to the pendant methyl groups on POPDA, as illustrated using radial distribution functions (RDF's) computed from the MD simulation trajectories. Methyl-methyl RDF's for non-PRS samples did not differ significantly from those of the prepolymerized liquid, but the methyl-methyl RDF's for the PRS-samples showed stronger methyl-methyl correlation at all distances, signifying better intra- and intermolecular POPDA packing. This results in lower POP backbone flexibility in the PRS samples and consequently higher Tg's relative to the non-PRS samples. Further simulations aim to ultimately focus on the ductility enhancement conferred by PRS.