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Carbon can be used to create unusual nanostructures of Si–C–O by controlled pyrolysis of silsesquioxane organics. Unlike silica, these ceramics resist crystallization at ultrahigh temperatures. Their structure has been compared with that of polymers, where crosslinked chains of polymers in organics are replaced by crosslinked networks of graphene in the ceramics. The network sequesters nanoscale domains of SiO4 tetrahedra. The resistance to crystallization of these nanodomain networks has been attributed to kinetic factors, namely obstruction of long-range diffusion of silica. In this work, we identify a thermodynamic hindrance to crystallization. Calorimetric measurements of heats of dissolution in a molten oxide solvent show that these ceramics possess a negative enthalpy relative to their crystalline constituents (silicon carbide, cristobalite, and graphite). The thermodynamic stability of the nanodomain structure is explained by a low free energy of the graphene–silica interfaces, perhaps related to the presence of mixed bonds of silicon bonded to both carbon and oxygen.