A method of predicting the composition of hydrocarbon products of a complex carbonaceous material when exposed to specific time and temperature conditions is disclosed. In one embodiment, the material is characterized to obtain elemental, chemical and structural parameters. A representative chemical structure of the material is constructed based on the characterization information. The representative chemical structure is then stochastically expanded to a molecular ensemble chemical structural model that includes heteroatoms. The chemical structural model is coupled to a compositional yield model and the composition of the material products is determined using kinetic modeling. Methods are provided of constructing a chemical structural model of complex carbonaceous material, of coupling a molecular ensemble of chemical structures to a thermal chemical mechanism, of updating an ensemble of chemical structures during the kinetic modeling to reflect chemical reaction products and of eliminating molecules from the system.