Second-generation biofuels will be derived from lignocellulosic biomass using biological catalysts to convert the carbon in plant cell wall polysaccharides to ethanol or other biofuels. The Center for Direct Catalytic Conversion of Biomass to Biofuels (C3Bio) is a DOE-funded Energy Frontier Research Center, which aims to develop transformational technologies to maximize the energy and carbon efficiencies of biofuels production. Heterogeneous chemical catalysis using inorganic and robust catalysts provides an alternative strategy to biological fermentation routes for the production of advanced biofuels, including alkanes and the aromatic components characteristic of gasoline. Designing new catalysts for converting lignocellulosic biomass to biofuels requires understanding the interactions of catalysts with the chemical and physical structures of the biomass at scales ranging from atoms to macromolecules. We are also exploring thermal treatments, including fast-hydropyrolysis, that may generate a bio-crude oil suitable for catalytic upgrading. Our preliminary data show that the composition of maize stover impacts the spectrum of fragments derived from pyrolysis molecular-beam mass spectrometry (PyMBMS). This method relies on thermal degradation of the cell wall constituents under anoxic conditions to provide information about hexose and pentose content, and the content and composition of phenolic compounds derived from lignin and hydroxycinnamic acids. The fact that we can detect changes in spectral profiles from PyMBMS of different genetic lines of maize indicates that specific alterations in the carbohydrate-lignin architecture of the cell wall may improve the selectivity of reaction products and the efficiency of fast-hydropyrolytic and catalytic conversion. We are generating variants of cell wall structures by manipulation of endogeneous plant genes, in both Arabidopsis and maize, and transgenic lines that incorporate catalysts directly or functionalized sites for future catalysis as the plants grow, that is, biomass tailored for its end-use in new conversion processes.