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This study investigates the characteristics of bio-oils produced from wheat straw in an updraft pyrolysis process developed by the DTU Chemical Engineering Department and Stiesdal SkyClean. The process was demonstrated in two pilot plants (100 kW and 200 kW) and scaled to a 20 MW commercial facility. Experiments were conducted at 500–550 °C using pelletized straw, with and without fractional condensation, to evaluate operational stability, product yields, and bio-oil quality. Fractional condensation reduced the water content of the bio-oil to ≤17 wt %, improving phase stability during storage and lowering oxygen content relative to fast-pyrolysis oils. However, reduced water content was accompanied by increased viscosity and a greater abundance of heavy aromatic structures. GC-MS and13 CNMR analyses showed that updraft bio-oils contained fewer light oxygenates (≈6.5 wt %) than fast-pyrolysis oils (≈23 wt %) and were enriched in high-molecular-weight compounds. This is attributed to extensive secondary gas-phase reactions, catalyzed by the high inorganic content of the straw pellets and by recirculation of pyrolysis gas, which enhanced char-gas interactions. Elevated concentrations of polycyclic aromatic hydrocarbons (PAHs)─300–400 ppm, or 3–10 times higher than values reported for intermediate and fast pyrolysis of agricultural residues─further indicated increased process severity. Energy balances showed that 39–45% of the feedstock energy was retained in the biochar and 18–21% in the bio-oil, with char yields of 22–26 wt % and bio-oil yields of ≈15 wt %. Toxicological analysis of 44 biochars produced from biogas-residue fibers confirmed compliance with the European Biochar Certificate standards for soil application, demonstrating the viability of the SkyClean concept for carbon sequestration and soil amendment. Overall, the findings highlight a trade-off between bio-oil quality and process severity in updraft pyrolysis and provide guidance for optimizing fractional condensation to balance fuel upgrading potential with negative-emission performance.