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A numerical study was performed to compare the formation of nitric oxide (NO) and nitrogen dioxide (NO₂), collectively termed NOx, resulting from biodiesel and diesel combustion in an internal combustion engine. It has been shown that biodiesel tends to increase NOx compared to diesel, and to-date, there is no widely accepted explanation. Many factors can lead to increased NOx formation and it was of interest to determine if fuel chemistry plays a significant role. Therefore, in order to isolate the fuel chemistry from mixing processes typical in a compression ignition engine, sprays were not considered in the present investigation. The current study compares the NOx formation of surrogates for biodiesel (as represented by methyl butanoate and n-heptane) and diesel (n-heptane) under completely homogeneous conditions. Combustion of each fuel was simulated using the Senkin code for both an adiabatic, constant volume reactor, and an adiabatic, single-zone HCCI engine model.