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Synthetic bio-fuels, which can be obtained through the gasification of biomass into synthesis gas and the subsequent catalytic reaction of the synthesis gas into liquid fuel molecules, could play a key-role in providing a sustainable source of automotive fuels during the coming decades. This paper presents an attempt to understand the effect of molecular structure of potential oxygenated synthetic bio-fuel molecules of different structure on the diesel combustion process in both stratified and homogeneous combustion modes. Specifically, the effects of molecular structure on the energy release rates, gaseous exhaust emissions and the sub-micron particulate matter distribution were examined. The experiments were carried out on a single-cylinder direct-injection diesel engine using a specially adapted common-rail fuel-system which allowed the injection of small single-molecule fuel samples at high pressure.