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Numerous previous studies have reported that the reduction of emissions by adapting oxygenated bio-fuels chiefly depend on the overall oxygen percentage of the blended oxygenates. However, the effect of molecular structures of the fuels has sometimes only been attributed to differences in auto-ignition quality (i.e. cetane number). In this paper, fuels with two kinds of molecular structures, namely linear and cyclic, have been studied. It reports on emissions tests on a modified in-line 6-cylinder DAF HD Diesel engine with several selected oxygenates mixed with diesel. Fuels in question here are from the non-oxygenates group: n-hexane and cyclohexane, and the oxygenate group: 1-hexanol and cyclohexanol. In order to isolate the effect of molecular structure, the blend compositions are chosen such that the overall oxygen fraction of all blends is the same.