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 inline 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. In the conclusions, some suggestions for adoption of appropriate bio-fuels as alternatives of diesel for lower emissions have been proposed by being observed differences in soot emission propensities.