This study relates to the development of future biofuels and it reports the effects of fuel molecular structure of various oxygenated compounds on compression auto ignition and exhaust emissions. The experimental study was conducted on a single cylinder compression ignition research engine. Ethers and various carbonyl compounds were investigated, including ketones, carboxylic acids and methyl esters. The results for these compounds were also compared to those for alcohol and alkane combustion obtained in a previous study. It was found that oxygen-bearing functional groups within various C8-C16 fuel molecules have a significant influence on the ignition delay and on engine in-cylinder temperatures. Carbonyl compounds had longer ignition delays compared to the corresponding alkanes, whereas ether compounds decreased the ignition delay. It is suggested that these observations relate to the changes in the relative ease of hydrogen abstraction and the ability of a fuel peroxy radical to undergo isomerization during the low-temperature combustion chemistry preceding ignition. In addition, it was observed that, both moving a carbonyl group closer to the centre of the carbon chain of a molecule and adding a double bond to a carboxylic acid increased the ignition delay. Oxygen in the fuel molecule, excluding carboxylic acids, was observed to increase the NOx emissions and decrease the mass of particulates in the exhaust gas. (C) 2015 Elsevier Ltd. All rights reserved.