Diesel fuels usually comprise a wide range of compounds having different molecular structures which can affect both the fuel's physical properties and combustion characteristics. In future, as synthetic fuels from fossil and sustainable sources become increasingly available, it could be possible to control the fuel's molecular structure to achieve clean and efficient combustion.This paper presents experimental results of combustion and emissions studies undertaken on a single cylinder diesel engine supplied with 18 different fuels each comprising a single, acyclic, non-oxygenated hydrocarbon molecule. These molecules were chosen to highlight the effect of straight carbon chain length, degree of saturation and the addition of methyl groups as branches to a straight carbon chain.The engine tests were carried out at constant injection timing and they were repeated at constant ignition timing and at constant ignition delay, the latter being achieved through the addition to the various fuels of small quantities of ignition improver (2-ethylhexyl nitrate). In tests conducted at constant injection and constant ignition timing the ignition delay of the molecule was found to be the primary driver of combustion phasing, the balance between premixed and diffusion-controlled combustion and, thereby, exhaust emissions. However, the elimination of ignition delay as a variable, using ignition improver, revealed further, subtler, secondary combustion effects also attributable to the molecular structure of the fuels tested. For example, with constant ignition delay, the premixed burn fraction and oxides of nitrogen in the exhaust for the various fuels correlated well with the volatility and the adiabatic flame temperature.