Computational and experimental studies on the effects of oxygenated fuels with single and split high-pressure fuel injections were conducted at both high and low load engine operating conditions. The oxygenates were a long chained ester and ether blended with conventional diesel fuel. An improved version of the KIVA-II multidimensional engine code was used in the study, and the soot model was modified to account for the influence of the oxygenate. Overall, very good agreement between measured and predicted soot emissions was achieved, including prediction of the substantial reductions in soot seen with the oxygenated fuels and with split injections. The measured NO trends as a function of fuel injection timing were captured in the computations. However, the magnitudes of the NO emissions were under-predicted for the oxygenated fuels when using the thermal Zeldo'vich mechanism with the largest discrepancy observed for the fuels with the highest concentration of oxygen. Experiments show that the contribution of soluble organics to the particulate matter is significant at light load. Practical models are proposed and evaluated for the calculation and prediction of soluble organic fractions (SOF) in the particulate matter. The models depend on accurate predictions of unburned hydrocarbon emissions. The predicted SOF agreed well with measured SOF values, especially at earlier fuel injection timings.