Synthetic diesel fuel produced from natural gas via gas-to-liquid (GTL) technology is referred to as ultraclean fuel but is still challenged for full certification as diesel fuel. GTL diesel lacks certain hydrocarbons and chemical constituents, which although are benign to the environment, result in a trade-off in performance when used in a diesel engine. To boost GTL diesel physicochemical properties and thereby enable its use in conventional diesel engines, GTL diesel needs improvement. This can be achieved by mixing suitable additives to the GTL diesel and through the development of surrogate fuels that have fewer components. Screening of thousands of additives is a tedious task and can be done efficiently via computer based modeling to quickly and reliably identify a small number of promising candidates. These models are used to guide the formulation of five surrogates and predict their physicochemical properties. These surrogates are further verified using rigorous mathematical tools as well as through advanced experimental techniques. An optimal surrogate MI-5 is identified, which closely mimics GTL diesel-conventional diesel blends in terms of its physicochemical properties. An engine study for the surrogate is also performed to understand the effect of physicochemical properties on combustion as well as the emission behavior of the fuel. MI-5 exhibited an optimal torque at higher load conditions. A reduction of 11.26% NOx emission for MI-5 is observed when compared to conventional fuel. At higher loads, diesel fuel surpasses the total hydrocarbon (THC) emissions for both the surrogate and the GTL fuel. No significant variation in CO and CO2 emissions for MI-5, GTL diesel and conventional diesel is observed. Analysis of combustion as well as emission behavior of the fuels helps to understand the role of physicochemical properties on the performance of the fuel.