Detailed combustion studies have historically been conducted in simplified reacting systems, such as shock-tubes and rapid compression machines. The reciprocating internal combustion engine presents many challenges when used to isolate the effects of fuel chemistry from thermodynamics. On the other hand, the conditions in such engines are the most representative in terms of pressure and temperature histories. This paper describes the use of a single-cylinder research engine as an advanced reactor to better determine fuel effects experimentally. In particular, a single-cylinder engine was operated in a manner that allowed the effects of changes in charge composition and temperatures to be isolated from changes in equivalence ratio. An example study is presented where the relative effects of low-temperature and high-temperature chemistry, and their effects on combustion phasing, are isolated and examined. A single-zone homogeneous model based on Chemkin™ code with detailed chemistry was interrogated to better understand some of the trends identified.The engine was operated in HCCI mode under both steady-state conditions and in an alternate-fired mode. The technique allows the effect of fuel/air equivalence ratio to be isolated from other parameters such as trapped residual content and wall temperatures. The Chemkin™ model was run with a 5-component mechanism from the Reaction Design Model Fuels Consortium and was calibrated using data from the steady-state engine tests. Results showed good correlation with combustion start and phasing for both the low- and high-temperature zones. The model was then used to explain the relationship between energy released and equivalence ratio in both the low- and high-temperature regimes.