In partially premixed combustion engines high octane number fuels are injected into the cylinder during the late part of the compression cycle, giving the fuel and oxidizer enough time to mix into a desirable stratified mixture. If ignited by auto-ignition such a gas composition can react in a combustion mode dominated by ignition wave propagation. 3D-CFD modeling of such a combustion mode is challenging as the rate of fuel consumption can be dependent on both mixing history and turbulence acting on the reaction wave. This paper presents a large eddy simulation (LES) study of the effects of stratification in scalar concentration (enthalpy and reactant mass fraction) due to large scale turbulence on the propagation of reaction waves in PPC combustion engines. The studied case is a closed cycle simulation of a single cylinder of a Scania D13 engine running PRF81 (81% iso-octane and 19% n-heptane). Two injection timings are investigated; start of injection at -17 CAD aTDC and -30 CAD aTDC. One-equation transported turbulence sub-grid closure is used for the unresolved momentum and scalar fluxes and the fuel spray is modelled using a Lagrangian particle tracking (LPT) approach. Initial flow conditions (prior to intake valve closing) are generated using a scale forcing method with a prescribed large-scale swirl mean flow motion. Fuel reactivity is modeled using finite rate chemistry based on a skeletal chemical kinetic mechanism (44 species, 140 reactions). The results are compared with optical engine experimental data and satisfactory agreement with the experiments is obtained in terms of the liquid spray length, cylinder pressure trace and ignition location. A majority of the fuel consumption is found to be in ignition fronts where small variations in temperature at low fuel concentrations are observed to cause large stratification in ignition delay time.