The emissions of modern Diesel engines, which are known to have various health effects, are beside the drivers torque demands and low fuel consumptions one of the most challenging issues for combustion and after treatment control. To comply with legal requirements, emission control for heavy duty engines is not feasible without additional hardware, usually consisting of a Diesel oxidation catalyst (DOC), a Diesel particulate filter (DPF) and a selective catalytic reduction (SCR) system. In contrast to other NOx reduction systems, e.g. lean NOx traps, the SCR system requires an additional ingredient, namely ammonia (NH3), to reduce the NOx emissions to non harmful components. Consequently, the correct amount of NH3 dosing in the SCR catalyst is one of the critical components to reach high conversion rates and avoid ammonia slip.Against this background and in contrast to existing proposals in which the NH3 dosing is often calculated based on a NOx emission sensor, this work presents a strategy to adopt the set point estimation of the NH3 dosing, based on a virtual NOx sensor extended by a virtual DOC model. On basis of that structure the NO/NO2 ratio and the NOx mass flow entering the SCR is estimated and accordingly the correct dosing amount of ammonia.Furthermore a model predictive controller - including the set point calculation, calibrated with a SCR model and the feedback from a NH3 sensor at the outlet of the SCR - is developed and tested in simulation on a dynamical driving cycle. To validate the advantages of the NO/NO2 value estimation for the SCR control the methods are compared in different aspects like the conversion efficiency and the NH3 slip for dynamical load changes.