In this work, we present mixed integer linear programming methods for the synthesis of processes that involve complex reaction networks. Specifically, we consider the modeling of reactors and interconnecting streams in systems where the composition of the reactor inlet streams can vary substantially, thereby making the determination of the limiting component as well as the calculation of the stream heating/cooling and power requirements challenging. First, towards the modeling of reactors, we develop an extent-based method which detects the limiting reactant of each reaction occurring in parallel with others, based on the inlet flows of the reactants. Second, we develop a computationally tractable method for the calculation of the work and heating/cooling duty needed to condition any stream of a process based on simple calculations that can be performed offline. Finally, we present how the two aforementioned components can be integrated in an optimization model generated based on a process superstructure. We demonstrate the application of the developed methods for the synthesis of a biorefinery. (C) 2018 Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.