Several technologies for synthesis gas (syngas) refining are introduced into a thermochemical based superstructure that will convert biomass, coal, and natural gas to liquid transportation fuels using Fischer-Tropsch (FT) synthesis or methanol synthesis. The FT effluent can be (i) refined into gasoline, diesel, and kerosene or (ii) catalytically converted to gasoline and distillate over a ZSM-5 zeolite. Methanol can be converted using ZSM-5 (i) directly to gasoline or to (ii) distillate via olefin intermediates. A mixed-integer nonlinear optimization model that includes simultaneous heat, power, and water integration is solved to global optimality to determine the process topologies that will produce the liquid fuels at the lowest cost. Twenty-four case studies consisting of different (a) liquid fuel combinations, (b) refinery capacities, and (c) superstructure possibilities are analyzed to identify important process topological differences and their effect on the overall system cost, the process material/energy balances, and the well-to-wheel greenhouse gas emissions. (C) 2012 Elsevier Ltd. All rights reserved.