We have studied the adsorption of n-butane and isobutane in the mesoporous silica SBA-2. Our work has two purposes: (i) to better understand the structure of the material, and in particular the impact of calcination on the evolution of the pore network, and (ii) to investigate our ability to tune the structure of SBA-2 to separate normal and isoalkanes by molecular sieving. By a combination of experimental adsorption measurements, molecular simulation, and percolation analysis, we determined the evolution of the sizes of the pores and the connectivity of the pore network as the calcination temperature increases. For a certain range of calcination temperatures, the pore network drops below its percolation threshold for isobutane, while allowing the percolation of n-butane, giving an extremely high selectivity for n-butane over isobutane. This suggests that tuning the window size of SBA-2 and other structured mesoporous materials of this general type has the potential to generate optimized adsorbents for particular applications.