Chemical reactions are often carried out in nanostructured materials, which can enhance reactions due to their large specific surface area, their interactions with the reacting mixture and confinement effects. In this work, we present a systematic study of the effect that the geometrical restrictions imposed by the pore walls can have on reactions that involve a three dimensional rearrangement of the atoms in a molecule. In particular, we consider the isomerization of three 4-membered hydrocarbons-n-butane, 1-butene and 1,3-butadiene confined in carbon nanopores of slit geometry. Our results illustrate the fact that, in the molecular sieving limit, the reaction rates change as the double exponential of the pore size (Santiso et al., in J. Chem. Phys., 2007a, submitted), and therefore the transition rates in nanopores can be many orders of magnitude different from the corresponding bulk values. These results can be used as a guideline for the molecular-level design of improved catalytic materials.