Ab initio quantum mechanical methods with the B3LYP/6-31G* method were used to model the reactants, transition states, and products of Claisen rearrangements of allyl vinyl ethers substituted at all positions with CN, NH2 or CF3 groups. The calculations predict that 1-CN, 1-CF3-cis, 5-NH2, 6-CN, and 6-CF3 substituents increase the activation barriers, in agreement with experimental results on substituent effects by CN, CF3, and the related 5-OCH3 example. All other substituents lower activation energies. A Marcus theory type analysis was applied to separate the intrinsic and thermodynamic contributions to the activation energies.