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, NH 2 or CF 3 groups. The calculations predict that 1-CN, 1-CF 3 -cis, 5-NH 2 , 6-CN, and 6-CF 3 substituents increase the activation barriers, in agreement with experimental results on substituent effects by CN, CF 3 , and the related 5-OCH 3 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.