Ab initio quantum mechanics and ONIOM calculations were used to study solvent and substituent effects on the reactions of 1,4-Benzoquinone with Cyclopentadiene and Cyclohexadiene derivatives in tetrahydrofuran and greater water solvents. These calculations revealed (i) that increasing the number of electron donating methyl group substituents and (ii) the proximity of substituents to the reacting carbons (carbon atoms which contribute to the forming C-C bonds) on the diene, promote charge transfer from the diene to the dienophile in the transition state. These effects increase the negative charge on the oxygen atoms, destabilize the transition state in the organic solvent by increasing steric interactions, and stabilize the transition state in water solvent by increasing the strength of hydrogen bonding. These results, along with consideration of variations in the solvent-accessible surface area (SASA) confirmed that the dramatic acceleration in the rate of the studied reactions in water solvent arise in part from hydrophobic association of the reactants, but predominantly arise from hydrogen bonding between water molecules and the polarized transition state.