Zero-point energies (ZPEs) of hydroxyl ion and hydrogen and water molecules, free and compressed in C60 cages, are computed; the excess energy acquired by molecules under compression is in the range 2–3 kcal/mol and depends on the isotopes. The differences in ZPE of compressed isotopic molecules strongly exceed those of the free molecules, resulting in the large deuterium and tritium isotope effects. These effects induced by compression are suggested as a probe for testing molecular compression of enzymatic sites; they may be important for understanding enormously large isotope effects observed in some enzymatic reactions, where they are attributed to the tunneling.