The chiral transition of lysine molecules confined in water and MOR zeolite combined environment was studied in the paper by introducing the ONIOM methods using combination of quantum mechanics and molecular mechanics. The molecular structure researches show that hydrogen bond angle of the transition state molecules in the hydrogen transfer reactions with the help of two water molecules is significantly larger than that with the help of one water molecule. The study of reaction channels shows there are three channels a

b and c in the title reaction where lysine is confined in MOR zeolite

protons transfer with the help of water molecules from one side to the other of the chiral C with amino

carbonyl and hydroxyl as a bridge

and at last the chiral transition is achieved. Calculations of potential energy surface show that channel a is the dominant reaction path and protons transfer the chiral C to amino is the stepdetermining where gibbs free energy barrier of two water-assisted proton transfers reaction is reduced to the minimum value 101.9 kJ·mol

-1

that is significantly lower than the gibbs free energy barrier 252.6

229.7 and 123.9 kJ·mol

-1

respectively corresponding to the bare reaction

confined in MOR zeolite and confined in water environment. The results show that water and MOR zeolite combined environment has a good co-catalysis on the chiral transition of lysine molecules

and SLys in vivo can be slowly optical isomerism.