Abstract: We studied the chiral transition mechanism of two conformations of lysine (Lys) molecules confined in the helically chiral SWBNNT by using the ONIOM methods of combination of quantum mechanics and molecular mechanics. The results show that the Lys molecular skeleton deformation
 of helically chiral SWBNNT in small tube diameter is obvious. When two conformations of Lys molecules confined in the SWBNNT(6,4), the apparent energy barriers of the optical isomerism reaction are 175.90,230.44 kJ/mol, respectively, the intrinsic energy barriers of the ratedetermining step of the optical isomerism reaction are 211.40,230.44 kJ/mol, which come from the transition states that the proton transfer from the chiral C to amino N and are low
er than the energy barrier of the ratedetermining step of bare reaction (252.60 kJ/mol). The smaller  tube diameter of the helically chiral SWNT, the better  confined catalytic action, and Lys molecules that confined in SWBNNT(6,4) with the single hydrogen bonds between amino group and carboxyl are optical isomerism in the first place.

Key words: lysine, helically chiral, chiral transition, perturbation theory, ONIOM method, transition state, nanotube, density functional