Abstract:  Methods of combined quantum chemistry ONIOM (Our own N-layered Integrated molecule Orbit and molecule Mechanics) are widely used to study the chemical reaction system associated with nanotubes. This work will study the system which is divided into two layers. The inner layer is α-alanine, using the B3LYP method based on density functional theory, and basis set selection 6-31++G (d, p); The outer layer, a single arm boron nitride nanotubes SWBNNT (9,9) is processed by using molecular mechanics UFF (universal force field) force field, and then the molecular structure and the hiral transition reaction mechanism of α-alanine confined in SWBNNT (9,9) are studied, besides, the stable point and transition state of chiral shift reaction process has been optimized. By analyzing the imaginary frequency vibration mode of transition states and intrinsic reaction coordinate (IRC)calculation for the transition states, the reliability of the transition state has been determined. In order to obtain relatively high levels of energy of the system, here we depict potential energy surface of the relatively exact chirality process of transformation and calculate a single point energy of each Inclusion on the ONIOM (B3LYP /6-311++G(3df, 3pd): UFF) level. Then correcting the total system energy of zero-point vibrational energy, we draw the potential energy surface of the reaction process. The analysis to molecular structure shows that: compared with the monomer α-alanine, the bond lengths of skeleton C-N are shorten in different degree when α-alanine is confined in SWBNNT (9,9). At the same time, the bond angles of skeleton carbons and the dihedral angles of skeleton C-N increase slightly. The study of reaction channel of chiral shift shows that: there are two roughly same reaction with channels of chiral shift of α-alanine in SWBNNT (9,9), and only the reaction channel of collaborative transfer of hydrogen in carbonyl and methyl without monomer. The calculation of potential energy surface in chiral shift reaction shows that: compared the monomer α-alanine chiral transformation, when α-alanine is limited in SWBNNT (9,9), the energy barrier of outboard hydrogen which transfers from chiral carbon directly to oxygen in carbonyl reduces from 326.5 kJ?mol-1 to 319.7 kJ?mol-1. The energy barriers of hydrogen transfer inside the carboxyl and hydrogen in chiral carbon transfer from outboard to carbonyl respectively decrease from 198.0 kJ?mol-1 and 320.3 kJ?mol-1 to 135.5kJ?mol-1 and 302.7 kJ?mol-1. The results show that：the energy barriers of different hydrogen transfer decrease in different degree, when α-alanine is limited in SWBNNT (9, 9).