Theoretical Study of the Molecular Mechanism for the Oxygenation Chemistry in Rubisco

Abstract

A set of transition structures (TSs) related to the oxygenation reaction catalyzed by Rubisco is characterized theoretically. The TSs correspond to dioxygen fixation at the C2 center, hydrolysis, and C2−C3 bond breaking; reaction intermediates were found from TSs using the intrinsic reaction coordinate approach. Hydroxypropanone and 3,4-dihydroxy-2-pentanone are used as molecular models for the substrate d-ribulose-1,5-bisphosphate. Ab initio SCF MO calculations at a 3-21G and 6-31G** basis set level of theory were used; the correlation energy has been included at the MP2/6-31G** level. The set of TSs can be docked at the active site of the enzyme without steric hindrance. The geometries of the fully optimized reactants and intermediates differ to a large extent when compared with the saddle point structures. It is inferred that a molding work would be required in order to give them a molecular surface that is complementary in shape to that of the active site. A comparison of the theoretically determined ...