Theoretical study of the molecular mechanism for the oxygenation chemistryin rubisco

A set of transition structures (TSs) related to the oxygenation reaction ca talyzed by Rubisco is characterized theoretically. The TSs correspond to di oxygen fixation at the C2 center, hydrolysis, and C2-C3 bond breaking; reac tion intermediates were found from TSs using the intrinsic reaction coordin ate approach. Hydroxypropanone and 3,4-dihydroxy-2-pentanone are used as mo lecular 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 se t of TSs can be docked at the active site of the enzyme without steric hind rance. The geometries of the fully optimized reactants and intermediates di ffer to a large extent when compared with the saddle point structures. It i s inferred that a molding work would be required in order to give them a mo lecular surface that is complementary in shape to that of the active site. A comparison of the theoretically determined transition structures and the transition state analogue 2'-carboxy-D-arabinitol 1,5-bisphosphate (CABP), whose X-ray structure at the active site is known, suggests that all aspect s of the reaction pathway can be achieved without changes in volume. There is a good correspondence between the intermediates suggested by experiments and those obtained here with both molecular models. The present results re present a mechanistic alternative to the catalytic process as it is current ly accepted in the literature.