A theoretical study of the molecular mechanism for the carboxylation chemistry in Rubisco

Stereochemical and structural aspects for the carbon dioxide fixation follo wed by hydration of D-ribulose 1,5-bisphosphate catalyzed by Rubisco are an alyzed by using two model substrates, hydroxypropanone and 3,4-dihydroxy-2- pentanone. The molecular mechanisms for the carboxylation, C3-hydration and C2-inversion processes, are theoretically characterized and discussed with saddle points of index I representing transition structures (TS) and relev ant (molded) intermediates mirroring the experimentally proposed mechanism. Ab initio SCF MO calculations at 3-21C and 6-31G** basis set levels of the ory were used, while the correlation energy is included at the MP2/6-31G** level. The mapping starts from TS1, the carboxylation transition structure, which describes now the coupling of the carbon dioxide attack to the subst rate C2-center in its dienol form with st synchronous interconversion of th e C3 hydroxyl into a ketone group. Thereafter, water addition leads to a ge m-diol followed by another step of intramolecular hydrogen transfer coupled with the C2-C3 bond breaking process. This TS breaks into one model of 3-D -phosphoglycerate product and an intermediate. The configuration inversion at the C2-center is found to be possible via intramolecular hydrogen transf er, as suggested by the corresponding TS relating the intermediate to the C 2-inverted conformation. The complete set of steps found gives a self-conta ined description of the carboxylation followed by hydrolysis with proper st ereochemistry. Comparisons between the transition state analogue: 2-carboxy -D-arabinitol- 1,5-bisphosphate and TS I show that both structures can be s uperposed with minimal root-mean-square deviation for C-atoms. All other ca lculated stationary TSs share the gross conformational features of TS1? and consequently, all molecular rearrangements detected in a Vacuum can be acc ommodated without constraints into the active site of Rubisco. Transition s tructures invariances with respect to level of theory and molecular models are discussed.