ONIOM calculations have provided novel insights into the mechanism of homolytic Co-C5' bond cleavage in the 5'-deoxyadenosylcobalamin cofactor catalyzed by methylmalonyl-CoA mutase. We have shown that it is a stepwise process in which conformational changes in the 5'-deoxyadenosine moiety precede the actual homolysis step. In the transition state structure for homolysis, the Co-C5' bond elongates by approximately 0.5 Angstroms from the value found in the substrate-bound reactant complex. The overall barrier to homolysis is approximately 10 kcal/mol, and the radical products are approximately 2.5 kcal/mol less stable than the initial ternary complex of enzyme, substrate, and cofactor. The movement of the deoxyadenosine moiety during the homolysis step positions the resulting 5'-deoxyadenosyl radical for the subsequent hydrogen atom transfer from the substrate, methylmalonyl-CoA.

Naturally‐occurring variations in the abundances of the stable isotopes of carbon and other elements can be used to understand the dynamics of natural processes in chemistry, biochemistry, biology, medicine, ecology and other fields. The use of carbon‐13 isotopic abundances as an indicator of photosynthetic function in plants has become common. The purpose of this article is to describe the physical and chemical processes that contribute to the abundances of carbon‐13 in plant materials, and to provide a framework for understanding how those processes control the isotopic contents of natural materials.

The cyclization of 2-hydroxypropyl-4-nitrophenyl phosphate (HpPNP) catalyzed by the dinuclear zinc complex of 1,3-bis(1,4,7-triazacyclonon-1-yl)-2-hydroxypropane (1) proceeds by a transition state that is different from that of the uncatalyzed reaction. Kinetic isotope effects (KIEs) measured in the nucleophilic atom and in the leaving group show that the uncatalyzed cyclization has a transition state (TS) with little phosphorus-oxygen bond fission to the leaving group (18klg = 1.0064 ± 0.0009 and 15k = 1.0002 ± 0.0002), and that nucleophilic bond formation occurs in the rate-determining step (18knuc = 1.0326 ± 0.0008). In the catalyzed reaction, larger leaving group isotope effects (18klg = 1.0113 ± 0.0005 and 15k = 1.0015 ± 0.0005) and a smaller nucleophile isotope effect (18knuc = 1.0116 ± 0.0010) indicate a later TS with greater leaving group bond fission, and greater nucleophilic bond formation. These observed nucleophile KIEs are the combined effect of the equilibrium effect on deprotonation of the 2’-hydroxyl nucleophile and the KIE on the nucleophilic step. An EIE of 1.0245 for deprotonation of the hydroxyl group of HPpNP was obtained computationally. The different KIEs for the two reactions indicate that the effective catalysis by 1 is accompanied by selection for an altered transition state, presumably arising from the preferential stabilization by the catalyst of charge away from the nucleophile and toward the leaving group. These results demonstrate the potential for a catalyst using biologically relevant metal ions to select for an altered transition state for phosphoryl transfer.