Molecular modeling of the mechanochemical triggering mechanism for catalysis of carbon–cobalt bond homolysis in coenzyme B12

Abstract

The possible contributions of the mechanochemical triggering effect to the enzymatic activation of the carbon–cobalt bond of coenzyme B12 (5′-deoxyadenosylcobalamin, AdoCbl) for homolytic cleavage have been studied by molecular modeling and semi-empirical molecular orbital calculations. Classically, this effect has envisioned enzymatic compression of the axial Co–N bond in the ground state to cause upward folding of the corrin ring and subsequent sterically induced distortion of the Co–C bond leading to its destabilization. The models of this process show that in both methylcobalamin (CH3Cbl) and AdoCbl, compression of the axial Co–N bond does engender upward folding of the corrin ring, and that the extent of such upward folding is smaller in an analog in which the normal 5,6-dimethylbenzimidazole axial ligand is replaced by the sterically smaller ligand, imidazole (CH3(Im)Cbl and Ado(Im)Cbl). Furthermore, in AdoCbl, this upward folding of the corrin is accompanied by increases in the carbon–cobalt bond length and in the Co–C–C bond angle (which are also less pronounced in Ado(Im)Cbl), and which indicate that the Co–C bond is indeed destabilized by this mechanism. However, these effects on the Co–C bond are small, and destabilization of this bond by this mechanism is unlikely to contribute more than ca. 3 kcal mol−1 towards the enzymatic catalysis of Co–C bond homolysis, far short of the observed ca. 14 kcal mol−1. A second version of mechanochemical triggering, in which compression of the axial Co–N bond in the transition state for Co–C bond homolysis stabilizes the transition state by increased Co–N orbital overlap, has also been investigated. Stretching the Co–C bond to simulate the approach to the transition state was found to result in an upward folding of the corrin ring, a slight decrease in the axial Co–N bond length, a slight displacement of the metal atom from the plane of the equatorial nitrogens towards the “lower” axial ligand, and a decrease in strain energy amounting to about 8 kcal mol−1 for both AdoCbl and Ado(Im)Cbl. In such modeled transition states, compression of the axial Co–N bond to just below 2.0 Å (the distance subsequently found to provide maximal stabilization of the transition state by increased orbital overlap) required about 4 kcal mol−1 for AdoCbl, and about 2.5 kcal mol−1 for Ado(Im)Cbl. ZINDO/1 calculations on slightly simplified structures showed that maximal electronic stabilization of the transition state by about 10 kcal mol−1 occurred at an axial Co–N bond distance of 1.96 Å for both AdoCbl and Ado(Im)Cbl. The net result is that this type of transition state mechanochemical triggering can provide 14 kcal mol−1 of transition state stabilization for AdoCbl, and about 15.5 kcal mol−1 for the Ado(Im)Cbl, enough to completely explain the observed enzymatic catalysis. These results are discussed in the light of current knowledge about class I AdoCbl-dependent enzymes, in which the coenzyme is bound in its “base-off” conformation, with the lower axial ligand position occupied by the imidazole moiety of an active site histidine residue, and the class II enzymes, in which AdoCbl binds to the enzyme in its “base-on” conformation, and the pendent 5,6-dimethylbenzimidazole base remains coordinated to the metal during Co–C bond activation.