Reductive Cleavage Mechanism of Methylcobalamin:  Elementary Steps of Co−C Bond Breaking

Abstract

Density functional theory has been applied to the investigation of the reductive cleavage mechanism of methylcobalamin (MeCbl). In the reductive cleavage of MeCbl, the Co-C bond is cleaved homolytically, and formation of the anion radical ([MeCbl]*-) reduces the dissociation energy by approximately 50%. Such dissociation energy lowering in [MeCbl]*- arises from the involvement of two electronic states: the initial state, which is formed upon electron addition, has dominant pi*corrin character, but when the Co-C bond is stretched the unpaired electron moves to the sigma*Co-C state, and the final cleavage involves the three-electron (sigma)2(sigma*)1 bond. The pi*corrin-sigma*Co-C states crossing does not take place at the equilibrium geometry of [MeCbl]*- but only when the Co-C bond is stretched to 2.3 A. In contrast to the neutral cofactor, the most energetically efficient cleavage of the Co-C bond is from the base-off form. The analysis of thermodynamic and kinetic data provides a rationale as to why Co-C cleavage in reduced form requires prior departure of the axial base. Finally, the possible connection of present work to B12 enzymatic catalysis and the involvement of anion-radical-like [MeCbl]*- species in relevant methyl transfer reactions is discussed.

Catalases versus peroxidases: DFT investigation of H2O2 oxidation in models systems and implications for heme protein engineering

“…The Becke and Perdew functional forms (BP86) were used for exchange and correlation interactions, respectively [28,29]. This functional form has been previously used in DFT studies on metal-based bioinorganic systems and showed to provide accurate geometries [16,[30][31][32][33][34][35][36]. Since the BP86 is known to underestimate the energy barrier for hydrogen atom transfers [37], the energy values were further refined using the hybrid B3LYP functional [38][39][40].…”

The Nature of the Co-C Bond Cleavage Processes in Methylcob(II)Alamin and Adenosylcob(III)Alamin

“…However, even with this barrier, a kinetic calculation shows that fast bond cleavage is improbable. Furthermore, the energy barrier of the Co-C bond breaking is much higher for base-on compared to the base-off species [39,68,106]. Our estimations show that the energy barrier of the geometry optimized 1e-reduced base-on specie is higher by about 0.5 eV compared to the energy barrier of the geometry optimized 1e-reduced base-off specie (see Figure 7 for single points calculations).…”

“…This enters a fl agrant contradiction with the experimental data, which demonstrates that the reaction rate constant of Co-C bond breaking is much higher in base-on species compared with the same reaction rate constant for base-off species [38]. Moreover, base-off methylcob(II)alamin compound cannot be considered in Co-C bond cleavage reaction of bio-reactions since is predicting a four coordinate vitamin B 12 specie immediately after a Co-C bond cleavage of methylcobalamin compound [39,68,106]. Instead, several experimental results show that methylco(II)calamine cofactor is fi ve coordinate [23][24][25][26][27][28]101,102] immediately after Co-C bond cleavage.…”

“…Consequently, various properties have been studied, including electron densities and reduction potentials determination [69,76,88,91,96], the comparison of DFT and CASSCF electronic structure data of truncated models of methylcobalamin species [70,71,74,81,85], the infl uence of various factors on the Co-C bond forming and cleavage in methyl-and 5-adenosylcobalamin models [68,[72][73][74][75][76]79,80,83,84,89,90,92,94,97,99,100], and excited states, spectroscopy and photo-dissociation analysis of vitamin B 12 species [78,82,86,87,93,95,98]. We used DFT calculations on Me-Cbl models to calculate total energy as a function of Co-C bond distance as the bond is stretched [39].…”

TD-DFT insight into photodissociation of the Co-C bond in coenzyme B12

“…The BP86 functional has been previously selected as the most appropriate for predicting both the structural and electronic properties of B 12 cofactors, including Co-C bond dissociation energy (BDE) (Jensen and Ryde, 2003; Rovira et al, 2004; Kuta et al, 2006; Kozlowski et al, 2007; Rovira and Kozlowski, 2007; Galezowski et al, 2008; Lodowski et al, 2009, 2011; Kornobis et al, 2011, 2013). To account for environmental effects on geometries and electronic properties, ground states of RibCbl model (Im-[Co III (corrin)]-Rib + , see Figure S1) were computed in the gas phase as well as in water via the Polarizable Continuum Model (PCM) (Miertuš et al, 1981; Cammi and Tomasi, 1995) as implemented in Gaussian 09.…”