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

The inorganic chemistry of the cobalt corrinoids - an update

The inorganic chemistry of the cobalt corrinoids, derivatives of vitamin B₁₂, is reviewed, with particular emphasis on equilibrium constants for, and kinetics of, their axial ligand substitution reactions. The role the corrin ligand plays in controlling and modifying the properties of the metal ion is emphasised. Other aspects of the chemistry of these compounds, including their structure, corrinoid complexes with metals other than cobalt, the redox chemistry of the cobalt corrinoids and their chemical redox reactions, and their photochemistry are discussed. Their role as catalysts in non-biological reactions and aspects of their organometallic chemistry are briefly mentioned. Particular mention is made of the role that computational methods - and especially DFT calculations - have played in developing our understanding of the inorganic chemistry of these compounds. A brief overview of the biological chemistry of the B₁₂-dependent enzymes is also given for the reader's convenience.

Methyl transfer reactions catalyzed by cobalamin-dependent enzymes: Insight from molecular docking

Methyl transfer reactions, mediated by methyltransferases (MeTrs), such as methionine synthase (MetH) or monomethylamine: CoM (MtmBC), constitute one of the most important classes of vitamin B₁₂-dependent reactions. The challenge in exploring the catalytic function of MeTrs is related to their modular structure. From the crystallographic point of view, the structure of each subunit has been determined, but there is a lack of understanding of how each subunit interacts with each other. So far, theoretical studies of methyl group transfer were carried out for the structural models of the active site of each subunit. However, those studies do not include the effect of the enzymatic environment, which is crucial for a comprehensive understanding of enzyme-mediated methyl transfer reactions. Herein, to explore how two subunits interact with each other and how the methyl transfer reaction is catalyzed by MeTrs, molecular docking of the functional units of MetH and MtmBC was carried out. Along with the interactions of the functional units, the reaction coordinates, including the Co-C bond distance for methylation of cob(I)alamin (Co^ICbl) and the C-S bond distance in demethylation reaction of cob(III)alamin (Co^IIICbl), were considered. The functional groups should be arranged so that there is an appropriate distance to transfer a methyl group and present results indicate that steric interactions can limit the number of potential arrangements. This calls into question the possibility of S_N2-type mechanism previously proposed for MeTrs. Further, it leads to the conclusion that the methyl transfer reaction involves some spatial changes of modules suggesting an alternate radical-based pathway for MeTrs-mediated methyl transfer reactions. The calculations also showed that changes in torsion angles induce a change in reaction coordinates, namely Co-C and C-S bond distances, for the methylation and demethylation reactions catalyzed both by MetH and MtmBC.

Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview

Nature has tailored a wide range of metalloenzymes that play a vast array of functions in all living organisms and from which their survival and evolution depends on. These enzymes catalyze some of the most important biological processes in nature, such as photosynthesis, respiration, water oxidation, molecular oxygen reduction, and nitrogen fixation. They are also among the most proficient catalysts in terms of their activity, selectivity, and ability to operate at mild conditions of temperature, pH, and pressure. In the absence of these enzymes, these reactions would proceed very slowly, if at all, suggesting that these enzymes made the way for the emergence of life as we know today. In this review, the structure and catalytic mechanism of a selection of diverse metalloenzymes that are involved in the production of highly reactive and unstable species, such as hydroxide anions, hydrides, radical species, and superoxide molecules are analyzed. The formation of such reaction intermediates is very difficult to occur under biological conditions and only a rationalized selection of a particular metal ion, coordinated to a very specific group of ligands, and immersed in specific proteins allows these reactions to proceed. Interestingly, different metal coordination spheres can be used to produce the same reactive and unstable species, although through a different chemistry. A selection of hand-picked examples of different metalloenzymes illustrating this diversity is provided and the participation of different metal ions in similar reactions (but involving different mechanism) is discussed.

Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation

The hemoprotein myoglobin is a model system for the study of protein dynamics. We used time-resolved serial femtosecond crystallography at an x-ray free-electron laser to resolve the ultrafast structural changes in the carbonmonoxy myoglobin complex upon photolysis of the Fe-CO bond. Structural changes appear throughout the protein within 500 femtoseconds, with the C, F, and H helices moving away from the heme cofactor and the E and A helices moving toward it. These collective movements are predicted by hybrid quantum mechanics/molecular mechanics simulations. Together with the observed oscillations of residues contacting the heme, our calculations support the prediction that an immediate collective response of the protein occurs upon ligand dissociation, as a result of heme vibrational modes coupling to global modes of the protein.

Tuning ligand electronics and peripheral substitution on cobalt salen complexes: structure and polymerisation activity

A series of cobalt salen complexes, where salen represents an N2O2 bis-Schiff-base bis-phenolate framework, are prepared, characterised and investigated for reversible-termination organometallic mediated radical polymerisation (RT-OMRP). The salen ligands contain a cyclohexane diimine bridge and systematically altered para-substituted phenoxide moieties as a method to examine the electronic impact of the ligand on complex structure and reactivity. The complexes are characterised by single crystal X-ray diffraction, cyclic voltammetry, X-ray photoelectron spectroscopy, electron paramagnetic resonance spectroscopy and computational methods. Structural studies all support a tailorable metal centre reactivity altered by the electron-donating ability of the salen ligand. RT-OMRP of styrene, methyl methacrylate and vinyl acetate is reported and suggests that cobalt-carbon bond strength varies with the ligand substitution. Competing β-hydrogen abstraction affords long-chain olefin-terminated polymer chains and well controlled vinyl acetate polymerisations, contrasting with the lower temperature associative exchange mechanism of degenerative transfer OMRP.

Co-C dissociation of adenosylcobalamin (coenzyme B12): role of dispersion, induction effects, solvent polarity, and relativistic and thermal corrections

Quantum-chemical cluster modeling is challenged in the limit of large, soft systems by the effects of dispersion and solvent, and well as other physical interactions. Adenosylcobalamin (AdoCbl, coenzyme B12), as one of the most complex cofactors in life, constitutes such a challenge. The cleavage of its unique organometallic Co-C bond has inspired multiple studies of this cofactor. This paper reports the fully relaxed potential energy surface of Co-C cleavage of AdoCbl, including for the first time all side-chain interactions with the dissociating Ado group. Various methods and corrections for dispersion, relativistic effects, solvent polarity, basis set superposition error, and thermal and vibrational effects were investigated, totaling more than 550 single-point energies for the large model. The results show immense variability depending on method, including solvation, functional type, and dispersion, challenging the conceived accuracy of methods used for such systems. In particular, B3LYP-D3 seems to severely underestimate the Co-C bond strength, consistent with previous results, and BP86 remains accurate for cobalamins when dispersion interactions are accounted for.

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

Coenzyme B₁₂ (AdoCbl) is one of the most biologically active forms of vitamin B₁₂, and continues to be a topic of active research interest. The mechanism of Co-C bond cleavage in AdoCbl, and the corresponding enzymatic reactions are however, not well understood at the molecular level. In this work, time-dependent density functional theory (TD-DFT) has been applied to investigate the photodissociation of coenzyme B₁₂. To reduce computational cost, while retaining the major spectroscopic features of AdoCbl, a truncated model based on ribosylcobalamin (RibCbl) was used to simulate Co-C photodissociation. Equilibrium geometries of RibCbl were obtained by optimization at the DFT/BP86/TZVP level of theory, and low-lying excited states were calculated by TD-DFT using the same functional and basis set. The calculated singlet states, and absorption spectra were simulated in both the gas phase, and water, using the polarizable continuum model (PCM). Both spectra were in reasonable agreement with experimental data, and potential energy curves based on vertical excitations were plotted to explore the nature of Co-C bond dissociation. It was found that a repulsive ³(σ_Co−C → σ^*_Co−C) triplet state became dissociative at large Co-C bond distance, similar to a previous observation for methylcobalamin (MeCbl). Furthermore, potential energy surfaces (PESs) obtained as a function of both Co-C_Rib and Co-N_Im distances, identify the S₁ state as a key intermediate generated during photoexcitation of RibCbl, attributed to a mixture of a metal-to-ligand charge transfer (MLCT) and a σ bonding-ligand charge transfer (SBLCT) states.

Mercury methylation by HgcA: theory supports carbanion transfer to Hg(II)

Many proteins use corrinoid cofactors to facilitate methyl transfer reactions. Recently, a corrinoid protein, HgcA, has been shown to be required for the production of the neurotoxin methylmercury by anaerobic bacteria. A strictly conserved Cys residue in HgcA was predicted to be a lower-axial ligand to Co(III), which has never been observed in a corrinoid protein. Here, we use density functional theory to study homolytic and heterolytic Co-C bond dissociation and methyl transfer to Hg(II) substrates with model methylcobalamin complexes containing a lower-axial Cys or His ligand to cobalt, the latter of which is commonly found in other corrinoid proteins. We find that Cys thiolate coordination to Co facilitates both methyl radical and methyl carbanion transfer to Hg(II) substrates, but carbanion transfer is more favorable overall in the condensed phase. Thus, our findings are consistent with HgcA representing a new class of corrinoid protein capable of transferring methyl groups to electrophilic substrates.

Co-C bond energies in adenosylcobinamide and methylcobinamide in the gas phase and in silico

Essential to biological activity of adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl) is the Co-C bond cleavage step. Hence, we report an accurate determination of the homolytic gas-phase Co-C bond dissociation energies in the related adenosyl- and methylcobinamides (41.5 ± 1.2 and 44.6 ± 0.8 kcal/mol, respectively) utilizing an energy-resolved threshold collision-induced dissociation technique. This approach allows for benchmarking of electronic structure methods separate from (often ill-defined) solvent effects. Adequacy of various density functional theory methods has been tested with respect to the experimentally obtained values.

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

Catalases and peroxidases are ubiquitous heme enzymes that catalyze the removal of hydrogen peroxide (H(2)O(2)). Both enzymes use one molecule of hydrogen peroxide to form a high valent iron intermediate named Compound I (Cpd I). However, whereas catalase Cpd I oxidizes a second H(2)O(2) molecule to oxygen, peroxidases use this intermediate to oxidize other substrates rather than H(2)O(2). The origin of the different reactivity of peroxidases and catalases is not known, but it is likely to be related to structural differences between the two heme active sites. Recent modeling studies suggest that the oxidation of H(2)O(2) by catalase Cpd I may take place by two hydrogen atom transfer steps. In this work, we investigate how catalases and peroxidases compare along the same hydrogen transfer steps to give hints into the question why peroxidases cannot efficiently oxidize H(2)O(2). The use of simplified models allows us to probe the direct effect of the proximal ligand (tyrosinate in catalases and histidine in peroxidases) without masking from the protein environment. We show that the nature of the fifth ligand (His in peroxidase and Tyr in catalase) has little effect on the energy barriers of the hydrogen transfer steps. On the contrary, the Cpd I-hydrogen peroxide (O(Fe)-O(peroxide)) distance affects significantly the reaction barriers. We propose that the distal side architecture of peroxidases do not allow to attain short O(Cpd I)-O(peroxide) distances, thus resulting in a lower efficiency towards H(2)O(2) oxidation.

Charge Separation Propensity of the Coenzyme B12-Tyrosine Complex in Adenosylcobalamin-Dependent Methylmalonyl-CoA Mutase Enzyme

We report the electrophilic Fukui function analysis based on density functional reactivity theory (DFRT) to demonstrate the feasibility of the proton-coupled electron transfer (PCET) mechanism. To characterize the charge propensity of an electron-transfer site other than the proton-acceptor site of the coenzyme B12-tyrosine complex, several structural models (ranging from minimal to actual enzyme scaffolds) have been employed at DFT and QM/MM computations. It is shown, based on the methylmalonyl-CoA mutase (MCM) enzyme that substrate binding plays a significant role in displacing the phenoxyl proton of the tyrosine (Y89), which initiates the electron transfer from Y89 to coenzyme B12. PCET-based enzymatic reaction implies that one electron-reduced form of the AdoCbl cofactor induces the cleavage of the Co-C bond, as an alternative to its neutral analogue, which can assist in understanding the origin of the observed trillion-fold rate enhancement in MCM enzyme.

Corrin ring-induced redox tuning

The density functional calculations suggest that the expansion of the corrin macrocycle's N(4) core by 0.06-0.10 Å leads to an appreciable lowering of 100-150 mV vs. saturated calomel electrode in the reduction potentials of two biologically important B(12) cofactors namely methylcobalamin and adenosylcobalamin respectively. This redox tuning of B(12) cofactors may encourage the electron transfer-based activation mechanism for B(12)-dependent enzymes.

Role of the Axial Base in the Modulation of the Cob(I)alamin Electronic Properties: Insight from QM/MM, DFT, and CASSCF Calculations

Quantum chemical computations are used to study the electronic and structural properties of the cob(I)alamin intermediate of the cobalamin-dependent methionine synthase (MetH). QM(DFT)/MM calculations on the methylcobalamin (MeCbl) binding domain of MetH reveal that the transfer of the methyl group to the substrate is associated with the displacement of the histidine axial base (His759). The axial base oscillates between a His-on form in the Me-cob(III)lamin:MetH resting state, where the Co-N(His759) distance is 2.27 Å, and a His-off form in the cob(I)alamin:MetH intermediate (2.78 Å). Furthermore, QM/MM and gas phase DFT calculations based on an unrestricted formalism show that the cob(I)alamin intermediate exhibits a complex electronic structure, intermediate between the Co(I) and Co(II)-radical corrin states. To understand this complexity, the electronic structure of Im···[Cob(I)alamin] is investigated using multireference CASSCF/QDPT2 calculations on gas phase models where the axial histidine is modeled by imidazole (Im). It is found that the correlated ground state wave function consists of a closed-shell Co(I) (d(8)) configuration and a diradical contribution, which can be described as a Co(II) (d(7))-radical corrin (π*)(1) configuration. Moreover, the contribution of these two configurations depends on the Co-NIm distance. At short Co-NIm distances (<2.5 Å), the dominant electronic configuration is the diradical state, while for longer distances it is the closed-shell state. The implications of this finding are discussed in the context of the methyl transfer reaction between the Me-H4folate substrate and cob(I)alamin.

Reductive cleavage mechanism of Co-C bond in cobalamin-dependent methionine synthase

The key step in the catalytic cycle of methionine synthase (MetH) is the transfer of a methyl group from the methylcobalamin (MeCbl) cofactor to homocysteine (Hcy). This mechanism has been traditionally viewed as an S(N)2-type reaction, but a different mechanism based on one-electron reduction of the cofactor (reductive cleavage) has been recently proposed. In this work, we analyze whether this mechanism is plausible from a theoretical point of view. By means of a combination of gas-phase as well as hybrid QM/MM calculations, we show that cleavage of the Co-C bond in a MeCbl···Hcy complex (Hcy = methylthiolate substrate (Me-S(-)), a structural mimic of deprotonated homocysteine) proceeds via a [Co(III)(corrin(*-))]-Me···*S-Me diradical configuration, involving electron transfer (ET) from a π*(corrin)-type state to a σ*(Co-C) one, and the methyl transfer displays an energy barrier ≤8.5 kcal/mol. This value is comparable to the one previously computed for the alternative S(N)2 reaction pathway (10.5 kcal/mol). However, the ET-based reductive cleavage pathway does not impose specific geometrical and distance constraints with respect to substrate and cofactor, as does the S(N)2 pathway. This might be advantageous from the enzymatic point of view because in that case, a methyl group can be transferred efficiently at longer distances.

Axial bonding in alkylcobalamins: DFT analysis of the inverse versus normal trans influence

Density functional theory has been applied to study the origin of the inverse and normal trans influence in alkylcobalamins. In order to cover the X-ray structural data available for alkylcobalamins with a variety of axial substituents, geometries of 28 related corrin-containing models have been optimized and analyzed. The BP86/6-31G(d) level of theory was applied which showed good reliability in reproducing the axial bond lengths. Comparison of experimental and calculated data allowed to conclude that the inverse trans influence is not a general feature of cobalamins, as it appeared from the experimental data analysis alone. Inverse trans influence is observed for the series of R groups with increasing bulk and electron donating ability. For the series of R groups having similar medium bulk, but differing significantly in the electron donating ability, normal trans influence was found. Finally, it was determined, that the axial bond lengths correlate well but differently in the two series of R groups with the orbital energies of the six molecular orbitals essential in axial interligand bonding.