Electronic and Steric Influence of Trans Axial Base on the Stereoelectronic Properties of Cobalamins

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.

Surprising Homolytic Gas Phase Co-C Bond Dissociation Energies of Organometallic Aryl-Cobinamides Reveal Notable Non-Bonded Intramolecular Interactions

Aryl-cobalamins are a new class of organometallic structural mimics of vitamin B12 designed as potential 'antivitamins B12 '. Here, the first cationic aryl-cobinamides are described, which were synthesized using the newly developed diaryl-iodonium method. The aryl-cobinamides were obtained as pairs of organometallic coordination isomers, the stereo-structure of which was unambiguously assigned based on homo- and heteronuclear NMR spectra. The availability of isomers with axial attachment of the aryl group, either at the 'beta' or at the 'alpha' face of the cobalt-center allowed for an unprecedented comparison of the organometallic reactivity of such pairs. The homolytic gas-phase bond dissociation energies (BDEs) of the coordination-isomeric phenyl- and 4-ethylphenyl-cobinamides were determined by ESI-MS threshold CID experiments, furnishing (Co-Csp 2 )-BDEs of 38.4 and 40.6 kcal mol-1 , respectively, for the two β-isomers, and the larger BDEs of 46.6 and 43.8 kcal mol-1 for the corresponding α-isomers. Surprisingly, the observed (Co-Csp 2 )-BDEs of the Coβ -aryl-cobinamides were smaller than the (Co-Csp 3 )-BDE of Coβ -methyl-cobinamide. DFT studies and the magnitudes of the experimental (Co-Csp 2 )-BDEs revealed relevant contributions of non-bonded interactions in aryl-cobinamides, notably steric strain between the aryl and the cobalt-corrin moieties and non-bonded interactions with and among the peripheral sidechains.

Cofactor Selectivity in Methylmalonyl Coenzyme A Mutase, a Model Cobamide-Dependent Enzyme

Cobamides, a uniquely diverse family of enzyme cofactors related to vitamin B12, are produced exclusively by bacteria and archaea but used in all domains of life. While it is widely accepted that cobamide-dependent organisms require specific cobamides for their metabolism, the biochemical mechanisms that make cobamides functionally distinct are largely unknown. Here, we examine the effects of cobamide structural variation on a model cobamide-dependent enzyme, methylmalonyl coenzyme A (CoA) mutase (MCM). The in vitro binding affinity of MCM for cobamides can be dramatically influenced by small changes in the structure of the lower ligand of the cobamide, and binding selectivity differs between bacterial orthologs of MCM. In contrast, variations in the lower ligand have minor effects on MCM catalysis. Bacterial growth assays demonstrate that cobamide requirements of MCM in vitro largely correlate with in vivo cobamide dependence. This result underscores the importance of enzyme selectivity in the cobamide-dependent physiology of bacteria.IMPORTANCE Cobamides, including vitamin B12, are enzyme cofactors used by organisms in all domains of life. Cobamides are structurally diverse, and microbial growth and metabolism vary based on cobamide structure. Understanding cobamide preference in microorganisms is important given that cobamides are widely used and appear to mediate microbial interactions in host-associated and aquatic environments. Until now, the biochemical basis for cobamide preferences was largely unknown. In this study, we analyzed the effects of the structural diversity of cobamides on a model cobamide-dependent enzyme, methylmalonyl-CoA mutase (MCM). We found that very small changes in cobamide structure could dramatically affect the binding affinity of cobamides to MCM. Strikingly, cobamide-dependent growth of a model bacterium, Sinorhizobium meliloti, largely correlated with the cofactor binding selectivity of S. meliloti MCM, emphasizing the importance of cobamide-dependent enzyme selectivity in bacterial growth and cobamide-mediated microbial interactions.

Theoretical analysis of C-F bond cleavage mediated by cob[I]alamin-based structures

In the present work, C-F bond cleavage mediated by the super-reduced form of cobalamin (i.e., Co^ICbl) was theoretically studied at the ONIOM(BP86/6-311++G(d,p):PM6) + SMD level of theory. Dispersion effects were introduced by employing Grimme's empirical dispersion at the ONIOM(BP86-D/6-311++G(d,p):PM6) + SMD level. In the first stage of the study, cobalamin was characterized in terms of the coordination number of the central cobalt atom. The ONIOM(BP86/6-311++G(d,p):PM6) results showed that the base-off form of the system is slightly more stable than its base-on counterpart (ΔE = E _base-off - E _base-on ~ -2 kcal/mol). The inclusion of dispersive forces in the description of the system stabilizes the base-on form, which becomes as stable as its base-off counterpart. Moreover, in the latter case, the energy barrier separating both structures was found to be negligible, with a computed value of 1.02 kcal/mol. In the second stage of the work, the reaction Co^ICbl + CH₃F → MeCbl + F^- was studied considering the base-off and the base-on forms of Co^ICbl. The reaction that occurs in the presence of the base-on form of Co^ICbl was found to be kinetically more favorable (ΔE ^≠ = 13.7 kcal/mol) than that occurring in the presence of the base-off form (ΔE ^≠ = 41.2 kcal/mol). Further reaction-force analyses of the processes showed that the energy barrier to C-F bond cleavage arises largely due to structural rearrangements when the reaction occurs on the base-on form of the Co^ICbl complex, but is mainly due to electronic rearrangements when the reaction takes place on the base-off form of the complex. The latter behavior emerges from differences in the synchronicity of the bond strengthening/weakening processes along the reaction path; the base-on mode of Co^ICbl is able to decrease the synchronicity of the chemical events. This work gives new molecular-level insights into the role of Cbl-based systems in the cleavage of C-F bonds. These insights have potential implications for research into processes for degrading fluorine-containing pollutants.

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.

DFT and ONIOM(DFT:MM) studies on Co-C bond cleavage and hydrogen transfer in B12-dependent methylmalonyl-CoA mutase. Stepwise or concerted mechanism?

The considerable protein effect on the homolytic Co-C bond cleavage to form the 5'-deoxyadenosyl (Ado) radical and cob(II)alamin and the subsequent hydrogen transfer from the methylmalonyl-CoA substrate to the Ado radical in the methylmalonyl-CoA mutase (MMCM) have been extensively studied by DFT and ONIOM(DFT/MM) methods. Several quantum models have been used to systematically study the protein effect. The calculations have shown that the Co-C bond dissociation energy is very much reduced in the protein, compared to that in the gas phase. The large protein effect can be decomposed into the cage effect, the effect of coenzyme geometrical distortion, and the protein MM effect. The largest contributor is the MM effect, which mainly consists of the interaction of the QM part of the coenzyme with the MM part of the coenzyme and the surrounding residues. In particular, Glu370 plays an important role in the Co-C bond cleavage process. These effects tremendously enhance the stability of the Co-C bond cleavage state in the protein. The initial Co-C bond cleavage and the subsequent hydrogen transfer were found to occur in a stepwise manner in the protein, although the concerted pathway for the Co-C bond cleavage coupled with the hydrogen transfer is more favored in the gas phase. The assumed concerted transition state in the protein has more deformation of the coenzyme and the substrate and has less interaction with the protein than the stepwise route. Key factors and residues in promoting the enzymatic reaction rate have been discussed in detail.

Spectroscopic studies of the corrinoid/iron-sulfur protein from Moorella thermoacetica

Methyl transfer reactions are important in a number of biochemical pathways. An important class of methyltransferases uses the cobalt cofactor cobalamin, which receives a methyl group from an appropriate methyl donor protein to form an intermediate organometallic methyl-Co bond that subsequently is cleaved by a methyl acceptor. Control of the axial ligation state of cobalamin influences both the mode (i.e., homolytic vs heterolytic) and the rate of Co-C bond cleavage. Here we have studied the axial ligation of a corrinoid iron-sulfur protein (CFeSP) that plays a key role in energy generation and cell carbon synthesis by anaerobic microbes, such as methanogenic archaea and acetogenic bacteria. This protein accepts a methyl group from methyltetrahydrofolate forming Me-Co(3+)CFeSP that then donates a methyl cation (Me) from Me-Co(3+)CFeSP to a nickel site on acetyl-CoA synthase. To unambiguously establish the binding scheme of the corrinoid cofactor in the CFeSP, we have combined resonance Raman, magnetic circular dichroism, and EPR spectroscopic methods with computational chemistry. Our results clearly demonstrate that the Me-Co3+ and Co2+ states of the CFeSP have an axial water ligand like the free MeCbi+ and Co(2+)Cbi+ cofactors; however, the Co-OH2 bond length is lengthened by about 0.2 angstroms for the protein-bound cofactor. Elongation of the Co-OH2 bond of the CFeSP-bound cofactor is proposed to make the cobalt center more "Co1+-like", a requirement to facilitate heterolytic Co-C bond cleavage.

Computational Mutation Analysis of Hydrogen Abstraction and Radical Rearrangement Steps in the Catalysis of Coenzyme B12-Dependent Diol Dehydratase

A mutation analysis of the catalytic functions of active-site residues of coenzyme B(12)-dependent diol dehydratase in the conversion of 1,2-propanediol to 1,1-propanediol has been carried out by using QM/MM computations. Mutants His143Ala, Glu170Gln, Glu170Ala, and Glu170Ala/Glu221Ala were considered to estimate the impact of the mutations of His143 and Glu170. In the His143Ala mutant the activation energy for OH migration increased to 16.4 from 11.5 kcal mol(-1) in the wild-type enzyme. The highest activation energy, 19.6 kcal mol(-1), was measured for hydrogen back-abstraction in this reaction. The transition state for OH migration is not sufficiently stabilized by the hydrogen-bonding interaction formed between the spectator OH group and Gln170 in the Glu170Gln mutant, which demonstrates that a strong proton acceptor is required to promote OH migration. In the Glu170Ala mutant, a new strong hydrogen bond is formed between the spectator OH group and Glu221. A computed activation energy of 13.6 kcal mol(-1) for OH migration in the Glu170Ala mutant is only 2.1 kcal mol(-1) higher than the corresponding barrier in the wild-type enzyme. Despite the low activation barrier, the Glu170Ala mutant is inactive because the subsequent hydrogen back-abstraction is energetically demanding in this mutant. OH migration is not feasible in the Glu170Ala/Glu221Ala mutant because the activation barrier for OH migration is greatly increased by the loss of COO(-) groups near the spectator OH group. This result indicates that the effect of partial deprotonation of the spectator OH group is the most important factor in reducing the activation barrier for OH migration in the conversion of 1,2-propanediol to 1,1-propanediol catalyzed by diol dehydratase.

Time-resolved measurements of the photolysis and recombination of adenosylcobalamin bound to glutamate mutase

Femtosecond to nanosecond transient absorption spectroscopy is used to investigate the photolysis of 5'-deoxyadenosylcobalamin (coenzyme B12, AdoCbl) bound to glutamate mutase. The photochemistry of AdoCbl is found to be inherently dependent upon the environment of the cofactor. Excitation of AdoCbl bound to glutamate mutase results in formation of a metal-to-ligand charge transfer intermediate state which decays to form cob(II)alamin with a time constant of 105 ps. This observation is in contrast to earlier measurements in water where the photohomolysis proceeds through an intermediate state in which the axial dimethylbenzimidazole ligand appears to have dissociated, and measurements in ethylene glycol where prompt bond homolysis is observed (Yoder, L. M.; Cole, A. G.; Walker, L. A., II; Sension, R. J. J. Phys. Chem. B 2001, 105, 12180-12188). The quantum yield for formation of stable radical pairs in the enzyme is found to be phi = 0.05 +/- 0.03, and the resulting intrinsic rate constants for geminate recombination and "cage escape" are 1.0 +/- 0.1 and 0.05 +/- 0.03 ns(-1), respectively. The rate constant for geminate recombination is 30% less than that observed for AdoCbl in water or ethylene glycol. This reduction is insufficient to account for the 10(12)-fold increase in the homolysis rate observed when substrate is bound to the protein. Finally, the protein provides a cage to prevent diffusive loss of the adenosyl radical; however, the ultimate yield for long-lived radicals is determined by the evolution from a singlet to a triplet radical pair as proposed for AdoCbl in ethylene glycol.

Performance of DFT in modeling electronic and structural properties of cobalamins

Computational modeling of the enzymatic activity of B12-dependent enzymes requires a detailed understanding of the factors that influence the strength of the Co--C bond and the limits associated with a particular level of theory. To address this issue, a systematic analysis of the electronic and structural properties of coenzyme B12 models has been performed to establish the performance of three different functionals including B3LYP, BP86, and revPBE. In particular the cobalt-carbon bond dissociation energies, axial bond lengths, and selected stretching frequencies have been analyzed in detail. Current analysis shows that widely used B3LYP functional significantly underestimates the strength of the Co--C bond while the nonhybrid BP86 functional produces very consistent results in comparison to experimental data. To explain such different performance of these functionals molecular orbital analysis associated with axial bonds has been performed to show differences in axial bonding provided by hybrid and nonhybrid functionals.

Time-resolved spectroscopic studies of B12 coenzymes: comparison of the influence of solvent on the primary photolysis mechanism and geminate recombination of methyl-, ethyl-, n-propyl-, and 5'-deoxyadenosylcobalamin

A transient absorption study of the photolysis of methylcobalamin (MeCbl), ethylcobalamin (EtCbl), and n-propylcobalamin (PrCbl) in ethylene glycol spanning six decades in time, from 10 fs to 10 ns, is reported. These measurements probe the influence of solvent on the formation and decay of the metal-to-ligand charge transfer (MLCT) intermediate observed following excitation of MeCbl, the photolysis mechanism in EtCbl and PrCbl, and the rate constants for geminate recombination of the alkyl radicals with cob(II)alamin and for the escape of the alkyl radicals from the initial solvent cage. Earlier investigations probed the dynamics of 5'-dexoyadenosylcobalamin (coenzyme B(12)) in water and ethylene glycol (Yoder, L. M.; Cole, A. G.; Walker, L. A., II; Sension, R. J. J. Phys. Chem. B 2001, 105, 12180-12188) and alkylcobalamins in water (Cole, A. G.; Yoder, L. M.; Shiang, J. J.; Anderson, N. A.; Walker, L. A., II; Banaszak Holl, M. M.; Sension, R. J. J. Am. Chem. Soc. 2002, 124, 434-441). The results of these investigations are discussed in the context of the literature on the frictional influence of solvent on chemical reaction dynamics. The measurements allow a separation of the influence of the solvent on the intrinsic rate constant for geminate recombination and the rate constant for escape from the initial solvent cage. The rate constant for the intrinsic geminate recombination of cob(II)alamin with the alkyl radical is weakly dependent on the solvent and on the nature of the alkyl radical (Me, Et, Pr, or Ado). The Et, Pr, and Ado radicals exhibit the behavior expected for diffusion-controlled escape from the initial solvent cage. In contrast, the magnitude of cage escape for the Me radical is much larger than anticipated on the basis of hydrodynamic arguments.

Influence of Environment on the Electronic Structure of Cob(III)alamins: Time-Resolved Absorption Studies of the S1 State Spectrum and Dynamics

Transient absorption spectroscopy has been used to elucidate the nature of the S1 intermediate state populated following excitation of cob(III)alamin (Cbl(III)) compounds. This state is sensitive both to axial ligation and to solvent polarity. The excited-state lifetime as a function of temperature and solvent environment is used to separate the dynamic and electrostatic influence of the solvent. Two distinct types of excited states are identified, both assigned to pi3d configurations. The spectra of both types of excited states are characterized by a red absorption band (ca. 600 nm) assigned to Co 3d --> 3d or Co 3d --> corrin pi* transitions and by visible absorption bands similar to the corrin pi-->pi* transitions observed for ground state Cbl(III) compounds. The excited state observed following excitation of nonalkyl Cbl(III) compounds has an excited-state spectrum characteristic of Cbl(III) molecules with a weakened bond to the axial ligand (Type I). A similar excited-state spectrum is observed for adenosylcobalamin (AdoCbl) in water and ethylene glycol. The excited-state spectrum of methyl, ethyl, and n-propylcobalamin is characteristic of a Cbl(III) species with a sigma-donating alkyl anion ligand (Type II). This Type II excited-state spectrum is also observed for AdoCbl bound to glutamate mutase. The results are discussed in the context of theoretical calculations of Cbl(III) species reported in the literature and highlight the need for additional calculations exploring the influence of the alkyl ligand on the electronic structure of cobalamins.

Photolysis of Methylcobalamin: Identification of the Relevant Excited States Involved in Co−C Bond Scission

The relevant excited states involved in the photolysis of methylcobalamin (MeCbl) have been examined by means of time-dependent density functional theory (TD-DFT). The low-lying singlet and triplet excited states have been calculated along the Co-C bond at the TD-DFT/BP86/6-31g(d) level of theory in order to investigate the dissociation process of MeCbl. These calculations have shown that the photodissociation is mediated by the repulsive 3(sigmaCo-C --> sigma*Co-C) triplet state. The key metastable photoproduct involved in Co-C bond photolysis was identified as an S1 state having predominantly dCo --> pi*corrin metal-ligand charge transfer (MLCT) character.

Computational insights into the mechanism of radical generation in B12-dependent methylmalonyl-CoA mutase

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.