Spectroscopic and Computational Studies of Cobalamin Species with Variable Lower Axial Ligation: Implications for the Mechanism of Co–C Bond Activation by Class I Cobalamin-Dependent Isomerases

Coordination-Induced Radical Generation: Selective Hydrogen Atom Abstraction via Controlled Ti-C σ-Bond Homolysis

A method for the generation of transient alkyl radicals via homolytic Ti-C bond cleavage was developed by employing a tailor-made organotitanium half-cage complex. In contrast to established metal-mediated radical initiation protocols via thermal or photochemical M-C σ-bond homolysis, radical formation is triggered solely by coordination of a solvent molecule (thf) to a titanium(IV) center. During the reaction, the nonstabilized alkyl radical is formed along with a persistent titanium(III) metalloradical, thus taming the former transient radical (persistent radical effect). Radical coupling and hydrogen atom abstraction (HAT) reactions have been explored not only experimentally but also computationally and by means of kinetic analysis. Exploiting these findings led to the development of selective HAT transformations, for example, with 9,10-dihydroanthracene. Deuterium labeling studies using selectively deuterated alkyls and 9,10-dihydroanthracene-d4 confirmed a radical pathway, which was underpinned by developing a radical-radical cross-coupling reaction for transferring the alkyl radical to a stable Sn-centered radical. To set the stage for an application in organic synthesis, a 5-endo-trig radical cyclization based on our methodology was established, and a dihydroxylated sesquiterpene was thus prepared in high diastereomeric excess.

Vibronic Coupling in Vitamin B12: A Combined Spectroscopic and Computational Study

Understanding the diverse reactivities of vitamin B12 and its derivatives, collectively called cobalamins, requires detailed knowledge of their geometric and electronic structures. Electronic absorption (Abs) and resonance Raman (rR) spectroscopies have proven invaluable in this area, particularly when used in concert with computational techniques such as density functional theory (DFT). There remain, however, lingering uncertainties in the computational description of electronic excited states of cobalamins, particularly surrounding the vibronic coupling that impacts the Abs bandshapes and gives rise to rR enhancement of vibrational modes. Past computational analyses of the vibrational spectra of cobalamins have either neglected rR enhancement or calculated rR enhancement for only a small number of modes. In the present study, we used the recently developed ORCA_ASA computational tool in conjunction with the popular B3LYP and BP86 functionals to predict Abs bandshapes and rR spectra for vitamin B12. The ORCA_ASA/B3LYP-computed Abs envelope in the visible spectral region and rR spectra of vitamin B12 agree remarkably well with our experimental data, while BP86 fails to reproduce both. This finding represents a significant advance in our understanding of how these two commonly used density functionals differently model the electronic properties of cobalamins. Guided by the computed frequencies for the Co-C stretching and Co-C-N bending modes, we identified, for the first time, isotope-sensitive features in our rR spectra of 12CNCbl and 13CNCbl that can be assigned to these modes. A normal coordinate analysis of the experimentally determined Co-C stretching and Co-C-N bending frequencies indicates that the Co-C force constant for vitamin B12 is 2.67 mdyn/Å, considerably larger than the Co-C force constants reported for alkylcobalamins.

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.

Photochemical hydrogen evolution from cobalt microperoxidase-11

A photochemical system utilizing the semisynthetic biomolecular catalyst acetylated cobalt microperoxidase-11 (CoMP11-Ac) along with [Ru(bpy)₃]²⁺ as a photosensitizer and ascorbic acid as an electron donor is shown to generate hydrogen from water in a visible light-driven reaction. The reductive quenching pathway facilitated by photoexcited [Ru(bpy)₃]²⁺ overcomes the high overpotential observed for CoMP11-Ac in electrocatalysis, yielding turnover numbers ranging from 606 to 2390 (2 μM - 0.1 μM CoMP11-Ac). The longevity of CoMP11-Ac in the photochemical system, sustaining catalysis for over 20 h, is in contrast to its previously reported behavior in an electrochemical system where catalysis slows after 15 min. Proton reduction turnover number and rate are highest at a neutral pH, a rare feature among cobalt catalysts in similar photochemical systems, which typically function best under acidic conditions. Incorporating biomolecular components into the design of catalysts for photochemical systems may address the need for hydrogen generation from neutral-pH water sources.

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.

Three Dimensional Triply Resonant Sum Frequency Spectroscopy Revealing Vibronic Coupling in Cobalamins: Toward a Probe of Reaction Coordinates

Triply resonant sum frequency (TRSF) spectroscopy is a fully coherent mixed vibrational-electronic spectroscopic technique that is ideally suited for probing the vibrational-electronic couplings that become important in driving reactions. We have used cyanocobalamin (CNCbl) and deuterated aquacobalamin (D₂OCbl⁺) as model systems for demonstrating the feasibility of using the selectivity of coherent multidimensional spectroscopy to resolve electronic states within the broad absorption spectra of transition metal complexes and identify the nature of the vibrational and electronic state couplings. We resolve three short and long axis vibrational modes in the vibrationally congested 1400-1750 cm^-1 region that are individually coupled to different electronic states in the 18 000-21 000 cm^-1 region but have minimal coupling to each other. Double resonance with the individual vibrational fundamentals and their overtones selectively enhances the corresponding electronic resonances and resolves features within the broad absorption spectrum. This work demonstrates the feasibility of identifying coupling between different pairs of vibrational states with different electronic states that together form the reaction coordinate surface of transition metal enzymes.

Modified vitamin B12 derivatives with a peptide backbone for biomimetic studies and medicinal applications

This short review highlights the author’s group research on modified vitamin B[Formula: see text] derivatives with a peptide backbone as (1) inhibitors of B[Formula: see text]-dependent enzymes and as (2) models of cofactor B[Formula: see text]-protein complexes.

Stabilizing intramolecular cobalt–imidazole coordination with a remote methyl group in the backbone of a cofactor B12–protein model

This communication describes the stabilizing effect of a remote methyl group in the backbone of a cobalamin–protein mimic on intramolecular imidazole–cobalt coordination.

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.

Resonance Raman spectroscopic study of the interaction between Co(II)rrinoids and the ATP:corrinoid adenosyltransferase PduO from Lactobacillus reuteri

The human-type ATP:corrinoid adenosyltransferase PduO from Lactobacillus reuteri (LrPduO) catalyzes the adenosylation of Co(II)rrinoids to generate adenosylcobalamin (AdoCbl) or adenosylcobinamide (AdoCbi(+)). This process requires the formation of "supernucleophilic" Co(I)rrinoid intermediates in the enzyme active site which are properly positioned to abstract the adeonsyl moiety from co-substrate ATP. Previous magnetic circular dichroism (MCD) spectroscopic and X-ray crystallographic analyses revealed that LrPduO achieves the thermodynamically challenging reduction of Co(II)rrinoids by displacing the axial ligand with a non-coordinating phenylalanine residue to produce a four-coordinate species. However, relatively little is currently known about the interaction between the tetradentate equatorial ligand of Co(II)rrinoids (the corrin ring) and the enzyme active site. To address this issue, we have collected resonance Raman (rR) data of Co(II)rrinoids free in solution and bound to the LrPduO active site. The relevant resonance-enhanced vibrational features of the free Co(II)rrinoids are assigned on the basis of rR intensity calculations using density functional theory to establish a suitable framework for interpreting rR spectral changes that occur upon Co(II)rrinoid binding to the LrPduO/ATP complex in terms of structural perturbations of the corrin ring. To complement our rR data, we have also obtained MCD spectra of Co(II)rrinoids bound to LrPduO complexed with the ATP analogue UTP. Collectively, our results provide compelling evidence that in the LrPduO active site, the corrin ring of Co(II)rrinoids is firmly locked in place by several amino acid side chains so as to facilitate the dissociation of the axial ligand.

Modulating the cobalt redox potential through imidazole hydrogen bonding interactions in a supramolecular biomimetic protein-cofactor model

This paper describes a supramolecular biomimetic model of the “His-on” configuration and the charge relay system present in certain types of B₁₂-dependent enzymes.

A realistic model for the active site of histidine-on cobalamin@protein complexes is reported and studied under homogeneous and immobilized conditions. Analysis of lower ligand modulation and its influence on the properties of the biomimetic compound are presented. The cofactor attachment by a protein's histidine residue was imitated by covalently linking an artificial imidazole-containing linker to cobyric acid. The resulting intramolecular coordination complex is an excellent structural model of its natural archetype, according to 2D ¹H-NMR studies and molecular modeling. The effect of deprotonation of the axially coordinating imidazole ligand – as proposed for natural cofactor complexes – tunes significantly the position of the cathodic peak (ΔV = –203 mV) and stabilizes thereby the Co^III form. Partial deprotonation of the imidazole moiety through hydrogen bonding interactions was then achieved by immobilizing the biomimetic model on hydrophobic C18 silica, which yielded an unprecedented insight on how this class of Cbl-dependent proteins may fine-tune their properties in biological systems.