Mechanism of Light Induced Radical Pair Formation in Coenzyme B12-Dependent Ethanolamine Ammonia-Lyase

Photoproduct formation in coenzyme B12-dependent CarH photoreceptor via a triplet pathway

CarH is a cobalamin-based photoreceptor which has attracted significant interest due to its complex mechanism involving its organometallic coenzyme-B₁₂ chromophore. While several experimental and computational studies have sought to understand CarH's mechanism of action, there are still many aspects of the mechanism which remain unclear. While light is needed to activate the Co-C_5' bond, it is not entirely clear whether reaction pathway involves singlet or triplet diradical states. A recent experimental study implicated triplet pathway and importance of intersystem crossing (ISC) as a viable mechanistic route for photoproduct formation in CarH. Herein, a combined quantum mechanics/molecular mechanics approach (QM/MM) was used to explore the involvement of triplet states in CarH. Two possibilities were explored. The first possibility involved photo-induced homolytic cleavage of the Co-C_5' where the radical pair (RP) would deactivate to a triplet state (T₀) on the ground state potential energy surface (PES). However, a pathway for the formation of the photoproduct, 4',5'-anhydroadenosine (anhAdo), on the triplet ground state PES was not energetically feasible. The second possibility involved exploring a manifold of low-lying triplet excited states computed using TD-DFT within the QM/MM framework. Viable crossings of triplet excited states with singlet excited states were identified using semiclassical Landau-Zener theory and the effectiveness of spin-orbit coupling by El-Sayed rules. Several candidates along both the Co-N_Im potential energy curve (PEC) and Co-C_5'/Co-N_Im PES were identified, which appear to corroborate experimental findings and implicate the possible role of triplet states in CarH.

Photoproduct formation in coenzyme B12-dependent CarH via a singlet pathway

The CarH photoreceptor exploits of the light-sensing ability of coenzyme B₁₂ ( adenosylcobalamin = AdoCbl) to perform its catalytic function, which includes large-scale structural changes to regulate transcription. In daylight, transcription is activated in CarH via the photo-cleavage of the Co-C_5' bond of coenzyme B₁₂. Subsequently, the photoproduct, 4',5'-anhydroadenosine (anhAdo) is formed inducing dissociation of the CarH tetramer from DNA. Several experimental studies have proposed that hydridocoblamin (HCbl) may be formed in process with anhAdo. The photolytic cleavage of the Co-C_5' bond of AdoCbl was previously investigated using photochemical techniques and the involvement of both singlet and triplet excited states were explored. Herein, QM/MM calculations were employed to probe (1) the photolytic processes which may involve singlet excited states, (2) the mechanism of anhAdo formation, and (3) whether HCbl is a viable intermediate in CarH. Time-dependent density functional theory (TD-DFT) calculations indicate that the mechanism of photodissociation of the Ado ligand involves the ligand field (LF) portion of the lowest singlet excited state (S₁) potential energy surface (PES). This is followed by deactivation to a point on the S₀ PES where the Co-C_5' bond remains broken. This species corresponds to a singlet diradical intermediate. From this point, the PES for anhAdo formation was explored, using the Co-C_5' and Co-C_4' bond distances as active coordinates, and a local minimum representing anhAdo and HCbl formation was found. The transition state (TS) for the formation of the Co-H bond of HCbl was located and its identity was confirmed by a single imaginary frequency of i1592 cm^-1. Comparisons to experimental studies and the potential role of rotation around the N-glycosidic bond of the Ado ligand were discussed.

Computational investigations of B12-dependent enzymatic reactions

Nature employs two biologically active forms of vitamin B₁₂, adenosylcobalamin (or coenzyme B₁₂) and methylcobalamin, as cofactors in molecular transformations both in bacteria and mammals. Computational chemistry, guided by experimental data, has been used to explore fundamental characteristics of these enzymatic reactions. In particular, the quantum mechanics/molecular mechanics (QM/MM) method has proven to be a powerful tool in elucidating important characteristics of B₁₂-dependent enzymatic reactions. Herein, we will present a brief tutorial in conducting QM/MM calculations for B₁₂ enzymatic reactions. We will summarize recent contributions that target the use of QM/MM calculations in both photochemical and enzymatic reactions including AdoCbl-dependent ethanolamine ammonia lyase, glutamate mutase, and photoreceptor CarH.

Aerobic photolysis of methylcobalamin: unraveling the photoreaction mechanism

The photo-reactivity of cobalamins (Cbls) is influenced by the nature of axial ligands and the cofactor's environment. While the biologically active forms of Cbls with alkyl axial ligands, such as methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl), are considered to be photolytically active, in contrast, the non-alkyl Cbls are photostable. In addition to these, the photolytic properties of Cbls can also be modulated in the presence of molecular oxygen, i.e., under aerobic conditions. Herein, the photoreaction of the MeCbl in the presence of oxygen has been explored using density functional theory (DFT) and time-dependent DFT (TD-DFT). The first stage of the aerobic photoreaction is the activation of the Co-C bond and the formation of the ligand field (LF) electronic state through the displacement of axial bonds. Once the photoreaction reaches the LF excited state, three processes can occur: namely the formation of OO-CH₃ through the reaction of CH₃ with molecular oxygen, de-activation of the {Im⋯[Co^II(corrin)]⋯CH₃}⁺ sub-system from the LF electronic state by changing the electronic configuration from (d_yz)¹(d_z²)² to (d_yz)²(d_z²)¹ and the formation of the deactivation complex (DC) complex via the recombination of OO-CH₃ species with the de-excited [Co^II(corrin)] system. In the proposed mechanism, the deactivation of the [Co^II(corrin)] subsystem may coexist with the formation of OO-CH₃, followed by immediate relaxation of the subsystems in the ground state. Moreover, the formation of the OO-CH₃ species followed by the formation of the {[Co^III(corrin)]-OO-CH₃}⁺ complex stabilizes the system compared to the reactant complex.

Role of the CarH photoreceptor protein environment in the modulation of cobalamin photochemistry

The photochemistry of cobalamins has recently been found to have biological importance, with the discovery of bacterial photoreceptor proteins, such as CarH and AerR. CarH and AerR, are involved in the light regulation of carotenoid biosynthesis and bacteriochlorophyll biosynthesis, respectively, in bacteria. Experimental transient absorption spectroscopic studies have indicated unusual photochemical behavior of 5'-deoxy-5'-adenosylcobalamin (AdoCbl) in CarH, with excited-state charge separation between cobalt and adenosyl and possible heterolytic cleavage of the Co-adenosyl bond, as opposed to the homolytic cleavage observed in aqueous solution and in many AdoCbl-based enzymes. We employ molecular dynamics and hybrid quantum mechanical/molecular mechanical calculations to obtain a microscopic understanding of the modulation of the excited electronic states of AdoCbl by the CarH protein environment, in contrast to aqueous solution and AdoCbl-based enzymes. Our results indicate a progressive stabilization of the electronic states involving charge transfer (CT) from cobalt/corrin to adenine on changing the environment from gas phase to water to solvated CarH. The solvent exposure of the adenosyl ligand in CarH, the π-stacking interaction between a tryptophan and the adenine moiety, and the hydrogen-bonding interaction between a glutamate and the lower axial ligand of cobalt are found to contribute to the stabilization of the states involving CT to adenine. The combination of these three factors, the latter two of which can be experimentally tested via mutagenesis studies, is absent in an aqueous solvent environment and in AdoCbl-based enzymes. The favored CT from metal and/or corrin to adenine in CarH may promote heterolytic cleavage of the cobalt-adenosyl bond proposed by experimental studies. Overall, this work provides novel, to our knowledge, physical insights into the mechanism of CarH function and directions for future experimental investigations. The fundamental understanding of the mechanism of CarH functioning will serve the development of optogenetic tools based on the new class of B₁₂-dependent photoreceptors.

Visible-to-NIR-Light Activated Release: From Small Molecules to Nanomaterials

Photoactivatable (alternatively, photoremovable, photoreleasable, or photocleavable) protecting groups (PPGs), also known as caged or photocaged compounds, are used to enable non-invasive spatiotemporal photochemical control over the release of species of interest. Recent years have seen the development of PPGs activatable by biologically and chemically benign visible and near-infrared (NIR) light. These long-wavelength-absorbing moieties expand the applicability of this powerful method and its accessibility to non-specialist users. This review comprehensively covers organic and transition metal-containing photoactivatable compounds (complexes) that absorb in the visible- and NIR-range to release various leaving groups and gasotransmitters (carbon monoxide, nitric oxide, and hydrogen sulfide). The text also covers visible- and NIR-light-induced photosensitized release using molecular sensitizers, quantum dots, and upconversion and second-harmonic nanoparticles, as well as release via photodynamic (photooxygenation by singlet oxygen) and photothermal effects. Release from photoactivatable polymers, micelles, vesicles, and photoswitches, along with the related emerging field of photopharmacology, is discussed at the end of the review.

Light Mediated Properties of a Thiolato-Derivative of Vitamin B12

Vitamin B₁₂ derivatives (Cbls = cobalamins) exhibit photolytic properties upon excitation with light. These properties can be modulated by several factors including the nature of the axial ligands. Upon excitation, homolytic cleavage of the organometallic bond to the upper axial ligand takes place in photolabile Cbls. The photosensitive nature of Cbls has made them potential candidates for light-activated drug delivery. The addition of a fluorophore to the nucleotide loop of thiolato Cbls has been shown to shift the region of photohomolysis to within the optical window of tissue (600-900 nm). With this possibility, there is a need to analyze photolytic properties of unique Cbls which contain a Co-S bond. Herein, the photodissociation of one such Cbl, namely, N-acetylcysteinylcobalamin (NACCbl), is analyzed based on density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations. The S₀ and S₁ potential energy surfaces (PESs), as a function of axial bond lengths, were computed to determine the mechanism of photodissociation. Like other Cbls, the S₁ PES contains metal-to-ligand charge transfer (MLCT) and ligand field (LF) regions, but there are some unique differences. Interestingly, the S₁ PES of NACCbl contains three distinct minima regions opening several possibilities for the mechanism of radical pair (RP) formation. The mild photoresponsiveness, observed experimentally, can be attributed to the small gap in energy between the S₁ and S₀ PESs. Compared to other Cbls, the gap shown for NACCbl is neither exactly in line with the alkyl Cbls nor the nonalkyl Cbls.

Aerobic photolysis of methylcobalamin: structural and electronic properties of the Cbl-O-O-CH3 intermediate

Photolysis of methylcobalamin (MeCbl) in the presence of molecular oxygen (O₂) has been investigated using density functional theory (DFT) and time-dependent DFT (TD-DFT). The key step involves the formation of the Cbl-O-O-CH₃ intermediate as a result of triplet O₂ insertion in the Co-C bond in the presence of light. Analysis of low-lying excited states shows that the presence of light is only needed to activate the Co-C bond via the formation of the ligand field (LF) state. The insertion of O₂, as well as the change in the spin state, takes place in the ground state. The analysis of the structural and electronic properties of the Cbl-O-O-CH₃ intermediate is presented and possible decomposition also discussed.

How does the mutation in the cap domain of methylcobalamin-dependent methionine synthase influence the photoactivation of the Co–C bond?

The topology of the S₁ PES is modulated by introducing a mutation at the F708 position. The mutation influences the photoactivation of the Co–C bond by decreasing the rate of geminate recombination and altering the rate of radical pair formation.