Intermediates in the catalytic cycle of methyl coenzyme M reductase: isotope exchange is consistent with formation of a σ-alkane-nickel complex

Oxidative C–C/C–X coupling in organometallic nickel complexes: insights from DFT

NiIII and NiIV-center complexes prefer direct reductive elimination than reacting through five-coordinate intermediates. 32+ complex in the presence of Cl− undergoes Cl–Csp2 elimination preferably over Cl–Csp3 and Csp3–Csp2 elimination.

Formation of Stable NiIII N-Confused Porphyrins Aided by a 3-Ethoxy Group

We report the synthesis, characterization, and reactivities of two stable Ni^III N-confused porphyrin (NCP) complexes. Metalation of 3-OEt NCP 1 with NiCl₂  ⋅ 6H₂ O in CHCl₃ /EtOH gave 3-OEt Ni^II NCP 3 initially, which was easily oxidized in air to form the Ni^III complex of NCP inner C-oxide 4. Bis-ethoxy-modified Ni^III complex 5 was synthesized by oxidation of 3 with PIFA in ethanol and CHCl₃ . The structures of 4 and 5 were determined by single-crystal X-ray diffraction analysis. An unusually long Ni^III -C bond (2.170(9) Å) was observed in 4. The g-factor (g>2.1) observed in the EPR spectra of 4 and 5 further confirmed that they are paramagnetic Ni^III complexes. Comparative experiments showed that the 3-ethoxy group plays an important role in the formation of 4 and 5. Reduction of 4 and 5 with NaBH₄ regenerated complex 3.

Reversible metal-centered reduction empowers a Ni-Corrin to mimic F430

This communication presents a novel truncated Ni^II-containing metbalamin and describes its reversible one electron reduction to a catalytically active Ni^I species, that features cofactor F430 model character. Our results strikingly demonstrate that stabilization of Ni^I is not restricted to the related hydroporhyrinoid ligands and is of relevance to the application of metallocorrins in (biomimetic) catalysis.

Efficient labeling of organic molecules using 13C elemental carbon: universal access to 13C2-labeled synthetic building blocks, polymers and pharmaceuticals

Synthetic methodology enabled by ¹³C-elemental carbon is reported. Calcium carbide Ca¹³C₂ was applied to introduce a universal ¹³C₂ unit in the synthesis of labeled alkynes, O,S,N-vinyl derivatives, labeled polymers and ¹³C₂-pyridazine drug core.

Theoretical Studies of Nickel-Dependent Enzymes

The advancements of quantum chemical methods and computer power allow detailed mechanistic investigations of metalloenzymes. In particular, both quantum chemical cluster and combined QM/MM approaches have been used, which have been proven to successfully complement experimental studies. This review starts with a brief introduction of nickel-dependent enzymes and then summarizes theoretical studies on the reaction mechanisms of these enzymes, including NiFe hydrogenase, methyl-coenzyme M reductase, nickel CO dehydrogenase, acetyl CoA synthase, acireductone dioxygenase, quercetin 2,4-dioxygenase, urease, lactate racemase, and superoxide dismutase.

Stabilizing Terminal Ni(III)-Hydroxide Complex Using NNN-Pincer Ligands: Synthesis and Characterization

The reaction of [Ni(COD)₂] (COD; cyclooctadiene) in THF with the NNN-pincer ligand bis(imino)pyridyl (L₁) reveals a susceptibility to oxidation in an inert atmosphere ([O₂] level <0.5 ppm), resulting in a transient Ni:dioxygen adduct. This reactive intermediate abstracts a hydrogen atom from THF and stabilizes an uncommon Ni(III) complex. The complex is crystallographically characterized by a molecular formula of [Ni^III(L_1^··)^2-(OH)] (1). Various isotopically labeled experiments (¹⁶O/¹⁸O) assertively endorse the origin of terminal oxygen based ligand in 1 due to the activation of molecular dioxygen. The presence of proton bound to the terminal oxygen in 1 is well supported by NMR, IR spectroscopy, DFT calculations, and hydrogen atom transfer (HAT) reactions promoted by 1. The observation of shakeup satellite peaks for the primary photoelectron lines of Ni(2p) in the X-ray photoelectron spectroscopy (XPS) unambiguously confirms the paramagnetic signature associated with the distorted square planar nickel ion, which is consistent with the trivalent oxidation state assigned for the nickel ion in 1. The variable temperature magnetic susceptibility data of 1 shows dominant antiferromagnetic interactions exist among the paramagnetic centers, resulting in an overall S = 1/2 ground state. Variable temperature X-band EPR studies performed on 1 show evidence for the S = 1/2 ground state, which is consistent with magnetic data. The unusual g-tensor extracted for the ground state S = 1/2 is analyzed under a strong exchange limit of spin-coupled centers. The electronic structure predicted for 1 is in good agreement with theoretical calculations.

Methyl (Alkyl)-Coenzyme M Reductases: Nickel F-430-Containing Enzymes Involved in Anaerobic Methane Formation and in Anaerobic Oxidation of Methane or of Short Chain Alkanes

Methyl-coenzyme M reductase (MCR) catalyzes the methane-forming step in methanogenic archaea. The active enzyme harbors the nickel(I) hydrocorphin coenzyme F-430 as a prosthetic group and catalyzes the reversible reduction of methyl-coenzyme M (CH₃–S-CoM) with coenzyme B (HS-CoM) to methane and CoM-S–S-CoB. MCR is also involved in anaerobic methane oxidation in reverse of methanogenesis and most probably in the anaerobic oxidation of ethane, propane, and butane. The challenging question is how the unreactive CH₃–S thioether bond in methyl-coenzyme M and the even more unreactive C–H bond in methane and the other hydrocarbons are anaerobically cleaved. A key to the answer is the negative redox potential (E_o′) of the Ni(II)F-430/Ni(I)F-430 couple below −600 mV and the radical nature of Ni(I)F-430. However, the negative one-electron redox potential is also the Achilles heel of MCR; it makes the nickel enzyme one of the most O₂-sensitive enzymes known to date. Even under physiological conditions, the Ni(I) in MCR is oxidized to the Ni(II) or Ni(III) states, e.g., when in the cells the redox potential (E′) of the CoM-S–S-CoB/HS-CoM and HS-CoB couple (E_o′ = −140 mV) gets too high. Methanogens therefore harbor an enzyme system for the reactivation of inactivated MCR in an ATP-dependent reduction reaction. Purification of active MCR in the Ni(I) oxidation state is very challenging and has been achieved in only a few laboratories. This perspective reviews the function, structure, and properties of MCR, what is known and not known about the catalytic mechanism, how the inactive enzyme is reactivated, and what remains to be discovered.

The deep, hot biosphere: Twenty-five years of retrospection

Twenty-five years ago this month, Thomas Gold published a seminal manuscript suggesting the presence of a "deep, hot biosphere" in the Earth's crust. Since this publication, a considerable amount of attention has been given to the study of deep biospheres, their role in geochemical cycles, and their potential to inform on the origin of life and its potential outside of Earth. Overwhelming evidence now supports the presence of a deep biosphere ubiquitously distributed on Earth in both terrestrial and marine settings. Furthermore, it has become apparent that much of this life is dependent on lithogenically sourced high-energy compounds to sustain productivity. A vast diversity of uncultivated microorganisms has been detected in subsurface environments, and we show that H₂, CH₄, and CO feature prominently in many of their predicted metabolisms. Despite 25 years of intense study, key questions remain on life in the deep subsurface, including whether it is endemic and the extent of its involvement in the anaerobic formation and degradation of hydrocarbons. Emergent data from cultivation and next-generation sequencing approaches continue to provide promising new hints to answer these questions. As Gold suggested, and as has become increasingly evident, to better understand the subsurface is critical to further understanding the Earth, life, the evolution of life, and the potential for life elsewhere. To this end, we suggest the need to develop a robust network of interdisciplinary scientists and accessible field sites for long-term monitoring of the Earth's subsurface in the form of a deep subsurface microbiome initiative.

Biocatalysts for methane conversion: big progress on breaking a small substrate

Nature utilizes two groups of enzymes to catalyze methane conversions, methyl-coenzyme M reductases (MCRs) and methane monooxygenases (MMOs). These enzymes have been difficult to incorporate into industrial processes due to their complexity, poor stability, and lack of recombinant tractability. Despite these issues, new ways of preparing and stabilizing these enzymes have recently been discovered, and new mechanistic insight into how MCRs and MMOs break the C-H bond in nature's most inert hydrocarbon have been obtained. This review focuses on recent findings in the methane biocatalysis field, and discusses the impact of these finding on designing MMO and MCR-based biotechnologies.

Influence of Ring-Expanded N-Heterocyclic Carbenes on the Structures of Half-Sandwich Ni(I) Complexes: An X-ray, Electron Paramagnetic Resonance (EPR), and Electron Nuclear Double Resonance (ENDOR) Study

Potassium graphite reduction of the half-sandwich Ni(II) ring-expanded diamino/diamidocarbene complexes CpNi(RE-NHC)Br gave the Ni(I) derivatives CpNi(RE-NHC) (where RE-NHC = 6-Mes (1), 7-Mes (2), 6-MesDAC (3)) in yields of 40%-50%. The electronic structures of paramagnetic 1-3 were investigated by CW X-/Q-band electron paramagnetic resonance (EPR) and Q-band ¹H electron nuclear double resonance (ENDOR) spectroscopy. While small variations in the g-values were observed between the diaminocarbene complexes 1 and 2, pronounced changes in the g-values were detected between the almost isostructural species (1) and diamidocarbene species (3). These results highlight the sensitivity of the EPR g-tensor to changes in the electronic structure of the Ni(I) centers generated by incorporation of heteroatom substituents onto the backbone ring positions. Variable-temperature EPR analysis also revealed the presence of a second Ni(I) site in 3. The experimental g-values for these two Ni(I) sites detected by EPR in frozen solutions of 3 are consistent with resolution on the EPR time scale of the disordered components evident in the X-ray crystallographically determined structure and the corresponding density functional theory (DFT)-calculated g-tensor. Q-band ¹H ENDOR measurements revealed a small amount of unpaired electron spin density on the Cp rings, consistent with the calculated SOMO of complexes 1-3. The magnitude of the ¹H A values for 3 were also notably larger, compared to 1 and 2, again highlighting the influence of the diamidocarbene on the electronic properties of 3.

The radical mechanism of biological methane synthesis by methyl-coenzyme M reductase

Methyl-coenzyme M reductase, the rate-limiting enzyme in methanogenesis and anaerobic methane oxidation, is responsible for the biological production of more than 1 billion tons of methane per year. The mechanism of methane synthesis is thought to involve either methyl-nickel(III) or methyl radical/Ni(II)-thiolate intermediates. We employed transient kinetic, spectroscopic, and computational approaches to study the reaction between the active Ni(I) enzyme and substrates. Consistent with the methyl radical-based mechanism, there was no evidence for a methyl-Ni(III) species; furthermore, magnetic circular dichroism spectroscopy identified the Ni(II)-thiolate intermediate. Temperature-dependent transient kinetics also closely matched density functional theory predictions of the methyl radical mechanism. Identifying the key intermediate in methanogenesis provides fundamental insights to develop better catalysts for producing and activating an important fuel and potent greenhouse gas.

An inhibitor persistently decreased enteric methane emission from dairy cows with no negative effect on milk production

A quarter of all anthropogenic methane emissions in the United States are from enteric fermentation, primarily from ruminant livestock. This study was undertaken to test the effect of a methane inhibitor, 3-nitrooxypropanol (3NOP), on enteric methane emission in lactating Holstein cows. An experiment was conducted using 48 cows in a randomized block design with a 2-wk covariate period and a 12-wk data collection period. Feed intake, milk production, and fiber digestibility were not affected by the inhibitor. Milk protein and lactose yields were increased by 3NOP. Rumen methane emission was linearly decreased by 3NOP, averaging about 30% lower than the control. Methane emission per unit of feed dry matter intake or per unit of energy-corrected milk were also about 30% less for the 3NOP-treated cows. On average, the body weight gain of 3NOP-treated cows was 80% greater than control cows during the 12-wk experiment. The experiment demonstrated that the methane inhibitor 3NOP, applied at 40 to 80 mg/kg feed dry matter, decreased methane emissions from high-producing dairy cows by 30% and increased body weight gain without negatively affecting feed intake or milk production and composition. The inhibitory effect persisted over 12 wk of treatment, thus offering an effective methane mitigation practice for the livestock industries.

The reaction mechanism of methyl-coenzyme M reductase: how an enzyme enforces strict binding order

Methyl-coenzyme M reductase (MCR) is a nickel tetrahydrocorphinoid (coenzyme F430) containing enzyme involved in the biological synthesis and anaerobic oxidation of methane. MCR catalyzes the conversion of methyl-2-mercaptoethanesulfonate (methyl-SCoM) and N-7-mercaptoheptanoylthreonine phosphate (CoB7SH) to CH4 and the mixed disulfide CoBS-SCoM. In this study, the reaction of MCR from Methanothermobacter marburgensis, with its native substrates was investigated using static binding, chemical quench, and stopped-flow techniques. Rate constants were measured for each step in this strictly ordered ternary complex catalytic mechanism. Surprisingly, in the absence of the other substrate, MCR can bind either substrate; however, only one binary complex (MCR·methyl-SCoM) is productive whereas the other (MCR·CoB7SH) is inhibitory. Moreover, the kinetic data demonstrate that binding of methyl-SCoM to the inhibitory MCR·CoB7SH complex is highly disfavored (Kd = 56 mM). However, binding of CoB7SH to the productive MCR·methyl-SCoM complex to form the active ternary complex (CoB7SH·MCR(Ni(I))·CH3SCoM) is highly favored (Kd = 79 μM). Only then can the chemical reaction occur (kobs = 20 s(-1) at 25 °C), leading to rapid formation and dissociation of CH4 leaving the binary product complex (MCR(Ni(II))·CoB7S(-)·SCoM), which undergoes electron transfer to regenerate Ni(I) and the final product CoBS-SCoM. This first rapid kinetics study of MCR with its natural substrates describes how an enzyme can enforce a strictly ordered ternary complex mechanism and serves as a template for identification of the reaction intermediates.

The characterization of the saddle shaped nickel(iii) porphyrin radical cation: an explicative NMR model for a ferromagnetically coupled metallo-porphyrin radical

Ni(iii)(OETPP˙)(Br)₂ is the first Ni(iii) porphyrin radical cation with structural and ¹H and ¹³C paramagnetic NMR data for porphyrinate systems.

Enzymes involved in the anaerobic oxidation of n-alkanes: from methane to long-chain paraffins

Anaerobic microorganisms play key roles in the biogeochemical cycling of methane and non-methane alkanes. To date, there appear to be at least three proposed mechanisms of anaerobic methane oxidation (AOM). The first pathway is mediated by consortia of archaeal anaerobic methane oxidizers and sulfate-reducing bacteria (SRB) via “reverse methanogenesis” and is catalyzed by a homolog of methyl-coenzyme M reductase. The second pathway is also mediated by anaerobic methane oxidizers and SRB, wherein the archaeal members catalyze both methane oxidation and sulfate reduction and zero-valent sulfur is a key intermediate. The third AOM mechanism is a nitrite-dependent, “intra-aerobic” pathway described for the denitrifying bacterium, ‘Candidatus Methylomirabilis oxyfera.’ It is hypothesized that AOM proceeds via reduction of nitrite to nitric oxide, followed by the conversion of two nitric oxide molecules to dinitrogen and molecular oxygen. The latter can be used to functionalize the methane via a particulate methane monooxygenase. With respect to non-methane alkanes, there also appear to be novel mechanisms of activation. The most well-described pathway is the addition of non-methane alkanes across the double bond of fumarate to form alkyl-substituted succinates via the putative glycyl radical enzyme, alkylsuccinate synthase (also known as methylalkylsuccinate synthase). Other proposed mechanisms include anaerobic hydroxylation via ethylbenzene dehydrogenase-like enzymes and an “intra-aerobic” denitrification pathway similar to that described for ‘Methylomirabilis oxyfera.’

Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective

"We'll never be able to know" is a truism that leads to resignation with respect to any experimental effort to search for the chemistry of life's origin. But such resignation runs radically counter to the challenge imposed upon chemistry as a natural science. Notwithstanding the prognosis according to which the shortest path to understanding the metamorphosis of the chemical into the biological is by way of experimental modeling of "artificial chemical life", the scientific search for the route nature adopted in creating the life we know will arguably never truly end. It is, after all, part of the search for our own origin.

Fundamentals of methanogenic pathways that are key to the biomethanation of complex biomass

The conversion of biomass to CH4 (biomethanation) involves an anaerobic microbial food chain composed of at least three metabolic groups of which the first two decompose the complex biomass primarily to acetate, formate, and H2. The thermodynamics of these conversions are unfavorable requiring a symbiosis with the CH4-producing group (methanogens) that metabolize the decomposition products to favorable concentrations. The methanogens produce CH4 by two major pathways, conversion of the methyl group of acetate and reduction of CO2 coupled to the oxidation of formate or H2. This review covers recent advances in the fundamental understanding of both methanogenic pathways with the view of stimulating research towards improving the rate and reliability of the overall biomethanation process.

Cyanobacterial alkane biosynthesis further expands the catalytic repertoire of the ferritin-like 'di-iron-carboxylate' proteins

Enzymes that activate dioxygen at carboxylate-bridged non-heme diiron clusters residing within ferritin-like, four-helix-bundle protein architectures have crucial roles in, among other processes, the global carbon cycle (e.g. soluble methane monooxygenase), fatty acid biosynthesis [plant fatty acyl-acyl carrier protein (ACP) desaturases], DNA biosynthesis [the R2 or β2 subunits of class Ia ribonucleotide reductases (RNRs)], and cellular iron trafficking (ferritins). Classic studies on class Ia RNRs showed long ago how this obligatorily oxidative di-iron/O2 chemistry can be used to activate an enzyme for even a reduction reaction, and more recent investigations of class Ib and Ic RNRs, coupled with earlier studies on dimanganese catalases, have shown that members of this protein family can also incorporate either one or two Mn ions and use them in place of iron for redox catalysis. These two strategies--oxidative activation for non-oxidative reactions and use of alternative metal ions--expand the catalytic repertoire of the family, probably to include activities that remain to be discovered. Indeed, a recent study has suggested that fatty aldehyde decarbonylases (ADs) from cyanobacteria, purported to catalyze a redox-neutral cleavage of a Cn aldehyde to the Cn-1 alkane (or alkene) and CO, also belong to this enzyme family and are most similar in structure to two other members with heterodinuclear (Mn-Fe) cofactors. Here, we first briefly review both the chemical principles underlying the O2-dependent oxidative chemistry of the 'classical' di-iron-carboxylate proteins and the two aforementioned strategies that have expanded their functional range, and then consider what metal ion(s) and what chemical mechanism(s) might be employed by the newly discovered cyanobacterial ADs.

Structural analysis of a Ni-methyl species in methyl-coenzyme M reductase from Methanothermobacter marburgensis

We present the 1.2 Å resolution X-ray crystal structure of a Ni-methyl species that is a proposed catalytic intermediate in methyl-coenzyme M reductase (MCR), the enzyme that catalyzes the biological formation of methane. The methyl group is situated 2.1 Å proximal of the Ni atom of the MCR coenzyme F(430). A rearrangement of the substrate channel has been posited to bring together substrate species, but Ni(III)-methyl formation alone does not lead to any observable structural changes in the channel.