Carbon monoxide dehydrogenase reaction mechanism: a likely case of abnormal CO2 insertion to a Ni-H(-) bond

Ni-containing carbon monoxide dehydrogenases (CODH), present in many anaerobic microorganisms, catalyze the reversible oxidation of CO to CO(2) at the so-called C-cluster. This atypical active site is composed of a [NiFe(3)S(4)] cluster and a single unusual iron ion called ferrous component II or Fe(u) that is bridged to the cluster via one sulfide ion. After additional refinement of recently published high-resolution structures of COOH(x)-, OH(x)-, and CN-bound CODH from Carboxydothermus hydrogenoformans (Jeoung and Dobbek Science 2007, 318, 1461-1464; J. Am. Chem. Soc. 2009, 131, 9922-9923), we have used computational methods on the predominant resulting structures to investigate the spectroscopically well-characterized catalytic intermediates, C(red1) and the two-electron more-reduced C(red2). Several models were geometry-optimized for both states using hybrid quantum mechanical/molecular mechanical potentials. The comparison of calculated Mo?ssbauer parameters of these active site models with experimental data allows us to propose that the C(red1) state has a Fe(u)-Ni(2+) bridging hydroxide ligand and the C(red2) state has a hydride terminally bound to Ni(2+). Using our combined structural and theoretical data, we put forward a revised version of an earlier proposal for the catalytic cycle of Ni-containing CODH (Volbeda and Fontecilla-Camps Dalton Trans. 2005, 21, 3443-3450) that agrees with available spectroscopic and structural data. This mechanism involves an abnormal CO(2) insertion into the Ni(2+)-H(-) bond.     

CODH‐IV: A High‐Efficiency CO‐Scavenging CO Dehydrogenase with Resistance to O2

CO dehydrogenases (CODHs) catalyse the reversible conversion between CO and CO₂. Genomic analysis indicated that the metabolic functions of CODHs vary. The genome of Carboxydothermus hydrogenoformans encodes five CODHs (CODH‐I–V), of which CODH‐IV is found in a gene cluster near a peroxide‐reducing enzyme. Our kinetic and crystallographic experiments reveal that CODH‐IV differs from other CODHs in several characteristic properties: it has a very high affinity for CO, oxidizes CO at diffusion‐limited rate over a wide range of temperatures, and is more tolerant to oxygen than CODH‐II. Thus, our observations support the idea that CODH‐IV is a CO scavenger in defence against oxidative stress and highlight that CODHs are more diverse in terms of reactivity than expected.     

O2 Inhibition of Ni‐Containing CO Dehydrogenase Is Partly Reversible

Ni‐containing CO dehydrogenases (CODHs) are very efficient metalloenzymes that catalyze the conversion between CO₂ and CO. They are a source of inspiration for designing CO₂‐reduction catalysts and can also find direct use in biotechnology. They are deemed extremely sensitive to O₂, but very little is known about this aspect of their reactivity. We investigated the reaction with O₂ of Carboxydothermus hydrogenoformans (Ch) CODH II and the homologous, recently characterized CODH from Desulfovibrio vulgaris (Dv) through protein film voltammetry and solution assays (in the oxidative direction). We found that O₂ reacts very quickly with the active site of CODHs, generating species that reactivate upon reduction—this was unexpected. We observed that distinct CODHs exhibit different behaviors: Dv CODH reacts half as fast with O₂ than Ch CODH, and only the former fully recovers the activity upon reduction. The results raise hope that fast CO/CO₂ biological conversion may be feasible under aerobic conditions.     

Effect of sodium sulfide on Ni-containing carbon monoxide dehydrogenases

The structure of the active-site C-cluster in CO dehydrogenase from Carboxydothermus hydrogenoformans includes a mu(2)-sulfide ion bridged to the Ni and unique Fe, whereas the same cluster in enzymes from Rhodospirillum rubrum (CODH(Rr)) and Moorella thermoacetica (CODH(Mt)) lack this ion. This difference was investigated by exploring the effects of sodium sulfide on activity and spectral properties. Sulfide partially inhibited the CO oxidation activity of CODH(Rr) and generated a lag prior to steady-state. CODH(Mt) was inhibited similarly but without a lag. Adding sulfide to CODH(Mt) in the C(red1) state caused the g(av) = 1.82 EPR signal to decline and new features to appear, including one with g = 1.95, 1.85 and (1.70 or 1.62). Removing sulfide caused the g(av) = 1.82 signal to reappear and activity to recover. Sulfide did not affect the g(av) = 1.86 signal from the C(red2) state. A model was developed in which sulfide binds reversibly to C(red1), inhibiting catalysis. Reducing this adduct causes sulfide to dissociate, C(red2) to develop, and activity to recover. Using this model, apparent K(I) values are 40 +/- 10 nM for CODH(Rr) and 60 +/- 30 microM for CODH(Mt). Effects of sulfide are analogous to those of other anions, including the substrate hydroxyl group, suggesting that these ions also bridge the Ni and unique Fe. This proposed arrangement raises the possibility that CO binding labilizes the bridging hydroxyl and increases its nucleophilic tendency toward attacking Ni-bound carbonyl.     

Carbon Monoxide Dehydrogenase Reduces Cyanate to Cyanide

The biocatalytic function of carbon monoxide dehydrogenase (CODH) has a high environmental relevance owing to its ability to reduce CO₂. Despite numerous studies on CODH over the past decades, its catalytic mechanism is not yet fully understood. In the present combined spectroscopic and theoretical study, we report first evidences for a cyanate (NCO⁻) to cyanide (CN⁻) reduction at the C-cluster. The adduct remains bound to the catalytic center to form the so-called CN⁻-inhibited state. Notably, this conversion does not occur in crystals of the Carboxydothermus hydrogenoformans CODH enzyme (CODHII_Ch), as indicated by the lack of the corresponding CN⁻ stretching mode. The transformation of NCO⁻, which also acts as an inhibitor of the two-electron-reduced C_red2 state of CODH, could thus mimic CO₂ turnover and open new perspectives for elucidation of the detailed catalytic mechanism of CODH.     

Structures and energetics of models for the active site of acetyl-coenzyme a synthase: role of distal and proximal metals in catalysis

Acetyl-coenzyme A (CoA) synthase/carbon monoxide dehydrogenase (ACS/CODH) is a bifunctional enzyme that generates CO from carbon dioxide in the C-cluster of the beta subunit and synthesizes acetyl-CoA from carbon monoxide (CO), CoA, and CH3+ at the active site of the A-cluster in the alpha subunit. On the basis of density functional calculations, we predict that methylation of Nip occurs first, and CO then adds to the NipII-CH3 species to form the intermediate, NipII(CO)(CH3), in which Nip deligates one of its SNid bonds. The CO-insertion/CH3-migration occurs on one metal, the proximal Ni, forming the trigonal planar NipII-acetyl intermediate. The thiolate can bind to NipII and reductively eliminate the thioester. Our calculations disfavor the unprecedented bimetallic CO-insertion/CH3-migration. Ni in the proximal site produces a better catalyst than does Cu.     

Binding of CO to structural models of the bimetallic subunit at the A-cluster of acetyl coenzyme A synthase/CO dehydrogenase

Trinuclear Ni-Cu-Ni and Ni-Ni-Ni complexes derived from an Ni(ii)-dicarboxamido-dithiolato metallosynthon exhibit redox behavior and CO binding properties similar to those of the A-cluster in acetyl coenzyme A synthase/CO dehydrogenase (ACS/CODH).     

Metalloproteins/metalloenzymes for the synthesis of acetyl-CoA in the Wood-Ljungdahl pathway

This paper focuses on the group of metalloproteins/metalloenzymes in the acetyl-coenzyme A synthesis pathway of anaerobic microbes called Wood-Ljungdahl pathway, including formate dehydrogenase (FDH), corrinoid iron sulfur protein (CoFeSP), acetyl-CoA synthase (ACS) and CO dehydrogenase (CODH). FDH, a key metalloenzyme involved in the conversion of carbon dioxide to methyltetrahydrofolate, catalyzes the reversible oxidation of formate to carbon dioxide. CoFeSP, as a methyl group transformer, accepts the methyl group from CH₃-H₄ folate and then transfers it to ACS. CODH reversibly catalyzes the reduction of CO₂ to CO and ACS functions for acetyl-coenzyme A synthesis through condensation of the methyl group, CO and coenzyme A, to finish the whole pathway. This paper introduces the structure, function and reaction mechanisms of these enzymes.     

Structural models of the bimetallic subunit at the A-cluster of acetyl coenzyme a synthase/CO dehydrogenase: binuclear sulfur-bridged Ni-Cu and Ni-Ni complexes and their reactions with CO

The Ni(II)-dicarboxamido-dithiolato complexes (Et4N)2[Ni(NpPepS)] (1) and (Et4N)2[Ni(PhPepS)] (2) were used as Nid metallosynthons in the construction of higher nuclearity dinuclear Ni-Cu and Ni-Ni species to model the bimetallic Mp-Nid site of the A-cluster of acetyl coenzyme A synthase/CO dehydrogenase (ACS/CODH). Reaction of 1 with [Cu(neo)Cl] and [Ni(terpy)Cl2] in MeCN affords the dinuclear complexes (Et4N)[Cu(neo)Ni(NpPepS)] (3) and [Ni(terpy)Ni(NpPepS)] (4), respectively. Reaction of 2 with [Ni(dppe)Cl2] in MeCN yields [Ni(dppe)Ni(PhPepS)] (6). The Ni-Cu complex 3 exhibits no redox chemistry at the Nid site and no reaction with CO. In contrast, the Nip sites in 4 and 6 are readily reduced (characterized by their Ni(I) EPR spectra) and bind CO, exhibiting nuco bands at 2044 and 1997 cm-1, respectively, indicating terminal CO binding. The present Ni-Ni systems replicate the structural and chemical properties of the A-cluster site in ACS/CODH and support the presence of Ni at Mp in the catalytically active enzyme.     

Computational Characterization of Reactive Intermediates of Carbon Monoxide Dehydrogenase

The catalytic oxidation of CO to CO2 by carbon monoxide dehydrogenases has been explored theoretically, and a large C-cluster model including the metal core [Ni-4Fe-4S] and surrounding residues and crystal water molecules was used in density functional calculations. The key species involved in the oxidation of CO at the C-cluster, Cred1, Cred2 and Cint, have been elucidated. On the basis of computational results, the plausible enzymatic mechanism for the CO oxidation was proposed. In the catalytic reaction, the first proton abstraction from the Fe（1）-bound water leads to a precursor to accommodate CO binding and the subsequently consecutive proton transfers from the metal-bound carboxylate to the amino acid residues facilitate the release of CO2. The hydrogen-bond network around the C-cluster formed by conserved residues His93, His96, Glu299, Lys563, and four water molecules in the active domain plays an important role in proton transfer and intermediate stabilization. Predicted geometries of key species show good agreement with the reported crystal structures.     

Structural and spectroscopic models of the A-cluster of acetyl coenzyme a synthase/carbon monoxide dehydrogenase: Nature's Monsanto acetic acid catalyst

Acetyl coenzyme A synthase/carbon monoxide dehydrogenase (ACS/CODH) is a bifunctional enzyme present in a number of anaerobic bacteria. The enzyme catalyzes two separate reactions namely, the reduction of atmospheric CO₂ to CO (CODH activity at the C-cluster) and the synthesis of acetyl coenzyme A (ACS activity at the A-cluster) from CO, CH₃ from a corrinoid iron-sulfur protein, and the thiol coenzyme A. The structure(s) of the A-cluster of ACS/CODH from Moorella thermoacetica revealed an unprecedented structure with three different metallic subunits linked to each other through bridging Cys-S residues comprising the active site. In these structure(s) a Fe₄S₄ cubane is bridged via Cys-S to a bimetallic metal cluster. This bimetallic cluster contains a four-coordinate Ni, Cu, or Zn as the proximal metal (to the Fe₄S₄ cluster; designated M_p), which in turn is bridged through two Cys-S residues to a terminal square planar Ni(II) (Ni_d, distal to Fe₄S₄) ligated by two deprotonated carboxamido nitrogens from the peptide backbone. It is now established that Ni is required at the M_p site for the ACS activity. Over the past several years modeling efforts by several groups have provided clues towards understanding the intrinsic properties of the unique site in ACS. To date most studies have focused on dinuclear compounds that model the M_p-Ni_d subsite. Synthesis of such models have revealed that the Ni_p sites (a) are readily removed when mixed with 1,10-phenanthroline (phen) and (b) can be reduced to the Ni(I) and/or Ni(0) oxidation state (deduced by EPR or electrochemical studies) and bind CO in terminal fashion with ν_co value similar to the enzyme. In contrast, the presence of Cu(I) centers at these M_p sites do not bind CO and are not removable with phen supporting a non-catalytic role for Cu(I) at the M_p site in the enzyme. The Ni_d site (coordinated by carboxamido-N/thiolato-S) in these models are very stable in the +2 oxidation state and not readily removed upon treatment with phen suggesting that the source of ‘labile Ni’ and the NiFeC signal arises from the presence of Ni at the M_p site in ACS. This review includes the results and implications of the modeling studies reported so far.     

脉冲电晕放电-催化转化CO2为CO

在常温、常压下，较系统地研究了CO2在脉冲电晕等离子体条件下的活化与转化，考察了反应器参数、脉冲成形电容、应用电压、气体流量、电晕极性对二氧化碳转化的影响。在本实验条件下，最佳反应器的有效长度为125mm,内径为22mm。二氧化碳转化率和一氧化碳产率随应用电压的增加而增加。另外，随着应用电压的增加，脉冲反应器的能量利用效率反而降低。随着气体流量的增大，二氧化碳的转化率及一氧化碳的产率下降。γ-Al2O3的存在大大促进了二氧化碳的转化，CO2的最高转化率达23％。由于γ-Al2O3在物化性质方面的特性，γ－Al2O3的存在对二氧化碳的转化有重要的作用。研究表明：脉冲电晕放电－催化转化CO2为CO是可行的。     

等离子法转化CO2为CO研究进展

评述了国内外等离子法转化CO2 为CO的发展状态与趋势 ,重点介绍了非平衡等离子体技术转化CO2 为CO的发展 ,探讨了它的基本反应机理 ,并提出了提高二氧化碳转化率的有效途径是负载型催化剂的研制及研究二氧化碳与有机物的氧化偶联反应 (如CO2 +2CH3 OH·(CH3 O) 2 CO +H2 O)具有重要意义。这为CO2 的化工利用开辟了一条广阔而有效的途径 ,也是控制温室效应 ,促进可持续发展的有效手段     

Iron Porphyrin Allows Fast and Selective Electrocatalytic Conversion of CO2 to CO in a Flow Cell

Molecular catalysts have been shown to have high selectivity for CO₂ electrochemical reduction to CO, but with current densities significantly below those obtained with solid-state materials. By depositing a simple Fe porphyrin mixed with carbon black onto a carbon paper support, it was possible to obtain a catalytic material that could be used in a flow cell for fast and selective conversion of CO₂ to CO. At neutral pH (7.3) a current density as high as 83.7 mA cm⁻² was obtained with a CO selectivity close to 98 %. In basic solution (pH 14), a current density of 27 mA cm⁻² was maintained for 24 h with 99.7 % selectivity for CO at only 50 mV overpotential, leading to a record energy efficiency of 71 %. In addition, a current density for CO production as high as 152 mA cm⁻² (>98 % selectivity) was obtained at a low overpotential of 470 mV, outperforming state-of-the-art noble metal based catalysts.     

EPR and infrared spectroscopic evidence that a kinetically competent paramagnetic intermediate is formed when acetyl-coenzyme A synthase reacts with CO

Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS) is a bifunctional enzyme which enables archaea and bacteria to grow autotrophically on CO and hydrogen/carbon dioxide using the Wood-Ljundahl pathway. CO produced from reduction of carbon dioxide by CODH is transferred to the active site of ACS through an intramolecular tunnel, where it combines with Coenzyme A and a methyl cation to produce acetyl-CoA. The active site of ACS contains a single [4Fe-4S] cluster bridged by a cysteine sulfur atom to a binuclear center. The binuclear center is composed of two Ni atoms bridged by two separate cysteine sulfurs. The Ni site attached to the [4Fe-4S] is referred to as proximal Ni, while the other Ni atom, which assumes a square-planar geometry, is referred to as the distal site. We report the characterization of the carbonylated form of highly active (0.67 spins/mol) heterologously expressed monomeric ACS from C. hydrogenoformans in E. coli by rapid-freeze quench EPR (RFQ-EPR) and stopped-flow infrared (SF-IR) spectroscopies. The reaction of ACS with CO produces a single metal-carbonyl species whose formation rate, measured by SF-IR, correlates with the rate of formation, measured by RFQ-EPR, of the paramagnetic state of the enzyme (NiFeC species). These results indicate that the NiFeC species is the predominant form observed in solution when ACS reacts with CO. The NiFeC species contains the proximal Ni in the +1 redox state and the [4Fe-4S] cluster in the 2+ state, thus there is no evidence for either a Ni(0) or a Ni(II) state in the active carbonylated form of the enzyme.     

Ligand-Based Reduction of CO(2) and Release of CO on Iron(II)

A synthetic cycle for the CO(2)-to-CO conversion (with subsequent release of CO) based on iron(II), a redox-active pydridinediimine ligand (PDI), and an O-atom acceptor is reported. This conversion is a passive-type ligand-based reduction, where the electrons for the CO(2) conversion are supplied by the reduced PDI ligand and the ferrous state of the iron is conserved.     

Carbon monoxide induced decomposition of the active site [Ni-4Fe-5S] cluster of CO dehydrogenase

During the past two years, crystal structures of Cu- and Mo-containing carbon monoxide dehydrogenases (CODHs) and Ni- and Fe-containing CODHs have been reported. The active site of CODHs from anaerobic bacteria (cluster C) is composed of Ni, Fe, and S for which crystallographic studies of the enzymes from Carboxydothermus hydrogenoformans, Rhodospirillum rubrum, and Moorella thermoaceticarevealed structural similarities in the overall protein fold but showed substantial differences in the essential Ni coordination environment. The [Ni-4Fe-5S] cluster C in the fully catalytically competent dithionite-reduced CODH II from C. hydrogenoformans (CODHII(Ch)) at 1.6 A resolution contains a characteristic mu(2)-sulfido ligand between Ni and Fe1, resulting in a square-planar ligand arrangement with four S-ligands at the Ni ion. In contrast, the [Ni-4Fe-4S] clusters C in CO-treated CODH from R. rubrum resolved at 2.8 A and in CO-treated acetyl-CoA synthase/CODH complex from M. thermoacetica at 2.2 and 1.9 A resolution, respectively, do not contain the mu(2)-sulfido ligand between Ni and Fe1 and display dissimilar geometries at the Ni ion. The [Ni-4Fe-4S] cluster is composed of a cubane [Ni-3Fe-4S] cluster linked to a mononuclear Fe site. The described coordination geometries of the Ni ion in the [Ni-4Fe-4S] cluster of R. rubrum and M. thermoacetica deviate from the square-planar ligand geometry in the [Ni-4Fe-5S] cluster C of CODHII(Ch). In addition, the latter was converted into a [Ni-4Fe-4S] cluster under specific conditions. The objective of this study was to elucidate the relationship between the structure of cluster C in CODHII(Ch) and the functionality of the protein. We have determined the CO oxidation activity of CODHII(Ch) under different conditions of crystallization, prepared crystals of the enzyme in the presence of dithiothreitol or dithionite as reducing agents under an atmosphere of N(2) or CO, and solved the corresponding structures at 1.1 to 1.6 A resolutions. Fully active CODHII(Ch) obtained after incubation of the enzyme with dithionite under N(2) revealed the [Ni-4Fe-5S] cluster. Short treatment of the enzyme with CO in the presence of dithiothreitol resulted in a catalytically competent CODHII(Ch) with a CO-reduced [Ni-4Fe-5S] cluster, but a prolonged treatment with CO caused the loss of CO-oxidizing activity and revealed a [Ni-4Fe-4S] cluster, which did not contain a mu(2)-S. These data suggest that the [Ni-4Fe-4S] cluster of CODHII(Ch) is an inactivated decomposition product originating from the [Ni-4Fe-5S] cluster.     

Analysis of the CO2 and NH3 reaction in an aqueous solution by 2D IR COS: formation of bicarbonate and carbamate

The two-dimensional (2D) infrared correlation spectra obtained from the reaction time- and concentration-dependent IR spectra elucidates the reaction of CO2 and NH3 in an aqueous solution for CO2 absorption. In the synchronous 2D correlation spectra, the interrelation of the proton with carbamate and bicarbonate indicates that the pH level affected the formation reactions of the two products. Furthermore, the interrelation of carbamate with bicarbonate confirmed the conversion of carbamate into bicarbonate with the release of protons (or the decrease of the pH). From the experimental results including the asynchronous 2D correlation spectra, the reaction of the CO2 and aqueous ammonia proceeded through the following steps: formation of carbamate, formation of bicarbonate, release of protons, and conversion of carbamate into bicarbonate. The analysis of the formation of carbamate and bicarbonate by 2D infrared correlation spectroscopy provides useful information on the reaction mechanism of CO2 and NH3 in aqueous solutions.     

多孔材料的二氧化碳吸附与光催化转化研究进展(英文)

太阳能光催化是CO_2转化和利用的新兴技术,直接利用洁净充足的太阳能将自然界富有的"温室气体"CO_2转化成化学燃料,不仅有利于消除大气温室效应,而且能缓解能源短缺问题,因而成为人们研究的一个重要方向.但目前CO_2的吸附和转换效率还很低,这是太阳能光催化CO_2资源化的最大障碍.高性能光催化剂的设计和合成是这项技术的关键.针对CO_2光还原反应的特异性,理想的光催化材料应该具有以下功能:强的CO_2吸附能力和高的光催化活性.将光催化剂与对CO_2具有高吸附性的多孔材料结合,就可以将CO_2吸附并富集在吸附剂周围的光催化剂表面上以进行催化转化,因此基于高效多孔吸附材料构筑光催化体系成为光催化转化CO_2的重要研究方向之一.CO_2的循环利用包括吸附和转化两方面,高吸附量的多孔材料是获得CO_2高转化效率的前提.本文首先以多孔材料结构参数及性能指标为主线,对无机多孔材料、金属有机框架材料及微孔有机聚合物材料的研究进展及应用前景进行了评述.通过对多孔材料的改性和新型多孔材料的开发,CO_2的吸附能力得到一定的提升,但是仅仅依靠多孔材料的吸附分离,不能实现CO_2中的碳资源循环.在此基础上,本文重点评述了多孔光催化材料在CO_2光催化转化中的最新研究进展.采用多孔材料与光催化剂结合,可增加材料的比表面积,在界面处暴露更多的活性位点,有利于光催化CO_2转化的进行;同时,通过孔结构和基团调控,可以调控光催化剂的反应活性和产物选择性.特别是金属有机框架材料与微孔有机聚合物材料,改变构建单元的官能团和制备技术还可以实现光谱响应范围的调控,提高太阳光的利用率.大量文献对比发现,引入较高CO_2吸附效率的多孔材料构建光催化体系,CO_2光催化转化的效率及产物选择性显著提高.最后,本文对多孔材料在CO_2光催化转化领域的研究现状与亟待解决的问题进行了剖析,提出了下一步可能的研究方向:(1)提高多孔材料自身的稳定性如耐水性能与光/热稳定性;(2)发展光催化材料在多孔载体的微观组装方法,不影响CO_2吸附效率的前提下提高光催化活性;(3)深入研究多孔光催化材料内部与表面的CO_2转化机理,为进一步提高吸附与转化效率提供理论指导.     

The Mutual Conversion of CO2 and CO in Dielectric Barrier Discharge (DBD)

Non-equilibrium plasma, which was engendered by dielectric barrier discharge (DBD) was used to analyze the mutual conversion between CO₂ and CO. The results showed that the conversion ratio of CO increased monotonously with the increasing voltage. But CO₂ was not so. Its conversion ratio reached maximum when the voltage was 3600 V in Ar system. It also showed that the existence of water molecules was more advanageous for the conversion of CO to CO₂ in Air system than in oxygen system, and the conversion ratio could reach 75.8% when the relative humidity was 100%. We also discussed the energy yield and energy efficiency, and the result was that high voltage and high concentration of reactant was disadvantageous for energy utilization.