Nature's carbonylation catalyst: Raman spectroscopic evidence that carbon monoxide binds to iron, not nickel, in CO dehydrogenase

Magnetic iron oxide nanoparticle enhanced microwave pretreatment for anaerobic digestion of meat industry sludge

Our study investigates the effects of iron oxide (Fe3O4) nanoparticles combined microwave pretreatment on the anaerobic digestibility and soluble chemical oxygen demand (SCOD) of meat industry sludge. One of our main objectives was to see whether the different microwave-based pretreatment procedures can enhance biogas production by improving the biological availability of organic compounds. Results demonstrated that combining microwave irradiation with magnetic iron oxide nanoparticles considerably increased SCOD (enhancement ratio was above 1.5), the rate of specific biogas production, and the total cumulative specific biogas volume (more than a threefold increment), while having no negative effect on the biomethane content. Furthermore, the assessment of the sludge samples' dielectric properties (dielectric constant and loss factor measured at the frequency of 500 MHz) showed a strong correlation with SCOD changes (r = 0.9942, R2 = 0.99), offering a novel method to evaluate pretreatment efficiency.

In situ topotactic formation of an inorganic intergrowth bulk NiS/FeS@MgFe-LDH heterojunction to simulate CODH for the photocatalytic reduction of CO2

Enzyme-mimetic photocatalysis has been attracting much attention in bionic research, in which carbon monoxide dehydrogenase (CODH) is a suitable prototype for simulation to meet environmental and energy needs. In this study, we utilized the structural memory effect of layered double hydroxides (LDHs) to build inorganic intergrowth bulk heterojunctions (IIBHs) NiS/FeS@MgFe-LDHs via a pyrolytic topological vulcanization (PTV) method that imitated active C-clusters [Ni-4Fe-4S] in CODH. Enzyme mimicry was evaluated in terms of the microstructure and catalytic reaction site. The similarity between the microstructure of NiS/FeS@MgFe-LDHs and the CODH active group was demonstrated through XRD, XAFS and other characterisations. Subsequently, the obtained in situ irradiated X-ray photoelectron spectra and transient absorption spectra indicated the photogenerated electron transfer of the IIBH, wherein electrons finally accumulated in the conduction band of the NiS domain for the photocatalytic CO2 reduction reaction, which was similar to that of C-clusters [Ni-4Fe-4S] in which the Ni2+ ion was the reactive site. As a result, NiS/FeS@MgFe-LDHs achieved a high yield of CO at a rate of 2151.974 μmol g-1 h-1, which was 39.8 and 9.7 times more than that of NiMgFe-LDHs and NiMgFe-MMO, respectively. The study offers an innovative design route for developing IIBHs, providing novel opportunities for enzyme-mimetic photocatalysis.

Two local minima for structures of [4Fe-4S] clusters obtained with density functional theory methods

[4Fe-4S] clusters are essential cofactors in many proteins involved in biological redox-active processes. Density functional theory (DFT) methods are widely used to study these clusters. Previous investigations have indicated that there exist two local minima for these clusters in proteins. We perform a detailed study of these minima in five proteins and two oxidation states, using combined quantum mechanical and molecular mechanical (QM/MM) methods. We show that one local minimum (L state) has longer Fe-Fe distances than the other (S state), and that the L state is more stable for all cases studied. We also show that some DFT methods may only obtain the L state, while others may obtain both states. Our work provides new insights into the structural diversity and stability of [4Fe-4S] clusters in proteins, and highlights the importance of reliable DFT methods and geometry optimization. We recommend r2SCAN for optimizing [4Fe-4S] clusters in proteins, which gives the most accurate structures for the five proteins studied.

Mono- and tri-β-substituted unsymmetrical metalloporphyrins: synthesis, structural, spectral and electrochemical properties

Mono-/tri-β-substituted metalloporphyrins have been synthesized and characterized. Dramatic reduction in the HOMO–LUMO gap with tunable electronic, spectral and electrochemical redox potentials were observed as the number of electron withdrawing groups increased.

Mineral-organic interfacial processes: potential roles in the origins of life

Life is believed to have originated on Earth ∼4.4-3.5 Ga ago, via processes in which organic compounds supplied by the environment self-organized, in some geochemical environmental niches, into systems capable of replication with hereditary mutation. This process is generally supposed to have occurred in an aqueous environment and, likely, in the presence of minerals. Mineral surfaces present rich opportunities for heterogeneous catalysis and concentration which may have significantly altered and directed the process of prebiotic organic complexification leading to life. We review here general concepts in prebiotic mineral-organic interfacial processes, as well as recent advances in the study of mineral surface-organic interactions of potential relevance to understanding the origin of life.

Iron and Cobalt Complexes of 2,6-Diacetylpyridine-bis(R-thiosemicarbazone) (R=H, phenyl) Showing Unprecedented Ligand Deviation from Planarity

The syntheses, characterization, and single-crystal X-ray crystal structures are reported for four complexes of iron and cobalt with the pentadentate ligands, 2,6-diacetylpyridinebis(thiosemicarbazone) (H(2)L(1)) and 2,6-diacetylpyridinebis-(phenylthiosemicarbazone) (H(2)L(2)), including a cobalt dimer displaying a deviation from planarity which is unprecedented for this class of ligands and allows the ligand to occupy five positions of a pseudo-octahedral coordination sphere. This dimer reacts with KCN to produce a mononuclear complex of relevance to the active site of cobalt nitrile hydratase.

Incorporation of thiolate donation using 2,2'-dithiodibenzaldehyde: complexes of a pentadentate N2S3 ligand with relevance to the active site of Co nitrile hydratase

The use of 2,2'-dithiodibenzaldehyde (DTDB) as a reactant for incorporating thiolate donors into the coordination sphere of a transition metal complex without the need for protecting groups is expanded to include the synthesis of complexes with pentadentate ligands. The ligand N,N'-bis(thiosalicylideneimine)-2,2'-thiobis(ethylamine) (tsaltp) is synthesized at a cobalt center by the reaction of DTDB with a Co complex of thiobis(ethylamine). The resulting Co complexes are thus coordinated by the N(2)S(3) pentadentate ligand through two imine N atoms, two thiolate S atoms, and one thioether S atom. A dimeric, bis-thiolate-bridged complex (1) is isolated and converted to a monomeric CN adduct (2) by treatment with KCN. The N(2)S(3) coordination environment provided by the tsaltp ligand is similar to that provided by the protein donors at the active site of the nitrile hydratase enzymes, with 2 being the first octahedral Co complex reported with such a coordination sphere.

Utilisation of CO2 as a chemical feedstock: opportunities and challenges

The need to reduce the accumulation of CO(2) into the atmosphere requires new technologies able to reduce the CO(2) emission. The utilization of CO(2) as a building block may represent an interesting approach to synthetic methodologies less intensive in carbon and energy. In this paper the general properties of carbon dioxide and its interaction with metal centres is first considered. The potential of carbon dioxide as a raw material in the synthesis of chemicals such as carboxylates, carbonates, carbamates is then discussed. The utilization of CO(2) as source of carbon for the synthesis of fuels or other C(1) molecules such as formic acid and methanol is also described and the conditions for its implementation are outlined. A comparison of chemical and biotechnological conversion routes of CO(2) is made and the barriers to their exploitation are highlighted.

Development of environmentally friendly syntheses: use of enzymes and biomimetic systems for the direct carboxylation of organic substrates

Carboxylation reactions widely occur in nature by the direct use of carbon dioxide or hydrogen carbonate and are mediated by enzymes, which may or may not have a metal as an active center. Such direct carboxylation reactions have found only very few applications for synthetic purposes at industrial level. In this paper we review a part of the work we have done on the use of carbon dioxide and describe: (i) the use of a carboxylation enzyme for the conversion of phenol into 4-OH benzoic acid; and (ii) the potential of biomimetic mixed anhydrides for the synthesis of compounds of industrial interest. The enzymatic production of acetic acid from carbon dioxide is compared with known and new transition metal catalyzed reactions that are fully biomimetic.

Primordial carbonylated iron-sulfur compounds and the synthesis of pyruvate

Experiments exploring the potential catalytic role of iron sulfide at 250 degrees C and elevated pressures (50, 100, and 200 megapascals) revealed a facile, pressure-enhanced synthesis of organometallic phases formed through the reaction of alkyl thiols and carbon monoxide with iron sulfide. A suite of organometallic compounds were characterized with ultraviolet-visible and Raman spectroscopy. The natural synthesis of such compounds is anticipated in present-day and ancient environments wherever reduced hydrothermal fluids pass through iron sulfide-containing crust. Here, pyruvic acid was synthesized in the presence of such organometallic phases. These compounds could have provided the prebiotic Earth with critical biochemical functionality.

Nickel biochemistry

Significant advances have been made in the past year in our understanding of the structure, function, and mode of regulation and assembly of nickel-containing enzymes. The highlight of 1997 was the elucidation of the methyl-CoM reductase structure.

Activated acetic acid by carbon fixation on (Fe,Ni)S under primordial conditions

In experiments modeling the reactions of the reductive acetyl-coenzyme A pathway at hydrothermal temperatures, it was found that an aqueous slurry of coprecipitated NiS and FeS converted CO and CH3SH into the activated thioester CH3-CO-SCH3, which hydrolyzed to acetic acid. In the presence of aniline, acetanilide was formed. When NiS-FeS was modified with catalytic amounts of selenium, acetic acid and CH3SH were formed from CO and H2S alone. The reaction can be considered as the primordial initiation reaction for a chemoautotrophic origin of life.

Enzymology of the fermentation of acetate to methane by Methanosarcina thermophila

Biologically-produced CH4 derives from either the reduction of CO2 or the methyl group of acetate by two separate pathways present in anaerobic mierobes from the Archaea domain. Elucidation of the pathway for CO2 reduction to CH4, the first to be investigated, has yielded several novel enzymes and cofactors. Most of the CH4 produced in nature derives from the methyl group of acetate. Methanosarcina thermophila is a moderate thermophile which ferments acetate by reducing the methyl group to CH4 with electrons derived from oxidation of the carbonyl group to CO2. The pathway in M. thermophila is now understood on a biochemical and genetic level comparable to understanding of the CO2-reducing pathway. Enzymes have been purified and characterized. The genes encoding these enzymes have been cloned, sequenced, transcriptionally mapped, and their regulation defined on a molecular level. This review emphasizes recent developments concerning the enzymes which are unique to the acetate fermentation pathway in M. thermophila.

Analysis of the CO dehydrogenase/acetyl-coenzyme A synthase operon of Methanosarcina thermophila

The cdhABC genes encoding the respective alpha, epsilon, and beta subunits of the five-subunit (alpha, beta, gamma, delta, and epsilon) CO dehydrogenase/acetyl-coenzyme synthase (CODH/ACS) complex from Methanosarcina thermophila were cloned and sequenced. Northern (RNA) blot analyses indicated that the cdh genes encoding the five subunits and an open reading frame (ORF1) with unknown function are cotranscribed during growth on acetate. Northern blot and primer extension analyses suggested that mRNA processing and multiple promoters may be involved in cdh transcript synthesis. The putative CdhA (alpha subunit) and CdhB (epsilon subunit) proteins each have 40% identity to CdhA and CdhB of the CODH/ACS complex from Methanosaeta soehngenii. The cdhC gene encodes the beta subunit (CdhC) of the CODH/ACS complex from M. thermophila. The N-terminal 397 amino acids of CdhC are 42% identical to the C-terminal half of the alpha subunit of CODH/ACS from the acetogenic anaerobe Clostridium thermoaceticum. Sequence analysis suggested potential structures and functions for the previously uncharacterized beta subunit from M. thermophila. The deduced protein sequence of ORF1, located between the cdhC and cdhD genes, has 29% identity to NifH2 from Methanobacterium ivanovii.

Multiple-Edge XAS Studies of Synthetic Iron-Copper Bridged Molecular Assemblies Relevant to Cytochrome c Oxidase. Structure Determination Using Multiple-Scattering Analysis with Statistical Evaluation of Errors

An X-ray absorption spectroscopy study has been carried out at the Fe and Cu K-edges for two bridged molecular assemblies, both of which contain an Fe-X-Cu (X = O(2)(-), OH(-)) bridge unit, some of whose features are relevant to the binuclear site of cytochrome c oxidase. The two complexes [(OEP)Fe-O-Cu(Me(6)tren)](1+) and [(OEP)Fe-(OH)-Cu(Me(5)tren)(OClO(3))](1+) have similar structural fragments around the metal centers except that they differ significantly in the bridge structure (the former contains a linear oxo bridge while the latter has a bent hydroxo bridge). We report a comparative study of these complexes using multiple-scattering (MS) EXAFS analysis and the program package GNXAS. It is found that there is a dramatic increase in the amplitude of the Fe-X-Cu MS pathway as the bridge unit approaches linearity. Full EXAFS MS analysis enables accurate quantitation of bridge metrical details and geometry for both complexes. These studies were done with an expanded version of GNXAS, which allows for simultaneous multiple-edge fitting. Such multiple-edge analysis (using both Fe and Cu edge data) allows common pathways (in this case involving the Fe-X-Cu bridge) to be constrained to be the same, thus improving the observation/variable ratio and enhancing sensitivity for determination of the bridge structure. The accuracy of the structural determination for the bridge units is evaluated by a statistical analysis methodology in which correlations among fitting parameters are identified and contour plots are used to determine random error. The overall error in the EXAFS structural determination is found by establishing the variance with the crystallographically determined values: for the EXAFS-determined parameters at distances below 4 Å, distances and angles deviated on average from crystallographic values by 0.014 Å and 1.5 degrees, respectively. It is also established that structural features in the Fe absorption preedge are diagnostic of oxo vs hydroxo ligation. The relevance of this study to the structural definition of binuclear bridged sites in cytochrome c oxidase and other metalloenzymes is considered.

A methylnickel intermediate in a bimetallic mechanism of acetyl-coenzyme A synthesis by anaerobic bacteria

Resonance Raman (RR) spectroscopy was used to identify a methylnickel adduct (upsilon Ni-C = 422 wave numbers) of carbon monoxide dehydrogenase (CODH) from Clostridium thermoaceticum. Formed at a nickel/iron-sulfur cluster on CODH called center A, the methylnickel species is the precursor of the methyl group of acetyl-coenzyme A in an anaerobic pathway of carbon monoxide or carbon dioxide fixation. Rapid kinetic and RR studies demonstrated that methylation of nickel occurs by heterolysis of the methyl-cobalt bond (upsilon Co-C = 429 wave numbers) of a methylated corrinoid/iron-sulfur protein. In combination with the earlier finding of an iron-carbonyl adduct at center A, detection of the methylnickel intermediate establishes a bimetallic mechanism for acetyl-coenzyme A synthesis.

Mechanism of CO oxidation by carbon monoxide dehydrogenase from Clostridium thermoaceticum and its inhibition by anions

Carbon monoxide dehydrogenase (CODH) performs two distinct reactions at two different metal centers. The synthesis of acetyl-CoA from a methyl group, CO, and coenzyme A occurs at center A and the oxidation of CO to CO2 occurs at center C. In the work reported here, we have studied the mechanism of CO oxidation by CODH and its inhibition by thiocyanate. Our data are consistent with a ping-pong mechanism. A scheme to explain the first half-reaction was developed that includes binding of water and CO to the oxidized form of center C, deprotonation of coordinated water to yield enzyme-bound hydroxyl, nucleophilic attack on coordinated CO by OH- to form enzyme-bound carboxyl, and deprotonation and decarboxylation to form CO2 and the reduced form of center C. In the second half-reaction, the reduced enzyme is reoxidized by an electron acceptor. CO oxidation was pH dependent. The pH dependence of kcat/Km for CO gave a single pKa of 7.7 and a maximum value at 55 degrees C and high pH of 9.1 x 10(6) M-1 s-1. The pH dependence of kcat followed a two-phase titration curve with pKa values of 7.1 and 9.5 and maximum value of kcat at 55 degrees C and high pH of 3250 s-1 (1310 mumol of CO oxidized min-1 mg-1). The pH dependencies of kcat/Km and kcat are interpreted to reflect the ionization of enzyme-bound water from binary and ternary complexes with center C. Reaction with thiocyanate, azide, or cyanate was found to cause a striking shift in the EPR spectrum of center C from gav = 1.82 (g = 2.01, 1.81, 1.65) to a two-component spectrum with gav = 2.15 (g = 2.34, 2.067, 2.03) and gav = 2.17 (g = 2.34, 2.115, 2.047). Thiocyanate acted as a mixed partial inhibitor with respect to CO. The inhibition constants were pH and temperature dependent. The pH dependencies of the inhibition constants gave pKa values of approximately 7.7. Binding of thiocyanate to the oxidized form of center C appears to be favored by a negative enthalpy that is offset by a decrease in entropy yielding a slightly unfavorable free energy of association.

Carbon monoxide-induced activation of gene expression in Rhodospirillum rubrum requires the product of cooA, a member of the cyclic AMP receptor protein family of transcriptional regulators

Induction of the CO-oxidizing system of the photosynthetic bacterium Rhodospirillum rubrum is regulated at the level of gene expression by the presence of CO. In this paper, we describe the identification of a gene that is required for CO-induced gene expression. An 11-kb deletion of the region adjacent to the previously characterized cooFSCTJ region resulted in a mutant unable to synthesize CO dehydrogenase in response to CO and unable to grow utilizing CO as an energy source. A 2.5-kb region that corresponded to a portion of the deleted region complemented this mutant for its CO regulation defect, restoring its ability to grow utilizing CO as an energy source. When the 2.5-kb region was sequenced, one open reading frame, designated cooA, predicted a product showing similarity to members of the cyclic AMP receptor protein (CRP) family of transcriptional regulators. The product, CooA, is 28% identical (51% similar) to CRP and 18% identical (45% similar) to FNR from Escherichia coli. The insertion of a drug resistance cassette into cooA resulted in a mutant that could not grow utilizing CO as an energy source. CooA contains a number of cysteine residues substituted at, or adjacent to, positions that correspond to residues that contact cyclic AMP in the crystal structure of CRP. A model based on this observation is proposed for the recognition of CO by Cooa. Adjacent to cooA are two genes, nadB and nadC, with predicted products similar to proteins in other bacteria that catalyze reactions in the de novo synthesis of NAD.(ABSTRACT TRUNCATED AT 250 WORDS)