1
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Chu S, Gao Q. Unveiling the Low-Lying Spin States of [Fe 3S 4] Clusters via the Extended Broken-Symmetry Method. Molecules 2024; 29:2152. [PMID: 38731643 PMCID: PMC11085573 DOI: 10.3390/molecules29092152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
Photosynthetic water splitting, when synergized with hydrogen production catalyzed by hydrogenases, emerges as a promising avenue for clean and renewable energy. However, theoretical calculations have faced challenges in elucidating the low-lying spin states of iron-sulfur clusters, which are integral components of hydrogenases. To address this challenge, we employ the Extended Broken-Symmetry method for the computation of the cubane-[Fe3S4] cluster within the [FeNi] hydrogenase enzyme. This approach rectifies the error caused by spin contamination, allowing us to obtain the magnetic exchange coupling constant and the energy level of the low-lying state. We find that the Extended Broken-Symmetry method provides more accurate results for differences in bond length and the magnetic coupling constant. This accuracy assists in reconstructing the low-spin ground state force and determining the geometric structure of the ground state. By utilizing the Extended Broken-Symmetry method, we further highlight the significance of the geometric arrangement of metal centers in the cluster's properties and gain deeper insights into the magnetic properties of transition metal iron-sulfur clusters at the reaction centers of hydrogenases. This research illuminates the untapped potential of hydrogenases and their promising role in the future of photosynthesis and sustainable energy production.
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Affiliation(s)
- Shibing Chu
- School of Physics and Electronic Engineering, Jiangsu University, Zhenjiang 212013, China;
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2
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Wilson DWN, Fataftah MS, Mathe Z, Mercado BQ, DeBeer S, Holland PL. Three-Coordinate Nickel and Metal-Metal Interactions in a Heterometallic Iron-Sulfur Cluster. J Am Chem Soc 2024; 146:4013-4025. [PMID: 38308743 PMCID: PMC10993082 DOI: 10.1021/jacs.3c12157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2024]
Abstract
Biological multielectron reactions often are performed by metalloenzymes with heterometallic sites, such as anaerobic carbon monoxide dehydrogenase (CODH), which has a nickel-iron-sulfide cubane with a possible three-coordinate nickel site. Here, we isolate the first synthetic iron-sulfur clusters having a nickel atom with only three donors, showing that this structural feature is feasible. These have a core with two tetrahedral irons, one octahedral tungsten, and a three-coordinate nickel connected by sulfide and thiolate bridges. Electron paramagnetic resonance (EPR), Mössbauer, and superconducting quantum interference device (SQUID) data are combined with density functional theory (DFT) computations to show how the electronic structure of the cluster arises from strong magnetic coupling between the Ni, Fe, and W sites. X-ray absorption spectroscopy, together with spectroscopically validated DFT analysis, suggests that the electronic structure can be described with a formal Ni1+ atom participating in a nonpolar Ni-W σ-bond. This metal-metal bond, which minimizes spin density at Ni1+, is conserved in two cluster oxidation states. Fe-W bonding is found in all clusters, in one case stabilizing a local non-Hund state at tungsten. Based on these results, we compare different M-M interactions and speculate that other heterometallic clusters, including metalloenzyme active sites, could likewise store redox equivalents and stabilize low-valent metal centers through metal-metal bonding.
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Affiliation(s)
- Daniel W. N. Wilson
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, Connecticut 06520, USA
| | - Majed S. Fataftah
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, Connecticut 06520, USA
| | - Zachary Mathe
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Brandon Q. Mercado
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, Connecticut 06520, USA
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Patrick L. Holland
- Department of Chemistry, Yale University, 225 Prospect St., New Haven, Connecticut 06520, USA
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3
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Villarreal DG, Rao G, Tao L, Liu L, Rauchfuss TB, Britt RD. Characterizing the Biosynthesis of the [Fe(II)(CN)(CO) 2(cysteinate)] - Organometallic Product of the Radical-SAM Enzyme HydG by EPR and Mössbauer Spectroscopy. J Phys Chem B 2023; 127:9295-9302. [PMID: 37861415 DOI: 10.1021/acs.jpcb.3c05495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
[FeFe]-hydrogenases employ a catalytic H-cluster, consisting of a [4Fe-4S]H cluster linked to a [2Fe]H subcluster with CO, CN- ligands, and an azadithiolate bridge, which mediates the rapid redox interconversion of H+ and H2. In the biosynthesis of this H-cluster active site, the radical S-adenosyl-l-methionine (radical SAM, RS) enzyme HydG plays the crucial role of generating an organometallic [Fe(II)(CN)(CO)2(cysteinate)]- product that is en route to forming the H-cluster. Here, we report direct observation of this diamagnetic organometallic Fe(II) complex through Mössbauer spectroscopy, revealing an isomer shift of δ = 0.10 mm s-1 and quadrupole splitting of ΔEQ = 0.66 mm s-1. These Mössbauer values are a change from the starting values of δ = 1.15 mm s-1 and ΔEQ = 3.23 mm s-1 for the ferrous "dangler" Fe in HydG. These values of the observed product complex B are in good agreement with Mössbauer parameters for the low-spin Fe2+ ions in synthetic analogues, such as 57Fe Syn-B, which we report here. These results highlight the essential role that HydG plays in converting a resting-state high-spin Fe(II) to a low-spin organometallic Fe(II) product that can be transferred to the downstream maturase enzymes.
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Affiliation(s)
- David G Villarreal
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Guodong Rao
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Lizhi Tao
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
| | - Liang Liu
- School of Chemical Sciences, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - Thomas B Rauchfuss
- School of Chemical Sciences, University of Illinois at Urbana─Champaign, Urbana, Illinois 61801, United States
| | - R David Britt
- Department of Chemistry, University of California Davis, Davis, California 95616, United States
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4
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Shiau AA, Lee HB, Oyala PH, Agapie T. Coordination Number in High-Spin-Low-Spin Equilibrium in Cluster Models of the S 2 State of the Oxygen Evolving Complex. J Am Chem Soc 2023; 145:14592-14598. [PMID: 37366634 PMCID: PMC10575483 DOI: 10.1021/jacs.3c04464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The S2 state of the Oxygen Evolving Complex (OEC) of Photosystem II (PSII) shows high-spin (HS) and low-spin (LS) EPR signals attributed to distinct structures based on computation. Five-coordinate MnIII centers are proposed in these species but are absent in available spectroscopic model complexes. Herein, we report the synthesis, crystal structure, electrochemistry, SQUID magnetometry, and EPR spectroscopy of a MnIIIMnIV3O4 cuboidal complex featuring five-coordinate MnIII. This cluster displays a spin ground state of S = 5/2, while conversion to a six-coordinate Mn upon treatment with water results in a spin state change to S = 1/2. These results demonstrate that coordination number, without dramatic changes within the Mn4O4 core, has a substantial effect on spectroscopy.
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Affiliation(s)
- Angela A Shiau
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd MC 127-72, Pasadena, California 91125, United States
| | - Heui Beom Lee
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd MC 127-72, Pasadena, California 91125, United States
| | - Paul H Oyala
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd MC 127-72, Pasadena, California 91125, United States
| | - Theodor Agapie
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E California Blvd MC 127-72, Pasadena, California 91125, United States
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5
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Brown AC, Suess DLM. An Open-Cuboidal [Fe 3S 4] Cluster Characterized in Both Biologically Relevant Redox States. J Am Chem Soc 2023; 145:2075-2080. [PMID: 36688844 DOI: 10.1021/jacs.2c13126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Synthetic analogues of the three common types of Fe-S clusters found in biology─diamond-core [Fe2S2] clusters, open-cuboidal [Fe3S4] clusters, and cuboidal [Fe4S4] clusters─have been reported in each biologically relevant redox state with one exception: the open-cuboidal [Fe3S4]+ cluster. Here, we describe the synthesis and characterization of an open-cuboidal [Fe3S4] cluster in both biologically relevant redox states: [Fe3S4]+ and [Fe3S4]0. Like their biological counterparts, the oxidized cluster has a spin-canted, S = 1/2 ground state, and the reduced cluster has an S = 2 ground state. Structural analysis reveals that the [Fe3S4] core undergoes substantial contraction upon oxidation, in contrast to the minimal structural changes observed for the only [Fe3S4] protein for which high-resolution structures are available in both redox states (Azotobacter vinelandii ferredoxin I; Av FdI). This difference between the synthetic models and Av FdI is discussed in the context of electron transfer by [Fe3S4] proteins.
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Affiliation(s)
- Alexandra C Brown
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Daniel L M Suess
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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6
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Schüren AO, Ridgway BM, Di Salvo F, Carella LM, Gramm VK, Metzger E, Doctorovich F, Rentschler E, Schünemann V, Ruschewitz U, Klein A. Structural insight into halide-coordinated [Fe 4S 4X nY 4-n] 2- clusters (X, Y = Cl, Br, I) by XRD and Mössbauer spectroscopy. Dalton Trans 2023; 52:1277-1290. [PMID: 36621931 DOI: 10.1039/d2dt03203a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Iron sulphur halide clusters [Fe4S4Br4]2- and [Fe4S4X2Y2]2- (X, Y = Cl, Br, I) were obtained in excellent yields (77 to 78%) and purity from [Fe(CO)5], elemental sulphur, I2 and benzyltrimethylammonium (BTMA+) iodide, bromide and chloride. Single crystals of (BTMA)2[Fe4S4Br4] (1), (BTMA)2[Fe4S4Br2Cl2] (2), (BTMA)2[Fe4S4Cl2I2] (3), and (BTMA)2[Fe4S4Br2I2] (4) were isostructural to the previously reported (BTMA)2[Fe4S4I4] (5) (monoclinic, Cc). Instead of the chloride cubane cluster [Fe4S4Cl4]2-, we found the prismane-shaped cluster (BTMA)3[Fe6S6Cl6] (6) (P1̄). 57Fe Mössbauer spectroscopy indicates complete delocalisation with Fe2.5+ oxidation states for all iron atoms. Magnetic measurements showed small χMT values at 298 K ranging from 1.12 to 1.54 cm3 K mol-1, indicating the dominant antiferromagnetic exchange interactions. With decreasing temperature, the χMT values decreased to reach a plateau at around 100 K. From about 20 K, the values drop significantly. Fitting the data in the Heisenberg-Dirac-van Vleck (HDvV) as well as the Heisenberg Double Exchange (HDE) formalism confirmed the delocalisation and antiferromagnetic coupling assumed from Mössbauer spectroscopy.
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Affiliation(s)
- Andreas O Schüren
- Universität zu Köln, Mathematisch-Naturwissenschaftliche Fakultät, Department für Chemie, Institut für Anorganische Chemie, Greinstraße 6, D-50939 Köln, Germany. .,INQUIMAE-CONICET-Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina
| | - Benjamin M Ridgway
- INQUIMAE-CONICET-Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina
| | - Florencia Di Salvo
- INQUIMAE-CONICET-Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina
| | - Luca M Carella
- Johannes Gutenberg Universität Mainz, Department Chemie, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Verena K Gramm
- Universität zu Köln, Mathematisch-Naturwissenschaftliche Fakultät, Department für Chemie, Institut für Anorganische Chemie, Greinstraße 6, D-50939 Köln, Germany.
| | - Elisa Metzger
- TU Kaiserlautern Department of Physics, 67663 Kaiserlautern, Germany
| | - Fabio Doctorovich
- INQUIMAE-CONICET-Universidad de Buenos Aires, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina.,Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física, Intendente Güiraldes 2160, Pabellón 2, Piso 3, C1428EGA, Buenos Aires, Argentina
| | - Eva Rentschler
- Johannes Gutenberg Universität Mainz, Department Chemie, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Volker Schünemann
- TU Kaiserlautern Department of Physics, 67663 Kaiserlautern, Germany
| | - Uwe Ruschewitz
- Universität zu Köln, Mathematisch-Naturwissenschaftliche Fakultät, Department für Chemie, Institut für Anorganische Chemie, Greinstraße 6, D-50939 Köln, Germany.
| | - Axel Klein
- Universität zu Köln, Mathematisch-Naturwissenschaftliche Fakultät, Department für Chemie, Institut für Anorganische Chemie, Greinstraße 6, D-50939 Köln, Germany.
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7
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Boncella AE, Sabo ET, Santore RM, Carter J, Whalen J, Hudspeth JD, Morrison CN. The expanding utility of iron-sulfur clusters: Their functional roles in biology, synthetic small molecules, maquettes and artificial proteins, biomimetic materials, and therapeutic strategies. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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8
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Bigness A, Vaddypally S, Zdilla MJ, Mendoza-Cortes JL. Ubiquity of cubanes in bioinorganic relevant compounds. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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9
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Balch A, Everett G, Power PP, Armstrong WH, Kovacs J, Stack TDP, Donahue JP, Gray TG, Groysman S, Deng L. Richard Hadley Holm: A Remembrance and A Tribute. COMMENT INORG CHEM 2021. [DOI: 10.1080/02603594.2021.1971203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Alan Balch
- Department of Chemistry, University of California, Davis, California, USA
| | - Grover Everett
- Department of Chemistry, University of Kansas, Lawrence, Kansas, USA
| | - Philip P. Power
- Department of Chemistry, University of California, Davis, California, USA
| | | | - Julie Kovacs
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - T. D. P. Stack
- Department of Chemistry, Stanford University, Stanford, California, USA
| | - James P. Donahue
- Department of Chemistry, Tulane University, New Orleans, Louisiana, USA
| | - Thomas G. Gray
- Department of Chemistry, Case Western Reserve University, Cleveland, Ohio, USA
| | | | - Liang Deng
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
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10
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Bartholomew AK, Musgrave RA, Anderton KJ, Juda CE, Dong Y, Bu W, Wang SY, Chen YS, Betley TA. Revealing redox isomerism in trichromium imides by anomalous diffraction. Chem Sci 2021; 12:15739-15749. [PMID: 35003606 PMCID: PMC8654065 DOI: 10.1039/d1sc04819h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/02/2021] [Indexed: 12/02/2022] Open
Abstract
In polynuclear biological active sites, multiple electrons are needed for turnover, and the distribution of these electrons among the metal sites is affected by the structure of the active site. However, the study of the interplay between structure and redox distribution is difficult not only in biological systems but also in synthetic polynuclear clusters since most redox changes produce only one thermodynamically stable product. Here, the unusual chemistry of a sterically hindered trichromium complex allowed us to probe the relationship between structural and redox isomerism. Two structurally isomeric trichromium imides were isolated: asymmetric terminal imide (tbsL)Cr3(NDipp) and symmetric, μ3-bridging imide (tbsL)Cr3(μ3–NBn) ((tbsL)6− = (1,3,5-C6H9(NC6H4-o-NSitBuMe2)3)6−). Along with the homovalent isocyanide adduct (tbsL)Cr3(CNBn) and the bisimide (tbsL)Cr3(μ3–NPh)(NPh), both imide isomers were examined by multiple-wavelength anomalous diffraction (MAD) to determine the redox load distribution by the free refinement of atomic scattering factors. Despite their compositional similarities, the bridging imide shows uniform oxidation of all three Cr sites while the terminal imide shows oxidation at only two Cr sites. Further oxidation from the bridging imide to the bisimide is only borne at the Cr site bound to the second, terminal imido fragment. Thus, depending on the structural motifs present in each [Cr3] complex, MAD revealed complete localization of oxidation, partial localization, and complete delocalization, all supported by the same hexadentate ligand scaffold. Application of high-resolution Multiwavelength Anomalous Diffraction (MAD) allows the assignment of localized, partly delocalized, and fully delocalized oxidation in a series of trichromium imide isomers.![]()
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Affiliation(s)
| | - Rebecca A Musgrave
- Department of Chemistry and Chemical Biology, Harvard University Cambridge MA 02139 USA
| | - Kevin J Anderton
- Department of Chemistry and Chemical Biology, Harvard University Cambridge MA 02139 USA
| | - Cristin E Juda
- Department of Chemistry and Chemical Biology, Harvard University Cambridge MA 02139 USA
| | - Yuyang Dong
- Department of Chemistry and Chemical Biology, Harvard University Cambridge MA 02139 USA
| | - Wei Bu
- ChemMatCARS, The University of Chicago Argonne Illinois 60439 USA
| | - Su-Yin Wang
- ChemMatCARS, The University of Chicago Argonne Illinois 60439 USA
| | - Yu-Sheng Chen
- ChemMatCARS, The University of Chicago Argonne Illinois 60439 USA
| | - Theodore A Betley
- Department of Chemistry and Chemical Biology, Harvard University Cambridge MA 02139 USA
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11
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Postbiosynthetic modification of a precursor to the nitrogenase iron-molybdenum cofactor. Proc Natl Acad Sci U S A 2021; 118:2015361118. [PMID: 33836573 DOI: 10.1073/pnas.2015361118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nitrogenases utilize Fe-S clusters to reduce N2 to NH3 The large number of Fe sites in their catalytic cofactors has hampered spectroscopic investigations into their electronic structures, mechanisms, and biosyntheses. To facilitate their spectroscopic analysis, we are developing methods for incorporating 57Fe into specific sites of nitrogenase cofactors, and we report herein site-selective 57Fe labeling of the L-cluster-a carbide-containing, [Fe8S9C] precursor to the Mo nitrogenase catalytic cofactor. Treatment of the isolated L-cluster with the chelator ethylenediaminetetraacetate followed by reconstitution with 57Fe2+ results in 57Fe labeling of the terminal Fe sites in high yield and with high selectivity. This protocol enables the generation of L-cluster samples in which either the two terminal or the six belt Fe sites are selectively labeled with 57Fe. Mössbauer spectroscopic analysis of these samples bound to the nitrogenase maturase Azotobacter vinelandii NifX reveals differences in the primary coordination sphere of the terminal Fe sites and that one of the terminal sites of the L-cluster binds to H35 of Av NifX. This work provides molecular-level insights into the electronic structure and biosynthesis of the L-cluster and introduces postbiosynthetic modification as a promising strategy for studies of nitrogenase cofactors.
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12
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Kerns SA, Rose MJ. Scaffold-Based Functional Models of [Fe]-Hydrogenase (Hmd): Building the Bridge between Biological Structure and Molecular Function. Acc Chem Res 2020; 53:1637-1647. [PMID: 32786339 DOI: 10.1021/acs.accounts.0c00315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The well-known dinuclear [FeFe] and [NiFe] hydrogenase enzymes are redox-based proton reduction and H2 oxidation catalysts. In comparison, the structural and functional aspects of the mononuclear nonredox hydrogenase, known as [Fe]-hydrogenase or Hmd, have been less explored because of the relatively recent crystallographic elucidation of the enzyme active site. Additionally, the synthetic challenges posed by the highly substituted and asymmetric coordination environment of the iron guanylylpyridinol (FeGP) cofactor have hampered functional biomimetic modeling studies to a large extent. The active site contains an octahedral low-spin Fe(II) center with the following coordination motifs: a bidentate acyl-pyridone moiety (C,N) and cysteinyl-S in a facial arrangement; two cis carbonyl ligands; and a H2O/H2 binding site. In [Fe]-hydrogenase, heterolytic H2 activation putatively by the pendant pyridone/pyridonate-O base serving as a proton acceptor. Following H2 cleavage, an intermediate Fe-H species is thought to stereoselectively transfer a hydride to the substrate methenyl-H4MPT+, thus forming methylene-H4MPT. In the past decade, chemists, inspired by the elegant organometallic chemistry inherent to the FeGP cofactor, have synthesized a number of faithful structural models. However, functional systems are still relatively limited and often rely on abiological ligands or metal centers that obfuscate a direct correlation to nature's design.Our group has developed a bioinspired suite of synthetic analogues of Hmd to better understand the effects of structure on the stability and functionality of the Hmd active site, with a special emphasis on using a scaffold-based ligand design. This systematic approach has contributed to a deeper understanding of the unique ligand array of [Fe]-hydrogenase in nature and has ultimately resulted in the first functional synthetic models without the aid of abiological ligands. This Account reviews the reactivity of the functional anthracene-scaffolded synthetic models developed by our group in the context of current mechanistic understanding drawn from both protein crystallography and computational studies. Furthermore, we introduce a novel thermodynamic framework to place the reactivity of our model systems in context and provide an outlook on the future study of [Fe]-hydrogenase synthetic models through both a structural and functional lens.
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Affiliation(s)
- Spencer A. Kerns
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Michael J. Rose
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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13
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Tang S, Hicks ND, Cheng YS, Silva A, Fortune SM, Sacchettini JC. Structural and functional insight into the Mycobacterium tuberculosis protein PrpR reveals a novel type of transcription factor. Nucleic Acids Res 2019; 47:9934-9949. [PMID: 31504787 PMCID: PMC6765138 DOI: 10.1093/nar/gkz724] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/19/2019] [Accepted: 08/07/2019] [Indexed: 01/15/2023] Open
Abstract
The pathogenicity of Mycobacterium tuberculosis depends upon its ability to catabolize host cholesterol. Upregulation of the methylcitrate cycle (MCC) is required to assimilate and detoxify propionyl-CoA, a cholesterol degradation product. The transcription of key genes prpC and prpD in MCC is activated by MtPrpR, a member of a family of prokaryotic transcription factors whose structures and modes of action have not been clearly defined. We show that MtPrpR has a novel overall structure and directly binds to CoA or short-chain acyl-CoA derivatives to form a homotetramer that covers the binding cavity and locks CoA tightly inside the protein. The regulation of this process involves a [4Fe4S] cluster located close to the CoA-binding cavity on a neighboring chain. Mutations in the [4Fe4S] cluster binding residues rendered MtPrpR incapable of regulating MCC gene transcription. The structure of MtPrpR without the [4Fe4S] cluster-binding region shows a conformational change that prohibits CoA binding. The stability of this cluster means it is unlikely a redox sensor but may function by sensing ambient iron levels. These results provide mechanistic insights into this family of critical transcription factors who share similar structures and regulate gene transcription using a combination of acyl-CoAs and [4Fe4S] cluster.
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Affiliation(s)
- Su Tang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77840, USA
| | - Nathan D Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Yu-Shan Cheng
- Department of Chemistry, Texas A&M University, College Station, TX 77840, USA
| | - Andres Silva
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77840, USA
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.,Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77840, USA.,Department of Chemistry, Texas A&M University, College Station, TX 77840, USA
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14
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DeRosha DE, Arnet NA, Mercado BQ, Holland PL. A [2Fe-1S] Complex That Affords Access to Bimetallic and Higher-Nuclearity Iron-Sulfur Clusters. Inorg Chem 2019; 58:8829-8834. [PMID: 31247861 DOI: 10.1021/acs.inorgchem.9b01212] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Small, coordinatively unsaturated iron-sulfur clusters are conceived as building blocks for the diverse set of shapes of iron-sulfur clusters in biological and synthetic chemistry. Here we describe a synthetic method for preparing [2Fe-1S] clusters containing two iron(II) ions, which are supported by a relatively unhindered β-diketiminate supporting ligand. The [2Fe-1S] cluster can be isolated in the presence of trimethylphosphine, and the compound with one PMe3 on each iron(II) ion has been crystallographically characterized. The PMe3 ligands may be removed with B(C6F5)3 to give a spectroscopically characterized species with solvent ligands. This species is a versatile synthon for [2Fe-2S], [4Fe-3S], and [10Fe-8S] clusters. Crystallographic characterization of the 10Fe cluster shows that it has all iron(II) ions, and the core has two [4Fe-4S] cubes that share a face in a novel arrangement. This cluster also has two iron sites that are coordinated to solvent donors, suggesting the potential for using this type of cluster for reactivity in the future.
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Affiliation(s)
- Daniel E DeRosha
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06511 , United States
| | - Nicholas A Arnet
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06511 , United States
| | - Brandon Q Mercado
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06511 , United States
| | - Patrick L Holland
- Department of Chemistry , Yale University , 225 Prospect Street , New Haven , Connecticut 06511 , United States
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15
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Oldengott J, Richthofen C, Walleck S, Stammler A, Bögge H, Glaser T. Trinuclear Triplesalophen Building Blocks with Terminal Cyanides and Implications for the Spin‐Polarization Mechanism for Low‐Spin Fe
III
and Cr
III
Ions. Eur J Inorg Chem 2018. [DOI: 10.1002/ejic.201801042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jan Oldengott
- Lehrstuhl für Anorganische Chemie I Fakultät für Chemie Universität Bielefeld Universitätsstr. 25 33615 Bielefeld Germany
| | - Carl‐Georg Richthofen
- Lehrstuhl für Anorganische Chemie I Fakultät für Chemie Universität Bielefeld Universitätsstr. 25 33615 Bielefeld Germany
| | - Stephan Walleck
- Lehrstuhl für Anorganische Chemie I Fakultät für Chemie Universität Bielefeld Universitätsstr. 25 33615 Bielefeld Germany
| | - Anja Stammler
- Lehrstuhl für Anorganische Chemie I Fakultät für Chemie Universität Bielefeld Universitätsstr. 25 33615 Bielefeld Germany
| | - Hartmut Bögge
- Lehrstuhl für Anorganische Chemie I Fakultät für Chemie Universität Bielefeld Universitätsstr. 25 33615 Bielefeld Germany
| | - Thorsten Glaser
- Lehrstuhl für Anorganische Chemie I Fakultät für Chemie Universität Bielefeld Universitätsstr. 25 33615 Bielefeld Germany
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16
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McSkimming A, Suess DLM. Selective Synthesis of Site-Differentiated Fe 4S 4 and Fe 6S 6 Clusters. Inorg Chem 2018; 57:14904-14912. [PMID: 30418746 DOI: 10.1021/acs.inorgchem.8b02684] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Obtaining rational control over the structure and nuclearity of metalloclusters is an ongoing challenge in synthetic Fe-S cluster chemistry. We report a new family of tridentate imidazolin-2-imine ligands L(NImR)3 that can bind [Fe4S4]2+ or [Fe6S6]3+ clusters, depending on the steric profile of the ligand and the reaction stoichiometry. A high-yielding synthetic route to L(NImR)3 ligands (where R is the imidazolyl N substituents) from trianiline and 2-chloroimidazolium precursors is described. For L(NImMe)3 (tris(1,3,5-(3-( N, N-dimethyl-4,5-diphenylimidazolin-2-imino)phenylmethyl))benzene), metalation with 1 equiv of [Ph4P]2[Fe4S4Cl4] and 3 equiv of NaBPh4 furnishes a mixture of products, but adjusting the stoichiometry to 1.5 equiv of [Ph4P]2[Fe4S4Cl4] provides (L(NImMe)3)Fe6S6Cl6 in high yield. Formation of an [Fe6S6]3+ cluster using L(NImTol)3 (tris(1,3,5-(3-( N, N-bis(4-methylphenyl)-4,5-diphenylimidazolin-2-imino)phenylmethyl))benzene) is not observed; instead, the [Fe4S4]2+ cluster [(L(NImTol)3)(Fe4S4Cl)][BPh4] is cleanly generated when 1 equiv of [Ph4P]2[Fe4S4Cl4] is employed. The selectivity for cluster nuclearity is rationalized by the orientation of the imidazolyl rings whereby long N-imidazolyl substituents preclude formation of [Fe6S6]3+ clusters but not [Fe4S4]2+ clusters. Thus, the structure and nuclearity of L(NImR)3-bound Fe-S clusters may be selectively controlled through rational modification the ligand's substituents.
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Affiliation(s)
- Alex McSkimming
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Daniel L M Suess
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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17
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Moula G, Matsumoto T, Miehlich ME, Meyer K, Tatsumi K. Synthesis of an All-Ferric Cuboidal Iron-Sulfur Cluster [Fe III4 S 4 (SAr) 4 ]. Angew Chem Int Ed Engl 2018; 57:11594-11597. [PMID: 29775229 DOI: 10.1002/anie.201803679] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Indexed: 11/11/2022]
Abstract
An unprecedented, super oxidized all-ferric iron-sulfur cubanoid cluster with all terminal thiolates, Fe4 S4 (STbt)4 (3) [Tbt=2,4,6-tris{bis(trimethylsilyl)methyl}phenyl], has been isolated from the reaction of the bis-thiolate complex Fe(STbt)2 (2) with elemental sulfur. This cluster 3 has been characterized by X-ray crystallography, zero-field 57 Fe Mössbauer spectroscopy, cyclic voltammetry, and other relevant physico-chemical methods. Based on all the data, the electronic ground state of the cluster has been assigned to be Stot =0.
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Affiliation(s)
- Golam Moula
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan),
| | - Tsuyoshi Matsumoto
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan
| | - Matthias E Miehlich
- Department of Chemistry and Pharmacy, Inorganic Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Egerlandstrasse 1, 91058, Erlangen, Bavaria, Germany
| | - Karsten Meyer
- Department of Chemistry and Pharmacy, Inorganic Chemistry, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Egerlandstrasse 1, 91058, Erlangen, Bavaria, Germany
| | - Kazuyuki Tatsumi
- Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan),
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18
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Moula G, Matsumoto T, Miehlich ME, Meyer K, Tatsumi K. Synthesis of an All-Ferric Cuboidal Iron-Sulfur Cluster [FeIII
4
S4
(SAr)4
]. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803679] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Golam Moula
- Research Center for Materials Science; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan),
| | - Tsuyoshi Matsumoto
- Institute of Transformative Bio-Molecules (WPI-ITbM); Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8601 Japan
| | - Matthias E. Miehlich
- Department of Chemistry and Pharmacy; Inorganic Chemistry; Friedrich-Alexander-University Erlangen-Nürnberg (FAU); Egerlandstrasse 1 91058 Erlangen Bavaria Germany
| | - Karsten Meyer
- Department of Chemistry and Pharmacy; Inorganic Chemistry; Friedrich-Alexander-University Erlangen-Nürnberg (FAU); Egerlandstrasse 1 91058 Erlangen Bavaria Germany
| | - Kazuyuki Tatsumi
- Research Center for Materials Science; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8602 Japan),
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19
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Lupan A, Silaghi-Dumitrescu R, King RB. Tetracapped tetrahedral ruthenium-sulfur clusters related to iron-sulfur structural units in metalloenzymes. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.10.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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20
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Kerns SA, Magtaan AC, Vong PR, Rose MJ. Functional Hydride Transfer by a Thiolate-Containing Model of Mono-Iron Hydrogenase featuring an Anthracene Scaffold. Angew Chem Int Ed Engl 2018; 57:2855-2858. [DOI: 10.1002/anie.201712948] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Spencer A. Kerns
- Department of Chemistry; The University of Texas at Austin; Austin TX 78712 USA
| | | | - Pisey R. Vong
- Department of Chemistry; The University of Texas at Austin; Austin TX 78712 USA
| | - Michael J. Rose
- Department of Chemistry; The University of Texas at Austin; Austin TX 78712 USA
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21
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Kerns SA, Magtaan AC, Vong PR, Rose MJ. Functional Hydride Transfer by a Thiolate-Containing Model of Mono-Iron Hydrogenase featuring an Anthracene Scaffold. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201712948] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Spencer A. Kerns
- Department of Chemistry; The University of Texas at Austin; Austin TX 78712 USA
| | | | - Pisey R. Vong
- Department of Chemistry; The University of Texas at Austin; Austin TX 78712 USA
| | - Michael J. Rose
- Department of Chemistry; The University of Texas at Austin; Austin TX 78712 USA
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22
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Ohta S, Ohki Y. Impact of ligands and media on the structure and properties of biological and biomimetic iron-sulfur clusters. Coord Chem Rev 2017. [DOI: 10.1016/j.ccr.2017.02.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Seo J, Manes TA, Rose MJ. Structural and functional synthetic model of mono-iron hydrogenase featuring an anthracene scaffold. Nat Chem 2017; 9:552-557. [DOI: 10.1038/nchem.2707] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 11/25/2016] [Indexed: 12/15/2022]
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24
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The competition between chemistry and biology in assembling iron-sulfur derivatives. Molecular structures and electrochemistry. Part IV. {[Fe3S4](SγCys)3} proteins. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2016.09.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Holm RH, Lo W. Structural Conversions of Synthetic and Protein-Bound Iron–Sulfur Clusters. Chem Rev 2016; 116:13685-13713. [DOI: 10.1021/acs.chemrev.6b00276] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. H. Holm
- Department
of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Wayne Lo
- Department
of Chemistry and
Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
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26
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Dance I. Mechanisms of the S/CO/Se interchange reactions at FeMo-co, the active site cluster of nitrogenase. Dalton Trans 2016; 45:14285-300. [PMID: 27534727 DOI: 10.1039/c6dt03159e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The active site of the N2 fixing enzyme nitrogenase is a C-centred Fe7MoS cluster (FeMo-co) containing a trigonal prism of six Fe atoms connected by a central belt of three doubly-bridging S atoms. The trigonal faces of the prism are capped via triply-bridging S atoms to Fe1 at one end and Mo at the other end. One of the central belt atoms, S2B, considered to be important in the chemical mechanism of the enzyme, has been shown by Spatzal, Rees et al. to undergo substitution by CO, and also substitution by Se in the presence of SeCN(-), under turnover conditions. Further, when turning over under C2H2 or N2/CO there is migration of Se to the other two belt bridging positions. These reactions are extraordinary, and unprecedented in metal chalcogenide cluster chemistry. Using density functional simulations, mechanisms for all of these reactions have been developed, involving the small molecules SCO, SeCO, C2H2S, C2H2Se, SeCN(-), SCN(-) functioning as carriers of S and Se atoms. The possibility that the S2B bridge position is vacant is discounted, because the barrier to formation of a bridge-void intermediate with two contiguous three-coordinate Fe atoms is too large. A bridging ligand is retained throughout the proposed mechanisms. Intermediates with Fe-C(O)-S/Se-Fe cycles and with SCO/SeCO C-bound to Fe are predicted. The energetics of the reaction trajectories show them to be feasible and easily reversible, consistent with experiment. Alternative mechanisms involving intramolecular differential rotatory rearrangements of the cluster to scramble the Se bridges are also examined, and shown to be very unlikely. The implications of these new facets of the reactivity of the FeMo-co cluster are discussed: it is considered that they are unlikely to be part of the mechanism of the physiological reactions of nitrogenase.
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Affiliation(s)
- Ian Dance
- School of Chemistry, UNSW Australia, Sydney 2052, Australia.
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27
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Tanifuji K, Tajima S, Ohki Y, Tatsumi K. Interconversion between [Fe4S4] and [Fe2S2] Clusters Bearing Amide Ligands. Inorg Chem 2016; 55:4512-8. [DOI: 10.1021/acs.inorgchem.6b00352] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Kazuki Tanifuji
- Department
of Chemistry, Graduate School of Science and Research Center for Materials
Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Shunichi Tajima
- Department
of Chemistry, Graduate School of Science and Research Center for Materials
Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yasuhiro Ohki
- Department
of Chemistry, Graduate School of Science and Research Center for Materials
Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kazuyuki Tatsumi
- Department
of Chemistry, Graduate School of Science and Research Center for Materials
Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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28
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Stüble P, Berroth A, Röhr C. Synthesis and crystal structure of new K and Rb selenido/tellurido ferrate cluster compounds. ZEITSCHRIFT FUR NATURFORSCHUNG SECTION B-A JOURNAL OF CHEMICAL SCIENCES 2016. [DOI: 10.1515/znb-2015-0223] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
In the course of a systematic study of alkali iron chalcogenido salts containing clusters [Fe4
Q
8] a series of new mixed-valent potassium and rubidium selenido and tellurido ferrates(II/III) was synthesized by carefully heating the pure elements enclosed in sample tubes under an argon atmosphere up to maximum temperatures of 800–900 °C. Their crystal structures have been determined by means of single crystal X-ray diffraction. The mixed-valent FeII/III tellurido ferrates A
7[Fe4Te8] form three different structure types. All structures contain tetramers of four edge sharing [FeTe4] tetrahedra, which are connected by common edges to form only slightly distorted tetrahedral [Fe4Te8]7− anions (‘stella quadrangula’) with a [Fe4Te4] cubane core. In all cases, these anions are surrounded by 26 alkali cations, which are located at the eight corners and the midpoints of the six faces and 12 edges of a cube. The three crystal structures can thus be described by three different packings of cuboid moieties: The monoclinic rubidium compound Rb7[Fe4Te8] (space group C2/c, a = 2000.16(7), b = 897.79(3), c = 1768.12(6) pm, β = 117.4995(10)°, Z = 4, R1 = 0.0296) is isotypic to the known cesium tellurido and sulfido ferrates Cs7[Fe4(S/Te)8]. Depending on the temperature, K7[Fe4Te8] forms two different but closely related new structure types: The tetragonal r.t. modification (space group P42/nmc, a = 1222.25(14), c = 872.1(2) pm, Z = 2, R1 = 0.0583) crystallizes in a supergroup of the orthorhombic l.t. (100 K) form (space group Pbcn, a = 1715.5, b = 866.76(3), c = 1715.50(7) pm, Z = 4, R1 = 0.0160). In all structures, the cluster centered cubes are stacked to form columns along the short (≈870 pm) axis. These columns are themselves densely packed with 4 (both K compounds) and 6 (A = Rb) adjacent face-sharing columns. According to these arrangements of cluster-centered cubes, a relation of the packing of K/Rb cations and cluster anions with the simple cubic packing can be established applying the crystallographic group-subgroup formalism. Attempts to synthesize the corresponding selenium compound K7[Fe4Se8] resulted in the formation of the likewise mixed-valent compound K6[Fe4Se8]. Despite the modified composition, the new orthorhombic structure (space group Pbcn, a = 1632.62(6), b = 821.10(3), c = 1592.75(6) pm, Z = 4, R1 = 0.0540) is almost isotypic to the l.t. form of K7[Fe4Te8], the only difference being a missing K site. K5Fe2Te5 crystallizes in a new structure type (cubic, space group Pa3̅, a = 1709.02(5) pm, Z = 4, R1 = 0.0594). According to K5Fe2Te5=K15[Fe3Te7]2(Te), its structure contains mixed-valent cuboidal trimers [Fe3Te7](6/7)− and isolated telluride ions, which are coordinated by cubes of K+ cations.
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Affiliation(s)
- Pirmin Stüble
- Institut für Anorganische und Analytische Chemie , Universität Freiburg , Albertstr. 21, D-79104 Freiburg, Germany
| | - Angela Berroth
- Institut für Anorganische und Analytische Chemie , Universität Freiburg , Albertstr. 21, D-79104 Freiburg, Germany
| | - Caroline Röhr
- Institut für Anorganische und Analytische Chemie , Universität Freiburg , Albertstr. 21, D-79104 Freiburg, Germany
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29
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Schüren AO, Gramm VK, Dürr M, Foi A, Ivanović-Burmazović I, Doctorovich F, Ruschewitz U, Klein A. Halide coordinated homoleptic [Fe4S4X4](2-) and heteroleptic [Fe4S4X2Y2](2-) clusters (X, Y = Cl, Br, I)--alternative preparations, structural analogies and spectroscopic properties in solution and solid state. Dalton Trans 2016; 45:361-75. [PMID: 26618565 DOI: 10.1039/c5dt02769a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
New facile methods to prepare iron sulphur halide clusters [Fe4S4X4](2-) from [Fe(CO)5] and elemental sulphur were elaborated. Reactions of ferrous precursors like tetrahalidoferrates(ii) or simple ferrous halides with [Fe(CO)5] and sulphur turned out to be efficient methods to prepare homoleptic [Fe4S4X4](2-) (X = Cl, Br) and heteroleptic clusters [Fe4S4X4-nYn](2-) (X = Cl, Br; Y = Br, I). Solid materials were obtained as salts of BTMA(+) (= benzyltrimethylammonium); the new compounds containing [Fe4S4Br4](2-) and [Fe4S4X2Y2](2-) (X, Y = Cl, Br, I) were all isostructural to (BTMA)2[Fe4S4I4] (monoclinic, Cc) as inferred from synchrotron X-ray powder diffraction. While the solid materials contain defined heteroleptic clusters with a halide X : Y ratio of 2 : 2, dissolving these compounds leads to rapid scrambling of the halide ligands forming mixtures of all five possible [Fe4S4X4-nYn](2-) clusters as could be shown by UHR-ESI MS. The variation of X and Y allowed assignment of the absorption bands in the visible and NIR; the long-wavelength bands around 1100 nm were tentatively assigned to intervalence charge transfer (IVCT) transitions.
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Affiliation(s)
- Andreas O Schüren
- Department für Chemie, Institut für Anorganische Chemie, Universität zu Köln, Greinstraße 6, 50939 Köln, Germany. and Departamento de Química Inorgánica, Analítica, y Química Física, Facultad de Ciencias Exactas y Naturales, INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Piso 3, C1428EHA Buenos Aires, Argentina
| | - Verena K Gramm
- Department für Chemie, Institut für Anorganische Chemie, Universität zu Köln, Greinstraße 6, 50939 Köln, Germany.
| | - Maximilian Dürr
- Department Chemie und Pharmazie, Lehrstuhl für Bioanorgansiche Chemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058 Erlangen, Germany
| | - Ana Foi
- Departamento de Química Inorgánica, Analítica, y Química Física, Facultad de Ciencias Exactas y Naturales, INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Piso 3, C1428EHA Buenos Aires, Argentina
| | - Ivana Ivanović-Burmazović
- Department Chemie und Pharmazie, Lehrstuhl für Bioanorgansiche Chemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, 91058 Erlangen, Germany
| | - Fabio Doctorovich
- Departamento de Química Inorgánica, Analítica, y Química Física, Facultad de Ciencias Exactas y Naturales, INQUIMAE-CONICET, Universidad de Buenos Aires, Ciudad Universitaria, Pabellón 2, Piso 3, C1428EHA Buenos Aires, Argentina
| | - Uwe Ruschewitz
- Department für Chemie, Institut für Anorganische Chemie, Universität zu Köln, Greinstraße 6, 50939 Köln, Germany.
| | - Axel Klein
- Department für Chemie, Institut für Anorganische Chemie, Universität zu Köln, Greinstraße 6, 50939 Köln, Germany.
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30
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Majumdar A. Bioinorganic modeling chemistry of carbon monoxide dehydrogenases: description of model complexes, current status and possible future scopes. Dalton Trans 2015; 43:12135-45. [PMID: 24984248 DOI: 10.1039/c4dt00729h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Carbon monoxide dehydrogenases (CODHs) use CO as their sole source of carbon and energy and are found in both aerobic and anaerobic carboxidotrophic bacteria. Reversible transformation of CO to CO2 is catalyzed by a bimetallic [Mo-(μ2-S)-Cu] system in aerobic and by a highly asymmetric [Ni-Fe-S] cluster in anaerobic CODH active sites. The CODH activity in the microorganisms effects the removal of almost 10(8) tons of CO annually from the lower atmosphere and earth and thus help to maintain a sub-toxic concentration of CO. Despite an appreciable amount of work, the mechanism of CODH activity is not clearly understood yet. Moreover, biomimetic chemistry directed towards the active sites of CODHs faces several synthetic challenges. The synthetic problems associated with the modeling chemistry and strategies adopted to overcome those problems are discussed along with their limitations. A critical analysis of the exciting results delineating the present status of CODH modeling chemistry and its future prospects are presented.
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Affiliation(s)
- Amit Majumdar
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata-700032, India.
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31
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Denny JA, Darensbourg MY. Metallodithiolates as ligands in coordination, bioinorganic, and organometallic chemistry. Chem Rev 2015; 115:5248-73. [PMID: 25948147 DOI: 10.1021/cr500659u] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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32
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Lee SC, Lo W, Holm RH. Developments in the biomimetic chemistry of cubane-type and higher nuclearity iron-sulfur clusters. Chem Rev 2014; 114:3579-600. [PMID: 24410527 PMCID: PMC3982595 DOI: 10.1021/cr4004067] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Wayne Lo
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1 Canada and the Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - R. H. Holm
- Corresponding Authors: S. C. Lee: . R. H. Holm:
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33
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Bioinspired greigite magnetic nanocrystals: chemical synthesis and biomedicine applications. Sci Rep 2013; 3:2994. [PMID: 24141204 PMCID: PMC3801133 DOI: 10.1038/srep02994] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Accepted: 10/02/2013] [Indexed: 11/17/2022] Open
Abstract
Large scale greigite with uniform dimensions has stimulated significant demands for applications such as hyperthermia, photovoltaics, medicine and cell separation, etc. However, the inhomogeneity and hydrophobicity for most of the as prepared greigite crystals has limited their applications in biomedicine. Herein, we report a green chemical method utilizing β-cyclodextrin (β-CD) and polyethylene glycol (PEG) to synthesize bioinspired greigite (Fe3S4) magnetic nanocrystals (GMNCs) with similar structure and magnetic property of magnetosome in a large scale. β-CD and PEG is responsible to control the crystal phase and morphology, as well as to bound onto the surface of nanocrystals and form polymer layers. The GMNCs exhibit a transverse relaxivity of 94.8 mM−1s−1 which is as high as iron oxide nanocrystals, and an entrapment efficiency of 58.7% for magnetic guided delivery of chemotherapeutic drug doxorubicin. Moreover, enhanced chemotherapeutic treatment of mice tumor was obtained via intravenous injection of doxorubicin loaded GMNCs.
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34
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Wang X, Zhou W, Chang Z, Zhou Z, Wu S. Solvent-free Synthesis of Hexagonal Iron Sulfide Nanoflowers. CHINESE J CHEM 2013. [DOI: 10.1002/cjoc.201300341] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Ohki Y, Tanifuji K, Yamada N, Cramer RE, Tatsumi K. Formation of a Nitrogenase P-cluster [Fe8S7] Core via Reductive Fusion of Two All-Ferric [Fe4S4] Clusters. Chem Asian J 2012; 7:2222-4. [DOI: 10.1002/asia.201200568] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Indexed: 11/06/2022]
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Zheng B, Chen XD, Zheng SL, Holm RH. Selenium as a structural surrogate of sulfur: template-assisted assembly of five types of tungsten-iron-sulfur/selenium clusters and the structural fate of chalcogenide reactants. J Am Chem Soc 2012; 134:6479-90. [PMID: 22424175 DOI: 10.1021/ja3010539] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Syntheses of five types of tungsten-iron-sulfur/selenium clusters, namely, incomplete cubanes, single cubanes, edge-bridged double cubanes (EBDCs), P(N)-type clusters, and double-cuboidal clusters, have been devised using the concept of template-assisted assembly. The template reactant is six-coordinate [(Tp*)W(VI)S(3)](1-) [Tp* = tris(3,5-dimethylpyrazolyl)hydroborate(1-)], which in the assembly systems organizes Fe(2+/3+) and sulfide/selenide into cuboidal [(Tp*)WFe(2)S(3)] or cubane [(Tp*)WFe(3)S(3)Q] (Q = S, Se) units. With appropriate terminal iron ligation, these units are capable of independent existence or may be transformed into higher-nuclearity species. Selenide is used as a surrogate for sulfide in cluster assembly in order to determine by X-ray structures the position occupied by an external chalcogenide nucleophile or an internal chalcogenide atom in the product clusters. Specific incorporation of selenide is demonstrated by the formation of [WFe(3)S(3)Se](2+/3+) cubane cores. Reductive dimerization of the cubane leads to the EBDC core [W(2)Fe(6)S(6)Se(2)](2+) containing μ(4)-Se sites. Reaction of these species with HSe(-) affords the P(N)-type cores [W(2)Fe(6)S(6)Se(3)](1+), in which selenide occupies μ(6)-Se and μ(2)-Se sites. The reaction of [(Tp*)WS(3)](1-), FeCl(2), and Na(2)Se yields the double-cuboidal [W(2)Fe(4)S(6)Se(3)](2+/0) core with μ(2)-Se and μ(4)-Se bridges. It is highly probable that in analogous sulfide-only assembly systems, external and internal sulfide reactants occupy corresponding positions in the cluster products. The results further demonstrate the viability of template-assisted cluster synthesis inasmuch as the reduced (Tp*)WS(3) unit is present in all of the clusters. Structures, zero-field Mössbauer data, and redox potentials are presented for each cluster type.
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Affiliation(s)
- Bo Zheng
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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Cao F, Hu W, Zhou L, Shi W, Song S, Lei Y, Wang S, Zhang H. 3D Fe3S4 flower-like microspheres: high-yield synthesis via a biomolecule-assisted solution approach, their electrical, magnetic and electrochemical hydrogen storage properties. Dalton Trans 2009:9246-52. [DOI: 10.1039/b912569h] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Pryadun R, Holm RH. A New Class of Binuclear and Trinuclear Iron−Sulfur Clusters Derived from Bis[bis(trimethylsilyl)amido]iron(II). Inorg Chem 2008; 47:3366-70. [DOI: 10.1021/ic7023742] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ruslan Pryadun
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
| | - R. H. Holm
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
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Jensen KP. Computational studies of modified [Fe3S4] clusters: Why iron is optimal. J Inorg Biochem 2008; 102:87-100. [PMID: 17723245 DOI: 10.1016/j.jinorgbio.2007.07.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2007] [Revised: 07/08/2007] [Accepted: 07/17/2007] [Indexed: 10/23/2022]
Abstract
This work reports density functional computations of metal-substituted models of biological [Fe3S4] clusters in oxidation states [MFe2S4](+/0/-1) (M=Mn, Fe, Co, Ni, Cu, Zn, and Mo). Geometry optimization with a dielectric screening model is shown to provide a substantial improvement in structure, compared to earlier used standard procedures. The error for average Fe-S bonds decreased from 0.038A to 0.016A with this procedure. Four density functionals were compared, B3LYP, BP86, TPSS, and TPSSh. B3LYP and to a lesser extent TPSSh energies were inconsistent with experiment for the oxidized [Fe3S4]+ cluster. BP86 (and to a slightly lesser extent TPSS) was within expected theoretical and experimental uncertainties for all oxidation states, the only qualitative error being 5kJ/mol in favor of the M(S)=3/2 configuration for the [Fe3S4]+ cluster, so BP86 was used for quantitative results. Computed reorganization energies and reduction potentials point directly towards the [Fe3S4] cluster as the superior choice of electron carrier, with the [ZnFe2S4] cluster a close second. In addition, partially and fully Mo-substituted clusters were investigated and found to have very low reorganization energies but too negative reduction potentials. The results provide a direct rationale why any substitution weakens the cluster as an electron carrier, and thus why the [Fe3S4] composition is optimal in the biological clusters.
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Affiliation(s)
- Kasper P Jensen
- Technical University of Denmark, Department of Chemistry, Building 207, 2800 Kgs. Lyngby, DK, Denmark.
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Meyer J. Iron-sulfur protein folds, iron-sulfur chemistry, and evolution. J Biol Inorg Chem 2007; 13:157-70. [PMID: 17992543 DOI: 10.1007/s00775-007-0318-7] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2007] [Accepted: 10/25/2007] [Indexed: 11/28/2022]
Abstract
An inventory of unique local protein folds around Fe-S clusters has been derived from the analysis of protein structure databases. Nearly 50 such folds have been identified, and over 90% of them harbor low-potential [2Fe-2S](2+,+) or [4Fe-4S](2+,+) clusters. In contrast, high-potential Fe-S clusters, notwithstanding their structural diversity, occur in only three different protein folds. These observations suggest that the extant population of Fe-S protein folds has to a large extent been shaped in the reducing iron- and sulfur-rich environment that is believed to have predominated on this planet until approximately two billion years ago. High-potential active sites are then surmised to be rarer because they emerged later, in a more oxidizing biosphere, in conditions where iron and sulfide had become poorly available, Fe-S clusters were less stable, and in addition faced competition from heme iron and copper active sites. Among the low-potential Fe-S active sites, protein folds hosting [4Fe-4S](2+,+) clusters outnumber those with [2Fe-2S](2+,+) ones by a factor of 3 at least. This is in keeping with the higher chemical stability and versatility of the tetranuclear clusters, compared with the binuclear ones. It is therefore suggested that, at least while novel Fe-S sites are evolving within proteins, the intrinsic chemical stability of the inorganic moiety may be more important than the stabilizing effect of the polypeptide chain. The discovery rate of novel Fe-S-containing protein folds underwent a sharp increase around 1995, and has remained stable to this day. The current trend suggests that the mapping of the Fe-S fold space is not near completion, in agreement with predictions made for protein folds in general. Altogether, the data collected and analyzed here suggest that the extant structural landscape of Fe-S proteins has been shaped to a large extent by primeval geochemical conditions on one hand, and iron-sulfur chemistry on the other.
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Affiliation(s)
- Jacques Meyer
- Commissariat à l'Energie Atomique, Université Joseph Fourier, UMR5249, CEA-Grenoble, 38054, Grenoble, France.
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41
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Kalyvas H, Coucouvanis D. Synthesis and characterization of new heterometallic iron sulfur nitrosyl clusters. Polyhedron 2007. [DOI: 10.1016/j.poly.2007.06.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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42
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The Chemistry of Synthetic Fe-Mo-S Clusters and their Relevance to the Structure and Function of the Fe-Mo-S Center in Nitrogenase. ACTA ACUST UNITED AC 2007. [DOI: 10.1002/9780470166512.ch6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
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Abstract
Persulfurated arenes have been known for about 50 years but they were underexploited in chemistry in spite of facile, mild, and high-yielding syntheses. Their properties (redox potentials, UV/Vis absorption, conductivity, nonlinear optical properties, etc.) are mainly due to the aromaticity of the ring with sp2-hybridized carbon atoms and to the electronic contribution from numerous divalent sulfur ligands, which also stabilize negative or positive charges. The characteristic conformational patterns of the sulfur ligands often facilitate preorganization in supramolecular assemblies, with or without thiophilic metal cations, for designing redox sensors, ion-selective membranes, clathrates, organic conductors, nonlinear optical materials, liquid crystals, coordination polymers, and bioinorganic systems. A new class of supramolecules with various molecular shapes such as asterisks, chains, wheels, and windmills were reported.
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Affiliation(s)
- Marc Gingras
- Chemistry Laboratory of Organic and Metallic Materials (CMOM), Faculty of Sciences, University of Nice-Sophia Antipolis, France.
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Meier R, Molinier M, Anson C, Powell AK, Kallies B, van Eldik R. Structure of sodium bis(N-methyl-iminodiacetato)iron(iii): trans-meridional N-coordination in the solid state and in solution. Dalton Trans 2006:5506-14. [PMID: 17117220 DOI: 10.1039/b605056e] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The results of a detailed solid state and solution structural study of the Fe(III) bis-mida complex [Fe(III)(mida)(2)]- (mida = N-methyl-iminodiacetate) are reported. The structure of the sodium salt Na[Fe(mida)2][NaClO4]2.3H2O (1) was determined by single-crystal X-ray analysis. The complex anion in 1 contains a six-coordinate Fe(III) centre bound to two tridentate mida ligands arranged in the meridional configuration, and the mer Fe(III)N2O4 chromophore shows a high degree of distortion from regular octahedral symmetry. Raman- and UV/VIS/NIR spectroscopic measurements showed that no gross changes take place in the Fe(III) coordination sphere upon redissolution in water. Quantum chemical calculations of all three possible configurations of the [Fe(mida)2]- complex ion in the gas phase support the finding that the mer isomer is more stable than the u-fac (cis) and s-fac (trans) isomers. Redox potential measurements of the Fe(III/II)(mida) couple in dependence of pH led to the following values for the equilibrium contants: log beta(III)(101) = 11.98 +/- 0.05, log beta(III)(102) = 20.49 +/- 0.01, pK(III)(a1 OH) = 7.81; log beta(II)(101) = 6.17 +/- 0.01, log beta(II)(102) = 11.39 +/- 0.01.
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Affiliation(s)
- Roland Meier
- Institut für Anorganische Chemie, Universität Erlangen-Nürnberg, Egerlandstrasse 1, 91058, Erlangen, Germany
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Heterometal cubane-type WFe3S4 and related clusters trigonally symmetrized with hydrotris(3,5-dimethylpyrazolyl)borate. Inorganica Chim Acta 2005. [DOI: 10.1016/j.ica.2004.11.051] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Takuma M, Ohki Y, Tatsumi K. Molybdenum Carbonyl Complexes with Citrate and Its Relevant Carboxylates. Organometallics 2005. [DOI: 10.1021/om049072f] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Motoki Takuma
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Yasuhiro Ohki
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Kazuyuki Tatsumi
- Department of Chemistry, Graduate School of Science and Research Center for Materials Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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Solomon EI, Hedman B, Hodgson KO, Dey A, Szilagyi RK. Ligand K-edge X-ray absorption spectroscopy: covalency of ligand–metal bonds. Coord Chem Rev 2005. [DOI: 10.1016/j.ccr.2004.03.020] [Citation(s) in RCA: 208] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Agarwalla S, Stroud RM, Gaffney BJ. Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies. J Biol Chem 2004; 279:34123-9. [PMID: 15181002 PMCID: PMC1237038 DOI: 10.1074/jbc.m405702200] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An unprecedented [4Fe-4S] iron-sulfur cluster was found in RumA, the enzyme that methylates U1939 in Escherichia coli 23 S ribosomal RNA (Agarwalla, S., Kealey, J. T., Santi, D. V., and Stroud, R. M. (2002) J. Biol. Chem. 277, 8835-8840; Lee, T. T., Agarwalla, S., and Stroud, R. M. (2004) Structure 12, 397-407). Methyltransferase reactions do not involve a redox step. To understand the structural and functional roles of the cluster in RumA, we have characterized redox reactions of the iron-sulfur cluster. As isolated aerobically, RumA exhibits a visible absorbance maximum at 390 nm and is EPR silent. It cannot be reduced by anaerobic additions of dithionite. Photoreduction by deazariboflavin/EDTA gives EPR spectra, the quantity (56% of S = 1/2 species) and details (g(av) approximately 1.96-1.93) of which indicate a [4Fe-4S](1+) cluster in the reduced RumA. Oxidation of RumA by ferricyanide leads to loss of the 390-nm band and appearance of lower intensity bands at 444 and 520 nm. EPR spectra of ferricyanide-oxidized RumA show a fraction (<8%) of the FeS cluster trapped in the [3Fe-4S](1+) form (g(av) approximately 2.011) together with unusual radical-like spectrum (g' values 2.015, 2.00, and 1.95). RumA also reacts with nitric oxide to give EPR spectra characteristic of the protein-bound iron dinitrosyl species. Oxidation of the cluster leads to its decomposition and that could be a mechanism for regulating the activity of RumA under conditions of oxidative stress in the cell. Sequence data base searches revealed that RumA homologs are widespread in various kingdoms of life and contain a conserved and unique iron-sulfur cluster binding motif, CX(5)CGGC.
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Affiliation(s)
- Sanjay Agarwalla
- From the Department of Biochemistry and Biophysics, University of California, San Francisco, California 94107 and the
- § To whom correspondence may be addressed: Dept. of Biochemistry and Biophysics, University of California, San Francisco, CA 94107. Tel.: 415-476-3937; Fax: 415-476-1902; E-mail:
| | - Robert M. Stroud
- From the Department of Biochemistry and Biophysics, University of California, San Francisco, California 94107 and the
| | - Betty J. Gaffney
- Biological Sciences Department, Florida State University, Tallahassee, Florida 32306
- || To whom correspondence may be addressed: Biological Sciences Department, Florida State University, Tallahassee, FL 32306. Tel.: 850-644-8547; E-mail:
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Meuwly M, Karplus M. Theoretical investigations on Azotobacter vinelandii ferredoxin I: effects of electron transfer on protein dynamics. Biophys J 2004; 86:1987-2007. [PMID: 15041642 PMCID: PMC1304053 DOI: 10.1016/s0006-3495(04)74261-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2003] [Accepted: 11/13/2003] [Indexed: 11/25/2022] Open
Abstract
Structural, energetic, and dynamical studies of Azotobacter vinelandii ferredoxin I are presented for native and mutant forms. The protein contains two iron-sulfur clusters, one of which ([3Fe-4S]) is believed to play a central role in the electron-coupled proton transfer. Different charge sets for the [3Fe-4S] cluster in its reduced and oxidized state are calculated with broken symmetry ab initio density functional theory methods and used in molecular dynamics (MD) simulations. The validity of the ab initio calculations is assessed by comparing partially optimized structures of the [3Fe-4S] clusters with x-ray structures. Possible proton transfer pathways between the protein and the iron-sulfur cluster are examined by both MD simulations and ab initio calculations. The MD simulations identify three main-chain hydrogen atoms--HN(13), HN(14), and HN(16)--that are within H-bonding distance of the [3Fe-4S] cluster throughout the MD simulations. They could thus play a role in the proton transfer from the protein to the iron-sulfur cluster. By contrast, the HD2(15) atom of the Asp-15 is seldom close enough to the [3Fe-4S] cluster to transfer a proton. Poisson-Boltzmann calculations indicate that there is a low, but nonzero probability, that Asp-15 is protonated at pH 7; this is a requirement for it to serve as a proton donor. Ab initio calculations with a fragment model for the protein find similar behavior for the transfer of a proton from the OH of the protonated side chain and the main-chain NH of Asp-15. The existence of a stable salt bridge between Asp-15 and Lys-84 in the D15E mutant, versus its absence in the wild-type, has been suggested as the cause of the difference in the rate of proton transfer. Extensive MD simulations were done to test this idea; the results do not support the proposal. The present findings, together with the available data, serve as the basis for an alternative proposal for the mechanism of the coupled electron-proton transfer reaction in ferredoxin I.
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Affiliation(s)
- Markus Meuwly
- Department of Chemistry, University of Basel, Basel, Switzerland.
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