1
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Le LN, Joyce JP, Oyala PH, DeBeer S, Agapie T. Highly Activated Terminal Carbon Monoxide Ligand in an Iron-Sulfur Cluster Model of FeMco with Intermediate Local Spin State at Fe. J Am Chem Soc 2024; 146:5045-5050. [PMID: 38358932 PMCID: PMC10910499 DOI: 10.1021/jacs.3c12025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/17/2024]
Abstract
Nitrogenases, the enzymes that convert N2 to NH3, also catalyze the reductive coupling of CO to yield hydrocarbons. CO-coordinated species of nitrogenase clusters have been isolated and used to infer mechanistic information. However, synthetic FeS clusters displaying CO ligands remain rare, which limits benchmarking. Starting from a synthetic cluster that models a cubane portion of the FeMo cofactor (FeMoco), including a bridging carbyne ligand, we report a heterometallic tungsten-iron-sulfur cluster with a single terminal CO coordination in two oxidation states with a high level of CO activation (νCO = 1851 and 1751 cm-1). The local Fe coordination environment (2S, 1C, 1CO) is identical to that in the protein making this system a suitable benchmark. Computational studies find an unusual intermediate spin electronic configuration at the Fe sites promoted by the presence the carbyne ligand. This electronic feature is partly responsible for the high degree of CO activation in the reduced cluster.
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Affiliation(s)
- Linh N.
V. Le
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Justin P. Joyce
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Paul H. Oyala
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Serena DeBeer
- Max
Planck Institute for Chemical Energy Conversion, Stiftstraße 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Theodor Agapie
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
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2
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Colussi A, Bokhari SNH, Mijovilovich A, Koník P, Küpper H. Acclimation to medium-level non-lethal iron limitation: Adjustment of electron flow around the PSII and metalloprotein expression in Trichodesmium erythraeum IMS101. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149015. [PMID: 37742749 DOI: 10.1016/j.bbabio.2023.149015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 09/26/2023]
Abstract
The aim of this study was to investigate how acclimation to medium-level, long-term, non-lethal iron limitation changes the electron flux around the Photosystem II of the oceanic diazotroph Trichodesmium erythraeum IMS101. Fe availability of about 5× and 100× lower than a replete level, i.e. conditions common in the natural environment of this cyanobacterium, were applied in chemostats. The response of the cells was studied not only in terms of growth, but also mechanistically, measuring the chlorophyll fluorescence of dark-adapted filaments via imaging fluorescence kinetic microscopy (FKM) with 0.3 ms time resolution. Combining these measurements with those of metal binding to proteins via online coupling of metal-free HPLC (size exclusion chromatography SEC) to sector-field ICP-MS allowed to track the fate of the photosystems, together with other metalloproteins. General increase of fluorescence has been observed, with the consequent decrease in the quantum yields φ of the PSII, while the efficiency ψ of the electron flux between PSII and the PSI remained surprisingly unchanged. This indicates the ability of Trichodesmium to cope with a situation that makes assembling the many iron clusters in Photosystem I a particular challenge, as shown by decreasing ratios of Fe to Mg in these proteins. The negative effect of Fe limitation on PSII may also be due to its fast turnover. A broader view was obtained from metalloproteomics via HPLC-ICP-MS, revealing a differential protein expression pattern under iron limitation with a drastic down-regulation especially of iron-containing proteins and some increase in low MW metal-binding complexes.
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Affiliation(s)
- Antonio Colussi
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Laboratory of Plant Biophysics and Biochemistry, České Budějovice, Czech Republic; University of South Bohemia, Faculty of Sciences, Department of Experimental Plant Biology, České Budějovice, Czech Republic
| | - Syed Nadeem Hussain Bokhari
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Laboratory of Plant Biophysics and Biochemistry, České Budějovice, Czech Republic
| | - Ana Mijovilovich
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Laboratory of Plant Biophysics and Biochemistry, České Budějovice, Czech Republic
| | - Peter Koník
- University of South Bohemia, Faculty of Sciences, Department of Chemistry, České Budějovice, Czech Republic
| | - Hendrik Küpper
- Czech Academy of Sciences, Biology Centre, Institute of Plant Molecular Biology, Laboratory of Plant Biophysics and Biochemistry, České Budějovice, Czech Republic; University of South Bohemia, Faculty of Sciences, Department of Experimental Plant Biology, České Budějovice, Czech Republic.
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3
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Barchenko M, Malcomson T, de Visser SP, O’Malley PJ. Computational Study on the Influence of Mo/V Centers on the Electronic Structure and Hydrazine Reduction Capability of [MFe 3S 4] 3+/2+ Complexes. Inorg Chem 2023; 62:16401-16411. [PMID: 37756478 PMCID: PMC10565805 DOI: 10.1021/acs.inorgchem.3c02072] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Indexed: 09/29/2023]
Abstract
[MFe3S4] cubanes have for some time been of interest for their ability to mimic the electronic and geometric structure of the active site of nitrogenase, the enzyme responsible for fixing N2 to NH3. Nitrogenase naturally occurs in three forms, with the major difference being that the metal ion present in the cofactor active site is either molybdenum (FeMoco), vanadium (FeVco), or iron. The molybdenum and vanadium versions of these cofactors are more closely studied, owing to their larger abundance and rate of catalysis. In this study, we compare free energy profiles and electronic properties of the Mo/V cubanes at various stages during the reduction of N2H4 to NH3. Our findings highlight the differences in how the complexes facilitate the reaction, in particular, vanadium's comparatively weaker ability to interact with the Fe/S network and stabilize reducing electrons prior to N-N bond cleavage, which may have implications when considering the lower efficiency of the vanadium-dependent nitrogenase.
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Affiliation(s)
- Maxim Barchenko
- Department
of Chemistry, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, U.K.
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.
| | - Thomas Malcomson
- Department
of Chemistry, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, U.K.
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.
- Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.
| | - Patrick J. O’Malley
- Department
of Chemistry, School of Natural Sciences, The University of Manchester, Manchester M13 9PL, U.K.
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4
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Yogendra S, Wilson DWN, Hahn AW, Weyhermüller T, Van Stappen C, Holland P, DeBeer S. Sulfur-Ligated [2Fe-2C] Clusters as Synthetic Model Systems for Nitrogenase. Inorg Chem 2023; 62:2663-2671. [PMID: 36715662 PMCID: PMC9930126 DOI: 10.1021/acs.inorgchem.2c03693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Indexed: 01/31/2023]
Abstract
Metal clusters featuring carbon and sulfur donors have coordination environments comparable to the active site of nitrogenase enzymes. Here, we report a series of di-iron clusters supported by the dianionic yldiide ligands, in which the Fe sites are bridged by two μ2-C atoms and four pendant S donors.The [L2Fe2] (L = {[Ph2P(S)]2C}2-) cluster is isolable in two oxidation levels, all-ferrous Fe2II and mixed-valence FeIIFeIII. The mixed-valence cluster displays two peaks in the Mössbauer spectra, indicating slow electron transfer between the two sites. The addition of the Lewis base 4-dimethylaminopyridine to the Fe2II cluster results in coordination with only one of the two Fe sites, even in the presence of an excess base. Conversely, the cluster reacts with 8 equiv of isocyanide tBuNC to give a monometallic complex featuring a new C-C bond between the ligand backbone and the isocyanide. The electronic structure descriptions of these complexes are further supported by X-ray absorption and resonant X-ray emission spectroscopies.
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Affiliation(s)
- Sivathmeehan Yogendra
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Daniel W. N. Wilson
- Department
of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Anselm W. Hahn
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Thomas Weyhermüller
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Casey Van Stappen
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Patrick Holland
- Department
of Chemistry, Yale University, 225 Prospect Street, New Haven, Connecticut 06520, United States
| | - Serena DeBeer
- Max
Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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5
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Su L, Yang D, Jiang Y, Li Y, Di K, Wang B, Ye S, Qu J. A Bioinspired Iron‐Molybdenum μ‐Nitrido Complex and Its Reactivity toward Ammonia Formation. Angew Chem Int Ed Engl 2022; 61:e202203121. [DOI: 10.1002/anie.202203121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Linan Su
- State Key Laboratory of Fine Chemicals Dalian University of Technology 2 Linggong Road Dalian 116024 China
| | - Dawei Yang
- State Key Laboratory of Fine Chemicals Dalian University of Technology 2 Linggong Road Dalian 116024 China
| | - Yang Jiang
- State Key Laboratory of Catalysis Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116024 China
| | - Yahui Li
- State Key Laboratory of Fine Chemicals Dalian University of Technology 2 Linggong Road Dalian 116024 China
| | - Kai Di
- State Key Laboratory of Fine Chemicals Dalian University of Technology 2 Linggong Road Dalian 116024 China
| | - Baomin Wang
- State Key Laboratory of Fine Chemicals Dalian University of Technology 2 Linggong Road Dalian 116024 China
| | - Shengfa Ye
- State Key Laboratory of Catalysis Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116024 China
| | - Jingping Qu
- State Key Laboratory of Fine Chemicals Dalian University of Technology 2 Linggong Road Dalian 116024 China
- State Key Laboratory of Bioreactor Engineering Shanghai Collaborative Innovation Centre for Biomanufacturing Frontiers Science Center for Materiobiology and Dynamic Chemistry East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
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6
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Su L, Yang D, Jiang Y, Li Y, Di K, Wang B, Ye S, Qu J. A Bioinspired Iron‐Molybdenum μ‐Nitrido Complex and Its Reactivity toward Ammonia Formation. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202203121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Linan Su
- State Key Laboratory of Fine Chemicals Dalian University of Technology 2 Linggong Road Dalian 116024 China
| | - Dawei Yang
- State Key Laboratory of Fine Chemicals Dalian University of Technology 2 Linggong Road Dalian 116024 China
| | - Yang Jiang
- State Key Laboratory of Catalysis Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116024 China
| | - Yahui Li
- State Key Laboratory of Fine Chemicals Dalian University of Technology 2 Linggong Road Dalian 116024 China
| | - Kai Di
- State Key Laboratory of Fine Chemicals Dalian University of Technology 2 Linggong Road Dalian 116024 China
| | - Baomin Wang
- State Key Laboratory of Fine Chemicals Dalian University of Technology 2 Linggong Road Dalian 116024 China
| | - Shengfa Ye
- State Key Laboratory of Catalysis Dalian Institute of Chemical Physics Chinese Academy of Sciences 457 Zhongshan Road Dalian 116024 China
| | - Jingping Qu
- State Key Laboratory of Fine Chemicals Dalian University of Technology 2 Linggong Road Dalian 116024 China
- State Key Laboratory of Bioreactor Engineering Shanghai Collaborative Innovation Centre for Biomanufacturing Frontiers Science Center for Materiobiology and Dynamic Chemistry East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
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7
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Benediktsson B, Bjornsson R. Analysis of the Geometric and Electronic Structure of Spin-Coupled Iron-Sulfur Dimers with Broken-Symmetry DFT: Implications for FeMoco. J Chem Theory Comput 2022; 18:1437-1457. [PMID: 35167749 PMCID: PMC8908755 DOI: 10.1021/acs.jctc.1c00753] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
![]()
The open-shell electronic
structure of iron–sulfur clusters
presents considerable challenges to quantum chemistry, with the complex
iron–molybdenum cofactor (FeMoco) of nitrogenase representing
perhaps the ultimate challenge for either wavefunction or density
functional theory. While broken-symmetry density functional theory
has seen some success in describing the electronic structure of such
cofactors, there is a large exchange–correlation functional
dependence in calculations that is not fully understood. In this work,
we present a geometric benchmarking test set, FeMoD11, of synthetic
spin-coupled Fe–Fe and Mo–Fe dimers, with relevance
to the molecular and electronic structure of the Mo-nitrogenase FeMo
cofactor. The reference data consists of high-resolution crystal structures
of metal dimer compounds in different oxidation states. Multiple density
functionals are tested on their ability to reproduce the local geometry,
specifically the Fe–Fe/Mo–Fe distance, for both antiferromagnetically
coupled and ferromagnetically coupled dimers via the broken-symmetry
approach. The metal–metal distance is revealed not only to
be highly sensitive to the amount of exact exchange in the functional
but also to the specific exchange and correlation functionals. For
the antiferromagnetically coupled dimers, the calculated metal–metal
distance correlates well with the covalency of the bridging metal–ligand
bonds, as revealed via the corresponding orbital analysis, Hirshfeld
S/Fe charges, and Fe–S Mayer bond order. Superexchange via
bridging ligands is expected to be the dominant interaction in these
dimers, and our results suggest that functionals that predict accurate
Fe–Fe and Mo–Fe distances describe the overall metal–ligand
covalency more accurately and in turn the superexchange of these systems.
The best performing density functionals of the 16 tested for the FeMoD11
test set are revealed to be either the nonhybrid functionals r2SCAN and B97-D3 or hybrid functionals with 10–15% exact
exchange: TPSSh and B3LYP*. These same four functionals are furthermore
found to reproduce the high-resolution X-ray structure of FeMoco well
according to quantum mechanics/molecular mechanics (QM/MM) calculations.
Almost all nonhybrid functionals systematically underestimate Fe–Fe
and Mo–Fe distances (with r2SCAN and B97-D3 being
the sole exceptions), while hybrid functionals with >15% exact
exchange
(including range-separated hybrid functionals) overestimate them.
The results overall suggest r2SCAN, B97-D3, TPSSh, and
B3LYP* as accurate density functionals for describing the electronic
structure of iron–sulfur clusters in general, including the
complex FeMoco cluster of nitrogenase.
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Affiliation(s)
- Bardi Benediktsson
- Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
| | - Ragnar Bjornsson
- Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland.,Max-Planck Institute for Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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8
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Sharma S, Baral M, Kanungo BK. Recent advances in therapeutical applications of the versatile hydroxypyridinone chelators. J INCL PHENOM MACRO 2022. [DOI: 10.1007/s10847-021-01114-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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9
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Yuan C, Jin WT, Zhou ZH. Comparisons of bond valences and distances for CO- and N 2-bound clusters of FeMo-cofactors. NEW J CHEM 2022. [DOI: 10.1039/d2nj00754a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By comparisons of N2 and isoelectronic substrate CO bound FeMo-cofactors (FeMo-cos) in nitrogenases, we have used a classical bond valence method to calculate the oxidation states of the iron and molybdenum atoms in FeMo-cos.
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Affiliation(s)
- Chang Yuan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Wan-Ting Jin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zhao-Hui Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
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10
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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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11
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Devi L, Kuzhalmozhi Madarasi P, Christopher Jeyakumar T. Computational studies of adsorption of dinitrogen over the group 8 metal-borazine complexes. CHEMICAL PAPERS 2021. [DOI: 10.1007/s11696-021-01953-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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12
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Chen X, Qi MY, Li YH, Tang ZR, Xu YJ. Enhanced ambient ammonia photosynthesis by Mo-doped Bi5O7Br nanosheets with light-switchable oxygen vacancies. CHINESE JOURNAL OF CATALYSIS 2021. [DOI: 10.1016/s1872-2067(21)63837-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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13
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Martín-Fernández C, Harvey JN. On the Use of Normalized Metrics for Density Sensitivity Analysis in DFT. J Phys Chem A 2021; 125:4639-4652. [PMID: 34018759 DOI: 10.1021/acs.jpca.1c01290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In the past years, there has been a discussion about how the errors in density functional theory might be related to errors in the self-consistent densities obtained from different density functional approximations. This, in turn, brings up the discussion about the different ways in which we can measure such errors and develop metrics that assess the sensitivity of calculated energies to changes in the density. It is important to realize that there cannot be a unique metric in order to look at this density sensitivity, simultaneously needing size-extensive and size-intensive metrics. In this study, we report two metrics that are widely applicable to any density functional approximation. We also show how they can be used to classify different chemical systems of interest with respect to their sensitivity to small variations in the density.
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Affiliation(s)
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan, 200F 3001 Leuven, Belgium
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14
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Weindl R, Khare R, Kovarik L, Jentys A, Reuter K, Shi H, Lercher JA. Zeolite‐Stabilized Di‐ and Tetranuclear Molybdenum Sulfide Clusters Form Stable Catalytic Hydrogenation Sites. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202015769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Roland Weindl
- Department of Chemistry and Catalysis Research Center Technical University of Munich 85747 Garching Germany
| | - Rachit Khare
- Department of Chemistry and Catalysis Research Center Technical University of Munich 85747 Garching Germany
| | - Libor Kovarik
- Institute for Integrated Catalysis Pacific Northwest National Laboratory Richland WA 99352 USA
| | - Andreas Jentys
- Department of Chemistry and Catalysis Research Center Technical University of Munich 85747 Garching Germany
| | - Karsten Reuter
- Department of Chemistry and Catalysis Research Center Technical University of Munich 85747 Garching Germany
- Fritz Haber Institute of the Max Planck Society 14195 Berlin Germany
| | - Hui Shi
- School of Chemistry and Chemical Engineering Yangzhou University Yangzhou Jiangsu 225009 China
| | - Johannes A. Lercher
- Department of Chemistry and Catalysis Research Center Technical University of Munich 85747 Garching Germany
- Institute for Integrated Catalysis Pacific Northwest National Laboratory Richland WA 99352 USA
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15
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Weindl R, Khare R, Kovarik L, Jentys A, Reuter K, Shi H, Lercher JA. Zeolite-Stabilized Di- and Tetranuclear Molybdenum Sulfide Clusters Form Stable Catalytic Hydrogenation Sites. Angew Chem Int Ed Engl 2021; 60:9301-9305. [PMID: 33576131 PMCID: PMC8252740 DOI: 10.1002/anie.202015769] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/05/2021] [Indexed: 11/24/2022]
Abstract
Supercages of faujasite (FAU)‐type zeolites serve as a robust scaffold for stabilizing dinuclear (Mo2S4) and tetranuclear (Mo4S4) molybdenum sulfide clusters. The FAU‐encaged Mo4S4 clusters have a distorted cubane structure similar to the FeMo‐cofactor in nitrogenase. Both clusters possess unpaired electrons on Mo atoms. Additionally, they show identical catalytic activity per sulfide cluster. Their catalytic activity is stable (>150 h) for ethene hydrogenation, while layered MoS2 structures deactivate significantly under the same reaction conditions.
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Affiliation(s)
- Roland Weindl
- Department of Chemistry and Catalysis Research Center, Technical University of Munich, 85747, Garching, Germany
| | - Rachit Khare
- Department of Chemistry and Catalysis Research Center, Technical University of Munich, 85747, Garching, Germany
| | - Libor Kovarik
- Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Andreas Jentys
- Department of Chemistry and Catalysis Research Center, Technical University of Munich, 85747, Garching, Germany
| | - Karsten Reuter
- Department of Chemistry and Catalysis Research Center, Technical University of Munich, 85747, Garching, Germany.,Fritz Haber Institute of the Max Planck Society, 14195, Berlin, Germany
| | - Hui Shi
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, Jiangsu, 225009, China
| | - Johannes A Lercher
- Department of Chemistry and Catalysis Research Center, Technical University of Munich, 85747, Garching, Germany.,Institute for Integrated Catalysis, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
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16
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Yang ZY, Jimenez-Vicente E, Kallas H, Lukoyanov DA, Yang H, Martin Del Campo JS, Dean DR, Hoffman BM, Seefeldt LC. The electronic structure of FeV-cofactor in vanadium-dependent nitrogenase. Chem Sci 2021; 12:6913-6922. [PMID: 34123320 PMCID: PMC8153082 DOI: 10.1039/d0sc06561g] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/26/2021] [Indexed: 01/01/2023] Open
Abstract
The electronic structure of the active-site metal cofactor (FeV-cofactor) of resting-state V-dependent nitrogenase has been an open question, with earlier studies indicating that it exhibits a broad S = 3/2 EPR signal (Kramers state) having g values of ∼4.3 and 3.8, along with suggestions that it contains metal-ions with valencies [1V3+, 3Fe3+, 4Fe2+]. In the present work, genetic, biochemical, and spectroscopic approaches were combined to reveal that the EPR signals previously assigned to FeV-cofactor do not correlate with active VFe-protein, and thus cannot arise from the resting-state of catalytically relevant FeV-cofactor. It, instead, appears resting-state FeV-cofactor is either diamagnetic, S = 0, or non-Kramers, integer-spin (S = 1, 2 etc.). When VFe-protein is freeze-trapped during high-flux turnover with its natural electron-donating partner Fe protein, conditions which populate reduced states of the FeV-cofactor, a new rhombic S = 1/2 EPR signal from such a reduced state is observed, with g = [2.18, 2.12, 2.09] and showing well-defined 51V (I = 7/2) hyperfine splitting, a iso = 110 MHz. These findings indicate a different assignment for the electronic structure of the resting state of FeV-cofactor: S = 0 (or integer-spin non-Kramers state) with metal-ion valencies, [1V3+, 4Fe3+, 3Fe2+]. Our findings suggest that the V3+ does not change valency throughout the catalytic cycle.
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Affiliation(s)
- Zhi-Yong Yang
- Department of Chemistry and Biochemistry, Utah State University Logan UT 84322 USA +1-435-797-3964
| | | | - Hayden Kallas
- Department of Chemistry and Biochemistry, Utah State University Logan UT 84322 USA +1-435-797-3964
| | - Dmitriy A Lukoyanov
- Department of Chemistry, Northwestern University Evanston IL 60208 USA +1-847-491-3104
| | - Hao Yang
- Department of Chemistry, Northwestern University Evanston IL 60208 USA +1-847-491-3104
| | | | - Dennis R Dean
- Department of Biochemistry, Virginia Tech Blacksburg VA 24061 USA +1-540-231-5895
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University Evanston IL 60208 USA +1-847-491-3104
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University Logan UT 84322 USA +1-435-797-3964
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17
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Molybdenum-Containing Metalloenzymes and Synthetic Catalysts for Conversion of Small Molecules. Catalysts 2021. [DOI: 10.3390/catal11020217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The energy deficiency and environmental problems have motivated researchers to develop energy conversion systems into a sustainable pathway, and the development of catalysts holds the center of the research endeavors. Natural catalysts such as metalloenzymes have maintained energy cycles on Earth, thus proving themselves the optimal catalysts. In the previous research results, the structural and functional analogs of enzymes and nano-sized electrocatalysts have shown promising activities in energy conversion reactions. Mo ion plays essential roles in natural and artificial catalysts, and the unique electrochemical properties render its versatile utilization as an electrocatalyst. In this review paper, we show the current understandings of the Mo-enzyme active sites and the recent advances in the synthesis of Mo-catalysts aiming for high-performing catalysts.
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18
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Lukoyanov DA, Yang ZY, Dean DR, Seefeldt LC, Raugei S, Hoffman BM. Electron Redistribution within the Nitrogenase Active Site FeMo-Cofactor During Reductive Elimination of H 2 to Achieve N≡N Triple-Bond Activation. J Am Chem Soc 2020; 142:21679-21690. [PMID: 33326225 DOI: 10.1021/jacs.0c07914] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nitrogen fixation by nitrogenase begins with the accumulation of four reducing equivalents at the active-site FeMo-cofactor (FeMo-co), generating a state (denoted E4(4H)) with two [Fe-H-Fe] bridging hydrides. Recently, photolytic reductive elimination (re) of the E4(4H) hydrides showed that enzymatic re of E4(4H) hydride yields an H2-bound complex (E4(H2,2H)), in a process corresponding to a formal 2-electron reduction of the metal-ion core of FeMo-co. The resulting electron-density redistribution from Fe-H bonds to the metal ions themselves enables N2 to bind with concomitant H2 release, a process illuminated here by QM/MM molecular dynamics simulations. What is the nature of this redistribution? Although E4(H2,2H) has not been trapped, cryogenic photolysis of E4(4H) provides a means to address this question. Photolysis of E4(4H) causes hydride-re with release of H2, generating doubly reduced FeMo-co (denoted E4(2H)*), the extreme limit of the electron-density redistribution upon formation of E4(H2,2H). Here we examine the doubly reduced FeMo-co core of the E4(2H)* limiting-state by 1H, 57Fe, and 95Mo ENDOR to illuminate the partial electron-density redistribution upon E4(H2,2H) formation during catalysis, complementing these results with corresponding DFT computations. Inferences from the E4(2H)* ENDOR results as extended by DFT computations include (i) the Mo-site participates negligibly, and overall it is unlikely that Mo changes valency throughout the catalytic cycle; and (ii) two distinctive E4(4H) 57Fe signals are suggested as associated with structurally identified "anchors" of one bridging hydride, two others with identified anchors of the second, with NBO-analysis further identifying one anchor of each hydride as a major recipient of electrons released upon breaking Fe-H bonds.
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Affiliation(s)
- Dmitriy A Lukoyanov
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Zhi-Yong Yang
- Department of Chemistry and Biocemistry, Utah State University, Logan, Utah 84322, United States
| | - Dennis R Dean
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
| | - Lance C Seefeldt
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Simone Raugei
- Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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19
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Zheng J, Wu S, Lu L, Huang C, Ho PL, Kirkland A, Sudmeier T, Arrigo R, Gianolio D, Edman Tsang SC. Structural insight into [Fe-S 2-Mo] motif in electrochemical reduction of N 2 over Fe 1-supported molecular MoS 2. Chem Sci 2020; 12:688-695. [PMID: 34163801 PMCID: PMC8178972 DOI: 10.1039/d0sc04575f] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The catalytic synthesis of NH3 from the thermodynamically challenging N2 reduction reaction under mild conditions is currently a significant problem for scientists. Accordingly, herein, we report the development of a nitrogenase-inspired inorganic-based chalcogenide system for the efficient electrochemical conversion of N2 to NH3, which is comprised of the basic structure of [Fe-S2-Mo]. This material showed high activity of 8.7 mgNH3 mgFe -1 h-1 (24 μgNH3 cm-2 h-1) with an excellent faradaic efficiency of 27% for the conversion of N2 to NH3 in aqueous medium. It was demonstrated that the Fe1 single atom on [Fe-S2-Mo] under the optimal negative potential favors the reduction of N2 to NH3 over the competitive proton reduction to H2. Operando X-ray absorption and simulations combined with theoretical DFT calculations provided the first and important insights on the particular electron-mediating and catalytic roles of the [Fe-S2-Mo] motifs and Fe1, respectively, on this two-dimensional (2D) molecular layer slab.
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Affiliation(s)
- Jianwei Zheng
- Wolfson Catalysis Centre, Department of Chemistry University of Oxford Oxford OX1 3QR UK
| | - Simson Wu
- Wolfson Catalysis Centre, Department of Chemistry University of Oxford Oxford OX1 3QR UK
| | - Lilin Lu
- College of Chemistry and Chemical Engineering, Wuhan University of Science and Technology China
| | - Chen Huang
- Department of Materials, University of Oxford Oxford OX1 PH UK
| | - Ping-Luen Ho
- Wolfson Catalysis Centre, Department of Chemistry University of Oxford Oxford OX1 3QR UK
| | - Angus Kirkland
- Department of Materials, University of Oxford Oxford OX1 PH UK
| | - Tim Sudmeier
- Wolfson Catalysis Centre, Department of Chemistry University of Oxford Oxford OX1 3QR UK
| | - Rosa Arrigo
- Diamond Light Source Harwell Campus, Chilton Oxfordshire OX11 0DE UK.,School of Science, Engineering and Environment, University of Salford Manchester M5 4WT UK
| | - Diego Gianolio
- Diamond Light Source Harwell Campus, Chilton Oxfordshire OX11 0DE UK
| | - Shik Chi Edman Tsang
- Wolfson Catalysis Centre, Department of Chemistry University of Oxford Oxford OX1 3QR UK
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20
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Castillo RG, Henthorn JT, McGale J, Maganas D, DeBeer S. Kβ X-Ray Emission Spectroscopic Study of a Second-Row Transition Metal (Mo) and Its Application to Nitrogenase-Related Model Complexes. Angew Chem Int Ed Engl 2020; 59:12965-12975. [PMID: 32363668 PMCID: PMC7496169 DOI: 10.1002/anie.202003621] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Indexed: 01/03/2023]
Abstract
In recent years, X-ray emission spectroscopy (XES) in the Kβ (3p-1s) and valence-to-core (valence-1s) regions has been increasingly used to study metal active sites in (bio)inorganic chemistry and catalysis, providing information about the metal spin state, oxidation state and the identity of coordinated ligands. However, to date this technique has been limited almost exclusively to first-row transition metals. In this work, we present an extension of Kβ XES (in both the 4p-1s and valence-to-1s [or VtC] regions) to the second transition row by performing a detailed experimental and theoretical analysis of the molybdenum emission lines. It is demonstrated in this work that Kβ2 lines are dominated by spin state effects, while VtC XES of a 4d transition metal provides access to metal oxidation state and ligand identity. An extension of Mo Kβ XES to nitrogenase-relevant model complexes shows that the method is sufficiently sensitive to act as a spectator probe for redox events that are localized at the Fe atoms. Mo VtC XES thus has promise for future applications to nitrogenase, as well as a range of other Mo-containing biological cofactors. Further, the clear assignment of the origins of Mo VtC XES features opens up the possibility of applying this method to a wide range of second-row transition metals, thus providing chemists with a site-specific tool for the elucidation of 4d transition metal electronic structure.
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Affiliation(s)
- Rebeca G. Castillo
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstrasse 34–3645470Mülheim an der RuhrGermany
| | - Justin T. Henthorn
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstrasse 34–3645470Mülheim an der RuhrGermany
| | - Jeremy McGale
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstrasse 34–3645470Mülheim an der RuhrGermany
| | - Dimitrios Maganas
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an der RuhrGermany
| | - Serena DeBeer
- Department of Inorganic SpectroscopyMax Planck Institute for Chemical Energy ConversionStiftstrasse 34–3645470Mülheim an der RuhrGermany
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21
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Castillo RG, Henthorn JT, McGale J, Maganas D, DeBeer S. Kβ X‐Ray Emission Spectroscopic Study of a Second‐Row Transition Metal (Mo) and Its Application to Nitrogenase‐Related Model Complexes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003621] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Rebeca G. Castillo
- Department of Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim an der Ruhr Germany
| | - Justin T. Henthorn
- Department of Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim an der Ruhr Germany
| | - Jeremy McGale
- Department of Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim an der Ruhr Germany
| | - Dimitrios Maganas
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Germany
| | - Serena DeBeer
- Department of Inorganic Spectroscopy Max Planck Institute for Chemical Energy Conversion Stiftstrasse 34–36 45470 Mülheim an der Ruhr Germany
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22
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Affiliation(s)
- Oliver Einsle
- Institute for Biochemistry, Albert-Ludwigs-University Freiburg, 79104 Freiburg, Germany
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, Howard Hughes Medical Institute, California Institute of Technology, Pasadena California 91125, United States
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23
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Jin WT, Yang M, Zhu SS, Zhou ZH. Bond-valence analyses of the crystal structures of FeMo/V cofactors in FeMo/V proteins. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:428-437. [PMID: 32355039 DOI: 10.1107/s2059798320003952] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/18/2020] [Indexed: 12/15/2022]
Abstract
The bond-valence method has been used for valence calculations of FeMo/V cofactors in FeMo/V proteins using 51 crystallographic data sets of FeMo/V proteins from the Protein Data Bank. The calculations show molybdenum(III) to be present in MoFe7S9C(Cys)(HHis)[R-(H)homocit] (where H4homocit is homocitric acid, HCys is cysteine and HHis is histidine) in FeMo cofactors, while vanadium(III) with a more reduced iron complement is obtained for FeV cofactors. Using an error analysis of the calculated valences, it was found that in FeMo cofactors Fe1, Fe6 and Fe7 can be unambiguously assigned as iron(III), while Fe2, Fe3, Fe4 and Fe5 show different degrees of mixed valences for the individual Fe atoms. For the FeV cofactors in PDB entry 5n6y, Fe4, Fe5 and Fe6 correspond to iron(II), iron(II) and iron(III), respectively, while Fe1, Fe2, Fe3 and Fe7 exhibit strongly mixed valences. Special situations such as CO-bound and selenium-substituted FeMo cofactors and O(N)H-bridged FeV cofactors are also discussed and suggest rearrangement of the electron configuration on the substitution of the bridging S atoms.
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Affiliation(s)
- Wan Ting Jin
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Min Yang
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Shuang Shuang Zhu
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Zhao Hui Zhou
- State Key Laboratory for Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
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24
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Jasniewski AJ, Lee CC, Ribbe MW, Hu Y. Reactivity, Mechanism, and Assembly of the Alternative Nitrogenases. Chem Rev 2020; 120:5107-5157. [PMID: 32129988 DOI: 10.1021/acs.chemrev.9b00704] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological nitrogen fixation is catalyzed by the enzyme nitrogenase, which facilitates the cleavage of the relatively inert triple bond of N2. Nitrogenase is most commonly associated with the molybdenum-iron cofactor called FeMoco or the M-cluster, and it has been the subject of extensive structural and spectroscopic characterization over the past 60 years. In the late 1980s and early 1990s, two "alternative nitrogenase" systems were discovered, isolated, and found to incorporate V or Fe in place of Mo. These systems are regulated by separate gene clusters; however, there is a high degree of structural and functional similarity between each nitrogenase. Limited studies with the V- and Fe-nitrogenases initially demonstrated that these enzymes were analogously active as the Mo-nitrogenase, but more recent investigations have found capabilities that are unique to the alternative systems. In this review, we will discuss the reactivity, biosynthetic, and mechanistic proposals for the alternative nitrogenases as well as their electronic and structural properties in comparison to the well-characterized Mo-dependent system. Studies over the past 10 years have been particularly fruitful, though key aspects about V- and Fe-nitrogenases remain unexplored.
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Affiliation(s)
- Andrew J Jasniewski
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States.,Department of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
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25
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Chen X, Li JY, Tang ZR, Xu YJ. Surface-defect-engineered photocatalyst for nitrogen fixation into value-added chemical feedstocks. Catal Sci Technol 2020. [DOI: 10.1039/d0cy01227k] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Surface-defect-engineered photocatalyst for nitrogen fixation.
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Affiliation(s)
- Xue Chen
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
- Fuzhou
- China
| | - Jing-Yu Li
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
- Fuzhou
- China
| | - Zi-Rong Tang
- College of Chemistry
- New Campus, Fuzhou University
- Fuzhou
- China
| | - Yi-Jun Xu
- State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fuzhou University
- Fuzhou
- China
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26
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Nagelski AL, Fataftah MS, Bollmeyer MM, McWilliams SF, MacMillan SN, Mercado BQ, Lancaster KM, Holland PL. The influences of carbon donor ligands on biomimetic multi-iron complexes for N 2 reduction. Chem Sci 2020; 11:12710-12720. [PMID: 34094466 PMCID: PMC8163302 DOI: 10.1039/d0sc03447a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The active site clusters of nitrogenase enzymes possess the only examples of carbides in biology. These are the only biological FeS clusters that are capable of reducing N2 to NH4+, implicating the central carbon and its interaction with Fe as important in the mechanism of N2 reduction. This biological question motivates study of the influence of carbon donors on the electronic structure and reactivity of unsaturated, high-spin iron centers. Here, we present functional and structural models that test the impacts of carbon donors and sulfide donors in simpler iron compounds. We report the first example of a diiron complex that is bridged by an alkylidene and a sulfide, which serves as a high-fidelity structural and spectroscopic model of a two-iron portion of the active-site cluster (FeMoco) in the resting state of Mo-nitrogenase. The model complexes have antiferromagnetically coupled pairs of high-spin iron centers, and sulfur K-edge X-ray absorption spectroscopy shows comparable covalency of the sulfide for C and S bridged species. The sulfur-bridged compound does not interact with N2 even upon reduction, but upon removal of the sulfide it becomes capable of reducing N2 to NH4+ with the addition of protons and electrons. This provides synthetic support for sulfide extrusion in the activation of nitrogenase cofactors. High-spin diiron alkylidenes give insight into the electronic structure and functional relevance of carbon in the FeMoco active site of nitrogenase.![]()
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Affiliation(s)
| | | | - Melissa M. Bollmeyer
- Department of Chemistry and Chemical Biology
- Baker Laboratory
- Cornell University
- Ithaca
- USA
| | | | - Samantha N. MacMillan
- Department of Chemistry and Chemical Biology
- Baker Laboratory
- Cornell University
- Ithaca
- USA
| | | | - Kyle M. Lancaster
- Department of Chemistry and Chemical Biology
- Baker Laboratory
- Cornell University
- Ithaca
- USA
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27
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Tsukada S, Abe T, Abe N, Nakashima S, Yamamoto K, Gunji T. Benzenedithiolate-bridged MoFe complexes: structures, oxidation states, and reactivities. Dalton Trans 2020; 49:9048-9056. [DOI: 10.1039/d0dt01428a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The benzenedithiolate-bridged MoFe complexes were synthesized and the oxidation states of the metal centers elucidated.
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Affiliation(s)
- Satoru Tsukada
- Graduate School of Engineering
- Chiba University
- Chiba 263-8522
- Japan
| | - Takayuki Abe
- Department of Pure and Applied Chemistry
- Faculty of Science and Technology
- Tokyo University of Science
- Chiba 278-8510
- Japan
| | - Naoya Abe
- Department of Pure and Applied Chemistry
- Faculty of Science and Technology
- Tokyo University of Science
- Chiba 278-8510
- Japan
| | - Satoru Nakashima
- Graduate School of Science
- Hiroshima University
- Higashi-Hiroshima
- Japan
- Natural Science Centre for Basic Research and Development
| | - Kazuki Yamamoto
- Department of Pure and Applied Chemistry
- Faculty of Science and Technology
- Tokyo University of Science
- Chiba 278-8510
- Japan
| | - Takahiro Gunji
- Department of Pure and Applied Chemistry
- Faculty of Science and Technology
- Tokyo University of Science
- Chiba 278-8510
- Japan
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28
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Thorhallsson AT, Benediktsson B, Bjornsson R. A model for dinitrogen binding in the E 4 state of nitrogenase. Chem Sci 2019; 10:11110-11124. [PMID: 32206260 PMCID: PMC7069239 DOI: 10.1039/c9sc03610e] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/14/2019] [Indexed: 12/27/2022] Open
Abstract
Molybdenum nitrogenase is one of the most intriguing metalloenzymes in nature, featuring an exotic iron-molybdenum-sulfur cofactor, FeMoco, whose mode of action remains elusive. In particular, the molecular and electronic structure of the N2-binding E4 state is not known. In this study we present theoretical QM/MM calculations of new structural models of the E4 state of molybdenum-dependent nitrogenase and compare to previously suggested models for this enigmatic redox state. We propose two models as possible candidates for the E4 state. Both models feature two hydrides on the FeMo cofactor, bridging atoms Fe2 and Fe6 with a terminal sulfhydryl group on either Fe2 or Fe6 (derived from the S2B bridge) and the change in coordination results in local lower-spin electronic structure at Fe2 and Fe6. These structures appear consistent with the bridging hydride proposal put forward from ENDOR studies and are calculated to be lower in energy than other proposed models for E4 at the TPSSh-QM/MM level of theory. We critically analyze the DFT method dependency in calculations of FeMoco that has resulted in strikingly different proposals for this state. Importantly, dinitrogen binds exothermically to either Fe2 or Fe6 in our models, contrary to others, an effect rationalized via the unique ligand field (from the hydrides) at the Fe with an empty coordination site. A low-spin Fe site is proposed as being important to N2 binding. Furthermore, the geometries of these states suggest a feasible reductive elimination step that could follow, as experiments indicate. Via this step, two electrons are released, reducing the cofactor to yield a distorted 4-coordinate Fe2 or Fe6 that partially activates N2. We speculate that stabilization of an N2-bound Fe(i) at Fe6 (not found for Fe2 model) via reductive elimination is a crucial part of N2 activation in nitrogenases, possibly aided by the apical heterometal ion (Mo or V). By using protons from the sulfhydryl group (to regenerate the sulfide bridge between Fe2 and Fe6) and the nearby homocitrate hydroxy group, we calculate a plausible route to yield a diazene intermediate. This is found to be more favorable with the Fe6-bound model than the Fe2-bound model; however, this protonation is uphill in energy, suggesting protonation of N2 might occur later in the catalytic cycle or via another mechanism.
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Affiliation(s)
- Albert Th Thorhallsson
- Science Institute , University of Iceland , Dunhagi 3 , 107 Reykjavik , Iceland
- Department of Inorganic Spectroscopy , Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany .
| | - Bardi Benediktsson
- Science Institute , University of Iceland , Dunhagi 3 , 107 Reykjavik , Iceland
| | - Ragnar Bjornsson
- Science Institute , University of Iceland , Dunhagi 3 , 107 Reykjavik , Iceland
- Department of Inorganic Spectroscopy , Max-Planck-Institut für Chemische Energiekonversion , Stiftstrasse 34-36 , 45470 Mülheim an der Ruhr , Germany .
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Abghoui Y, Sigtryggsson SB, Skúlason E. Biomimetic Nitrogen Fixation Catalyzed by Transition Metal Sulfide Surfaces in an Electrolytic Cell. CHEMSUSCHEM 2019; 12:4265-4273. [PMID: 31313891 DOI: 10.1002/cssc.201901429] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Indexed: 06/10/2023]
Abstract
The nitrogen reduction reaction was investigated on the surfaces of 18 different stable transition metal sulfides using density functional theory calculations. YS, ScS, and ZrS were modeled in the rocksalt structure with the (1 0 0) facet; TiS, VS, CrS, NbS, NiS, and FeS in NiAs-type structure with the (1 1 1) facet; and MnS2 , CoS2 , IrS2 , CuS2 , OsS2 , FeS2 , RuS2 , RhS2 , and NiS2 in pyrite structure for both the (1 0 0) and (1 1 1) orientations. As the first step towards determination of sulfides that are less prone to hydrogen evolution, the competition between adsorption of NNH and H (for the associative mechanism), and between adsorption of N and H (for the dissociative mechanism) on these surfaces was considered. The catalytic activity through both the associative and dissociative mechanisms was explored and the overpotential required for electrochemical ammonia formation is reported. The scaling relations and volcano plots were constructed with free energy of adsorption of NNH or N on the surface as the descriptor. RuS2 was observed as the most active sulfide that could catalyze nitrogen reduction to ammonia at potentials around -0.3 V through the associative mechanism. NbS, CrS, TiS, and VS are also promising candidates for both the associative and dissociative mechanisms with overpotentials for nitrogen reduction around 0.7-1.1 V.
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Affiliation(s)
- Younes Abghoui
- Science Institute, University of Iceland, VR-III, 107, Reykjavík, Iceland
| | | | - Egill Skúlason
- Science Institute, University of Iceland, VR-III, 107, Reykjavík, Iceland
- Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, VRIII, 107, Reykjavik, Iceland
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31
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Jin WT, Wang H, Wang SY, Dapper CH, Li X, Newton WE, Zhou ZH, Cramer SP. Preliminary Assignment of Protonated and Deprotonated Homocitrates in Extracted FeMo-Cofactors by Comparisons with Molybdenum(IV) Lactates and Oxidovanadium Glycolates. Inorg Chem 2019; 58:2523-2532. [PMID: 30726074 DOI: 10.1021/acs.inorgchem.8b03108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A similar pair of protonated and deprotonated mononuclear oxidovanadium glycolates [VO(Hglyc)(phen)(H2O)]Cl·2H2O (1) and [VO(glyc)(bpy)(H2O)] (2) and a mixed-(de)protonated oxidovanadium triglycolate (NH4)2[VO(Hglyc)2(glyc)]·H2O (3) were isolated and examined. The ≡C-O(H) (≡C-OH or ≡C-O) groups coordinated to vanadium were spectroscopically and structurally identified. The glycolate in 1 features a bidentate chelation through protonated α-hydroxy and α-carboxy groups, whereas the glycolate in 2 coordinates through deprotonated α-alkoxy and α-carboxy groups. The glycolates in 3 coordinate to vanadium through α-alkoxy or α-hydroxy and α-carboxy groups and thus have both protonated ≡C-OH and deprotonated ≡C-O bonds simultaneously. Structural investigations revealed that the longer protonated V-Oα-hydroxy bonds [2.234(2) Å and 2.244(2) Å] in 1 and 3 are close to those of FeV-cofactor (FeV-co) 2.17 Å1 (FeMo-co 2.17 Å2), while deprotonated V-Oα-alkoxy bonds [2, 1.930(2); 3, 1.927(2) Å] were obviously shorter. This shows a similar elongated trend as the Mo-O distances in the previously reported deprotonated vs protonated molybdenum lactates (Wang, S. Y. et al. Dalton Trans. 2018, 47, 7412-7421) and these vanadium and molybdenum complexes have the same local V/Mo-homocitrate structures as those of FeV/Mo-cos of nitrogenases. The IR spectra of these oxidovanadium and the previously synthesized molybdenum complexes including different substituted ≡C-O(H) model compounds show red-shifts for ≡C-OH vs ≡C-O alternation, which further assign the two IR bands of extracted FeMo-co at 1084 and 1031 cm-1 to ≡C-O and ≡C-OH vibrations, respectively. Although the structural data or IR spectra for some of the previously synthesized Mo/V complexes and extracted FeMo-co were measured earlier, this is the first time that the ≡C-O(H) coordinated peaks are assigned. The overall structural and IR results well suggest the coexistence of homocitrates coordinated with α-alkoxy (deprotonated) and α-hydroxy (protonated) groups in the extracted FeMo-co.
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Affiliation(s)
- Wan-Ting Jin
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Hongxin Wang
- Department of Chemistry , University of California , Davis , California 95616 , United States.,Physical Biosciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Si-Yuan Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Christie H Dapper
- Department of Biochemistry , Virginia Polytechnic Institute and State University , Blacksburg , Virginia 24061 , United States
| | - Xing Li
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - William E Newton
- Department of Biochemistry , Virginia Polytechnic Institute and State University , Blacksburg , Virginia 24061 , United States
| | - Zhao-Hui Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering , Xiamen University , Xiamen 361005 , China
| | - Stephen P Cramer
- Department of Chemistry , University of California , Davis , California 95616 , United States.,Physical Biosciences Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
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32
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Thorhallsson AT, Bjornsson R. Computational Mechanistic Study of [MoFe3S4] Cubanes for Catalytic Reduction of Nitrogenase Substrates. Inorg Chem 2019; 58:1886-1894. [DOI: 10.1021/acs.inorgchem.8b02669] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Albert Th. Thorhallsson
- Science Institute, University of Iceland, Dunhagi 3, Reykjavik 107, Iceland
- Department of Inorganic Spectroscopy, Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, Mülheim an der Ruhr 45470, Germany
| | - Ragnar Bjornsson
- Science Institute, University of Iceland, Dunhagi 3, Reykjavik 107, Iceland
- Department of Inorganic Spectroscopy, Max-Planck-Institut für Chemische Energiekonversion, Stiftstrasse 34-36, Mülheim an der Ruhr 45470, Germany
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33
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Bouchard S, Bruschi M, De Gioia L, Le Roy C, Pétillon FY, Schollhammer P, Talarmin J. FeMo Heterobimetallic Dithiolate Complexes: Investigation of Their Electron Transfer Chemistry and Reactivity toward Acids, a Density Functional Theory Rationalization. Inorg Chem 2019; 58:679-694. [PMID: 30561200 DOI: 10.1021/acs.inorgchem.8b02861] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The electrochemical behavior of complexes [FeMo(CO)5(κ2-dppe)(μ-pdt)] (1) and [FeMo(CO)4(MeCN)(κ2-dppe)(μ-pdt)] (2), in the absence and in the presence of acid, has been investigated. The reduction of 1 follows at slow scan rates, in CH2Cl2-[NBu4][PF6] and acid-free media, an ECrevE mechanism that is supported by cyclic voltammetry (CV) experiments and digital CV simulations. In MeCN-[NBu4][PF6], the electrochemical reduction of 1 is the same as in dichloromethane and follows an ECE mechanism at slow scan rates, but with a positive shift of the redox potentials. In contrast, the oxidation of 1 is strongly solvent-dependent. In dichloromethane, the oxidation of 1 is reversible and involves a single electron, while in acetonitrile, it is irreversible at moderate and slow scan rates ( v ≤ ca. 1 V s-1), and some chemical reversibility is apparent at higher scan rates ( v = 10 V s-1). Density functional theory calculations revealed that the chemical step in the ECrevE mechanism corresponds to the dissociation of one PPh2 end of the diphosphine ligand and the transfer of the semibridging CO to the Fe atom, similarly to the mechanism observed in the FeFe analogue complex. However, in the case of 1, the subsequent coordination of the phosphine ligand to the other metal is an unfavorable process.
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Affiliation(s)
- Solène Bouchard
- UMR CNRS 6521 "Chimie, Electrochimie Moléculaires et Chimie Analytique", Université de Bretagne Occidentale, UFR Sciences et Techniques , CS 93837, 29238 Brest-Cedex 3 , France
| | - Maurizio Bruschi
- Department of Earth and Environmental Sciences , University of Milano-Bicocca , Piazza della Scienza 1 , 20126 Milan , Italy
| | - Luca De Gioia
- Department of Biotechnology and Bioscience , University of Milano-Bicocca , Piazza della Scienza 2 , 20126 Milan , Italy
| | - Christine Le Roy
- UMR CNRS 6521 "Chimie, Electrochimie Moléculaires et Chimie Analytique", Université de Bretagne Occidentale, UFR Sciences et Techniques , CS 93837, 29238 Brest-Cedex 3 , France
| | - François Y Pétillon
- UMR CNRS 6521 "Chimie, Electrochimie Moléculaires et Chimie Analytique", Université de Bretagne Occidentale, UFR Sciences et Techniques , CS 93837, 29238 Brest-Cedex 3 , France
| | - Philippe Schollhammer
- UMR CNRS 6521 "Chimie, Electrochimie Moléculaires et Chimie Analytique", Université de Bretagne Occidentale, UFR Sciences et Techniques , CS 93837, 29238 Brest-Cedex 3 , France
| | - Jean Talarmin
- UMR CNRS 6521 "Chimie, Electrochimie Moléculaires et Chimie Analytique", Université de Bretagne Occidentale, UFR Sciences et Techniques , CS 93837, 29238 Brest-Cedex 3 , France
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34
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Foster SL, Bakovic SIP, Duda RD, Maheshwari S, Milton RD, Minteer SD, Janik MJ, Renner JN, Greenlee LF. Catalysts for nitrogen reduction to ammonia. Nat Catal 2018. [DOI: 10.1038/s41929-018-0092-7] [Citation(s) in RCA: 676] [Impact Index Per Article: 112.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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35
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Lee CC, Tanifuji K, Newcomb M, Liedtke J, Hu Y, Ribbe MW. A Comparative Analysis of the CO-Reducing Activities of MoFe Proteins Containing Mo- and V-Nitrogenase Cofactors. Chembiochem 2018; 19:649-653. [PMID: 29363247 DOI: 10.1002/cbic.201800035] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Indexed: 11/12/2022]
Abstract
The Mo and V nitrogenases are structurally homologous yet catalytically distinct in their abilities to reduce CO to hydrocarbons. Here we report a comparative analysis of the CO-reducing activities of the Mo- and V-nitrogenase cofactors (i.e., the M and V clusters) upon insertion of the respective cofactor into the same, cofactor-deficient MoFe protein scaffold. Our data reveal a combined contribution from the protein environment and cofactor properties to the reactivity of nitrogenase toward CO, thus laying a foundation for further mechanistic investigation of the enzymatic CO reduction, while suggesting the potential of targeting both the protein scaffold and the cofactor species for nitrogenase-based applications in the future.
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Affiliation(s)
- Chi Chung Lee
- Department of Molecular Biology and Biochemistry, University of California, 2230/2236 McGaugh Hall, Irvine, CA, 92697-3900, USA
| | - Kazuki Tanifuji
- Department of Molecular Biology and Biochemistry, University of California, 2230/2236 McGaugh Hall, Irvine, CA, 92697-3900, USA
| | - Megan Newcomb
- Department of Molecular Biology and Biochemistry, University of California, 2230/2236 McGaugh Hall, Irvine, CA, 92697-3900, USA.,Department of Chemistry, University of California, 2236 McGaugh Hall, Irvine, CA, 92697-2025, USA
| | - Jasper Liedtke
- Department of Molecular Biology and Biochemistry, University of California, 2230/2236 McGaugh Hall, Irvine, CA, 92697-3900, USA
| | - Yilin Hu
- Department of Molecular Biology and Biochemistry, University of California, 2230/2236 McGaugh Hall, Irvine, CA, 92697-3900, USA
| | - Markus W Ribbe
- Department of Molecular Biology and Biochemistry, University of California, 2230/2236 McGaugh Hall, Irvine, CA, 92697-3900, USA.,Department of Chemistry, University of California, 2236 McGaugh Hall, Irvine, CA, 92697-2025, USA
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36
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Pick FS, Leznoff DB, Fryzuk MD. Redox behaviour of ([fc(NPiPr2)2]Fe)2, formation of an iron–iron bond and cleavage of azobenzene. Dalton Trans 2018; 47:10925-10931. [DOI: 10.1039/c8dt00828k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The redox behaviour of the dimeric tetrairon complex, ([fc(NPiPr2)2]Fe)2 (where fc(NPiPr2)2 = 1,1′-(C5H4NPiPr2)2Fe) has been investigated.
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Affiliation(s)
- Fraser S. Pick
- Department of Chemistry
- The University of British Columbia
- Vancouver
- Canada
| | - Daniel B. Leznoff
- Deprtment of Chemistry
- Simon Fraser University
- 8888 University Drive
- Burnaby
- Canada V5A 1S6
| | - Michael D. Fryzuk
- Department of Chemistry
- The University of British Columbia
- Vancouver
- Canada
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37
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Kuwata S, Hidai M. Science of Nitrogen Fixation Developed by Cooperation between Chemistry and Biology. J SYN ORG CHEM JPN 2018. [DOI: 10.5059/yukigoseikyokaishi.76.346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shigeki Kuwata
- School of Materials and Chemical Technology, Tokyo Institute of Technology
- PRESTO, Japan Science and Technology Agency (JST)
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38
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Abstract
New perspectives for dinitrogen activation: an overview of photochemical pathways to cleave the strong N–N bond.
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39
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Benediktsson B, Bjornsson R. QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site. Inorg Chem 2017; 56:13417-13429. [DOI: 10.1021/acs.inorgchem.7b02158] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Bardi Benediktsson
- Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
| | - Ragnar Bjornsson
- Science Institute, University of Iceland, Dunhagi 3, 107 Reykjavik, Iceland
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40
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41
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Duan G, Hakoyama T, Kamiya T, Miwa H, Lombardo F, Sato S, Tabata S, Chen Z, Watanabe T, Shinano T, Fujiwara T. LjMOT1, a high-affinity molybdate transporter from Lotus japonicus, is essential for molybdate uptake, but not for the delivery to nodules. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:1108-1119. [PMID: 28276145 DOI: 10.1111/tpj.13532] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/01/2017] [Accepted: 03/01/2017] [Indexed: 05/06/2023]
Abstract
Molybdenum (Mo) is an essential nutrient for plants, and is required for nitrogenase activity of legumes. However, the pathways of Mo uptake from soils and then delivery to the nodules have not been characterized in legumes. In this study, we characterized a high-affinity Mo transporter (LjMOT1) from Lotus japonicus. Mo concentrations in an ethyl methanesulfonate-mutagenized line (ljmot1) decreased by 70-95% compared with wild-type (WT). By comparing the DNA sequences of four AtMOT1 homologs between mutant and WT lines, one point mutation was found in LjMOT1, which altered Trp292 to a stop codon; no mutation was found in the other homologous genes. The phenotype of Mo concentrations in F2 progeny from ljmot1 and WT crosses were associated with genotypes of LjMOT1. Introduction of endogenous LjMOT1 to ljmot1 restored Mo accumulation to approximately 60-70% of the WT. Yeast expressing LjMOT1 exhibited high Mo uptake activity, and the Km was 182 nm. LjMOT1 was expressed mainly in roots, and its expression was not affected by Mo supply or rhizobium inoculation. Although Mo accumulation in the nodules of ljmot1 was significantly lower than that of WT, it was still high enough for normal nodulation and nitrogenase activity, even for cotyledons-removed ljmot1 plants grown under low Mo conditions, in this case the plant growth was significantly inhibited by Mo deficiency. Our results suggest that LjMOT1 is an essential Mo transporter in L. japonicus for Mo uptake from the soil and growth, but is not for Mo delivery to the nodules.
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Affiliation(s)
- Guilan Duan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Tsuneo Hakoyama
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takehiro Kamiya
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hiroki Miwa
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Fabien Lombardo
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
- National Agriculture and Food Research Organization (NARO) Institute of Crop Science, Ibaraki, 305-8518, Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0812, Japan
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, 980-8577, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0812, Japan
| | - Zheng Chen
- Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, 010-8589, Japan
- Department of Environmental Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu, 215123, China
| | - Toshihiro Watanabe
- Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, 010-8589, Japan
| | - Takuro Shinano
- Graduate School of Agriculture, Hokkaido University, Kita-ku, Sapporo, 010-8589, Japan
- NARO Tohoku Agricultural Research Center, Arai, Fukushima, 960-2156, Japan
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
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42
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Cui Q. Perspective: Quantum mechanical methods in biochemistry and biophysics. J Chem Phys 2017; 145:140901. [PMID: 27782516 DOI: 10.1063/1.4964410] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
In this perspective article, I discuss several research topics relevant to quantum mechanical (QM) methods in biophysical and biochemical applications. Due to the immense complexity of biological problems, the key is to develop methods that are able to strike the proper balance of computational efficiency and accuracy for the problem of interest. Therefore, in addition to the development of novel ab initio and density functional theory based QM methods for the study of reactive events that involve complex motifs such as transition metal clusters in metalloenzymes, it is equally important to develop inexpensive QM methods and advanced classical or quantal force fields to describe different physicochemical properties of biomolecules and their behaviors in complex environments. Maintaining a solid connection of these more approximate methods with rigorous QM methods is essential to their transferability and robustness. Comparison to diverse experimental observables helps validate computational models and mechanistic hypotheses as well as driving further development of computational methodologies.
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Affiliation(s)
- Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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43
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Maia LB, Moura I, Moura JJ. EPR Spectroscopy on Mononuclear Molybdenum-Containing Enzymes. FUTURE DIRECTIONS IN METALLOPROTEIN AND METALLOENZYME RESEARCH 2017. [DOI: 10.1007/978-3-319-59100-1_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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44
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Layer G, Krausze J, Moser J. Reduction of Chemically Stable Multibonds: Nitrogenase-Like Biosynthesis of Tetrapyrroles. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 925:147-161. [DOI: 10.1007/5584_2016_175] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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45
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Amolegbe SA, Akinremi CA, Adewuyi S, Lawal A, Bamigboye MO, Obaleye JA. Some nontoxic metal-based drugs for selected prevalent tropical pathogenic diseases. J Biol Inorg Chem 2016; 22:1-18. [DOI: 10.1007/s00775-016-1421-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Accepted: 11/18/2016] [Indexed: 02/04/2023]
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46
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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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47
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Zhang RH, Zhou XW, Dong X, Zhou ZH. Solid and solution chemistry of protonated and deprotonated mononuclear molybdenum(VI) citrates. J COORD CHEM 2016. [DOI: 10.1080/00958972.2016.1246721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Rong-Hua Zhang
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, China
| | - Xin-Wen Zhou
- College of Biological and Pharmaceutical Sciences, China Three Gorges University, Yichang, China
| | - Xin Dong
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
| | - Zhao-Hui Zhou
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
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48
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Katz FEH, Owens CP, Tezcan FA. Electron Transfer Reactions in Biological Nitrogen Fixation. Isr J Chem 2016. [DOI: 10.1002/ijch.201600020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Faith E. H. Katz
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive San Diego CA 92093 USA
| | - Cedric P. Owens
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive San Diego CA 92093 USA
| | - F. A. Tezcan
- Department of Chemistry and Biochemistry; University of California, San Diego; 9500 Gilman Drive San Diego CA 92093 USA
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49
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Čorić I, Holland PL. Insight into the Iron-Molybdenum Cofactor of Nitrogenase from Synthetic Iron Complexes with Sulfur, Carbon, and Hydride Ligands. J Am Chem Soc 2016; 138:7200-11. [PMID: 27171599 PMCID: PMC5508211 DOI: 10.1021/jacs.6b00747] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nitrogenase enzymes are used by microorganisms for converting atmospheric N2 to ammonia, which provides an essential source of N atoms for higher organisms. The active site of the molybdenum-dependent nitrogenase is the unique carbide-containing iron-sulfur cluster called the iron-molybdenum cofactor (FeMoco). On the FeMoco, N2 binding is suggested to occur at one or more iron atoms, but the structures of the catalytic intermediates are not clear. In order to establish the feasibility of different potential mechanistic steps during biological N2 reduction, chemists have prepared iron complexes that mimic various structural aspects of the iron sites in the FeMoco. This reductionist approach gives mechanistic insight, and also uncovers fundamental principles that could be used more broadly for small-molecule activation. Here, we discuss recent results and highlight directions for future research. In one direction, synthetic iron complexes have now been shown to bind N2, break the N-N triple bond, and produce ammonia catalytically. Carbon- and sulfur-based donors have been incorporated into the ligand spheres of Fe-N2 complexes to show how these atoms may influence the structure and reactivity of the FeMoco. Hydrides have been incorporated into synthetic systems, which can bind N2, reduce some nitrogenase substrates, and/or reductively eliminate H2 to generate reduced iron centers. Though some carbide-containing iron clusters are known, none yet have sulfide bridges or high-spin iron atoms like the FeMoco.
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Affiliation(s)
- Ilija Čorić
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Patrick L. Holland
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
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50
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Tanabe Y, Nishibayashi Y. Catalytic Dinitrogen Fixation to Form Ammonia at Ambient Reaction Conditions Using Transition Metal-Dinitrogen Complexes. CHEM REC 2016; 16:1549-77. [DOI: 10.1002/tcr.201600025] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Indexed: 01/23/2023]
Affiliation(s)
- Yoshiaki Tanabe
- Department of Systems Innovation, School of Engineering; The University of Tokyo; Hongo, Bunkyo-ku Tokyo 113-8656 Japan
| | - Yoshiaki Nishibayashi
- Department of Systems Innovation, School of Engineering; The University of Tokyo; Hongo, Bunkyo-ku Tokyo 113-8656 Japan
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