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Taut J, Chambron J, Kersting B. Fifty Years of Inorganic Biomimetic Chemistry: From the Complexation of Single Metal Cations to Polynuclear Metal Complexes by Multidentate Thiolate Ligands. Eur J Inorg Chem 2023. [DOI: 10.1002/ejic.202200739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Josef Taut
- Institut für Anorganische Chemie Universität Leipzig Johannisallee 29 04103 Leipzig Germany
- Institut de Chimie de Strasbourg UMR 7177 CNRS-Université de Strasbourg 1, rue Blaise Pascal 67008 Strasbourg France
| | - Jean‐Claude Chambron
- Institut de Chimie de Strasbourg UMR 7177 CNRS-Université de Strasbourg 1, rue Blaise Pascal 67008 Strasbourg France
| | - Berthold Kersting
- Institut für Anorganische Chemie Universität Leipzig Johannisallee 29 04103 Leipzig Germany
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2
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Yu H, Zhang Q, Xu J, Wang X, Luo L. Assessment of density functional theory in studying on the transition states of a Diiron-mediated N N bond cleavage reaction. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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3
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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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4
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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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5
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Tanifuji K, Ohki Y. Metal–Sulfur Compounds in N2 Reduction and Nitrogenase-Related Chemistry. Chem Rev 2020; 120:5194-5251. [DOI: 10.1021/acs.chemrev.9b00544] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Kazuki Tanifuji
- Department of Molecular Biology and Biochemistry, University of California, Irvine, Irvine, California 92697-3900, United States
| | - Yasuhiro Ohki
- Department of Chemsitry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
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6
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Grunenberg J. The Interstitial Carbon of the Nitrogenase FeMo Cofactor is Far Better Stabilized than Previously Assumed. Angew Chem Int Ed Engl 2017; 56:7288-7291. [DOI: 10.1002/anie.201701790] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 03/16/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Jörg Grunenberg
- TU Braunschweig; Fakultät für Lebenswissenschaften; Institut für Organische Chemie, Abteilung Computerchemie; Hagenring 30 38106 Braunschweig Germany
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7
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Grunenberg J. Der interstitiell gebundene Kohlenstoff der Nitrogenase ist deutlich stabiler als bisher angenommen. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701790] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jörg Grunenberg
- TU Braunschweig; Fakultät für Lebenswissenschaften; Institut für Organische Chemie; Abteilung Computerchemie; Hagenring 30 38106 Braunschweig Deutschland
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8
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Bjornsson R, Neese F, Schrock RR, Einsle O, DeBeer S. The discovery of Mo(III) in FeMoco: reuniting enzyme and model chemistry. J Biol Inorg Chem 2014; 20:447-60. [PMID: 25549604 PMCID: PMC4334110 DOI: 10.1007/s00775-014-1230-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Accepted: 12/11/2014] [Indexed: 12/02/2022]
Abstract
Biological nitrogen fixation is enabled by molybdenum-dependent nitrogenase enzymes, which effect the reduction of dinitrogen to ammonia using an Fe7MoS9C active site, referred to as the iron molybdenum cofactor or FeMoco. In this mini-review, we summarize the current understanding of the molecular and electronic structure of FeMoco. The advances in our understanding of the active site structure are placed in context with the parallel evolution of synthetic model studies. The recent discovery of Mo(III) in the FeMoco active site is highlighted with an emphasis placed on the important role that model studies have played in this finding. In addition, the reactivities of synthetic models are discussed in terms of their relevance to the enzymatic system.
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Affiliation(s)
- Ragnar Bjornsson
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstr. 34-36, 45470, Mülheim and Der Ruhr, Germany,
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9
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Xu L, Wang YC, Ma W, Zhang WX, Xi Z. Mechanistic Insights into N—N Bond Cleavage in Catalytic Guanylation Reactions between 1,2-Diarylhydrazines and Carbodiimides. J Org Chem 2014; 79:12004-9. [DOI: 10.1021/jo501865b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ling Xu
- Beijing
National Laboratory for Molecular Sciences, MOE Key Laboratory of
Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China
| | - Yu-Chen Wang
- Beijing
National Laboratory for Molecular Sciences, MOE Key Laboratory of
Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China
| | - Wangyang Ma
- Beijing
National Laboratory for Molecular Sciences, MOE Key Laboratory of
Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China
| | - Wen-Xiong Zhang
- Beijing
National Laboratory for Molecular Sciences, MOE Key Laboratory of
Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China
- State
Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China
| | - Zhenfeng Xi
- Beijing
National Laboratory for Molecular Sciences, MOE Key Laboratory of
Bioorganic Chemistry and Molecular Engineering, College of Chemistry, Peking University, Beijing 100871, China
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10
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Asatryan R, Bozzelli JW, Ruckenstein E. Dihydrogen Catalysis: A Degradation Mechanism for N2-Fixation Intermediates. J Phys Chem A 2012; 116:11618-42. [DOI: 10.1021/jp303692v] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Rubik Asatryan
- Department of Chemical and Biological
Engineering, State University of New York, Buffalo, New York 14260, United States
- Department of Chemistry and
Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Joseph W. Bozzelli
- Department of Chemistry and
Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Eli Ruckenstein
- Department of Chemical and Biological
Engineering, State University of New York, Buffalo, New York 14260, United States
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11
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Luo Y, Li Y, Yu H, Zhao J, Chen Y, Hou Z, Qu J. DFT Studies on the Reduction of Dinitrogen to Ammonia by a Thiolate-Bridged Diiron Complex as a Nitrogenase Mimic. Organometallics 2011. [DOI: 10.1021/om200950q] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yi Luo
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical
Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Yang Li
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical
Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Hang Yu
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical
Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Jinfeng Zhao
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical
Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Yanhui Chen
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical
Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
| | - Zhaomin Hou
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical
Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
- Organometallic Chemistry Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako,
Saitama 351-0198, Japan
| | - Jingping Qu
- State Key Laboratory of Fine
Chemicals, School of Pharmaceutical
Science and Technology, Dalian University of Technology, Dalian 116024, People's Republic of China
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12
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Danyal K, Yang ZY, Seefeldt LC. Electron paramagnetic resonance spectroscopy. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2011; 766:191-205. [PMID: 21833869 DOI: 10.1007/978-1-61779-194-9_13] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
EPR spectroscopy has been an important tool in nitrogenase research for the last 50 years. The three metalloclusters in nitrogenase, the Fe protein [4Fe-4S] cluster, and the MoFe protein P-cluster, and FeMo-cofactor, all have EPR spectra when poised in the appropriate paramagnetic states. EPR spectroscopy can probe changes in the electronic properties of each metal cluster, such as when substrates bind, and can provide a definitive method for observing changes in the redox states of the clusters. In this chapter, the methods for analysis of the three metal clusters of nitrogenase by EPR spectroscopy are described, along with methods for trapping substrate-derived intermediates on the active site that are amenable to characterization by EPR and other magnetic resonance spectroscopy techniques.
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Affiliation(s)
- Karamatullah Danyal
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA.
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13
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Field LD, Guest RW, Turner P. Mixed-valence dinitrogen-bridged Fe(0)/Fe(II) complex. Inorg Chem 2011; 49:9086-93. [PMID: 20815362 DOI: 10.1021/ic101646p] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reactions of a dinitrogen-bridged Fe(II)/Fe(II) complex [(FeH(PP(3)))(2)(μ-N(2))](2+) (3) (PP(3) = P(CH(2)CH(2)PMe(2))(3)) with base were investigated using (15)N labeling techniques to enhance characterization. In the presence of base, 3 is initially deprotonated to the Fe(II)/Fe(0) dinitrogen-bridged complex [(FeH(PP(3)))(μ-N(2))(Fe(PP(3)))](+) (4) and then to the symmetrical Fe(0)/Fe(0) dinitrogen-bridged complex (Fe(PP(3)))(2)(μ-N(2)) (5). [(FeH(PP(3)))(μ-N(2))(Fe(PP(3)))](+) (4) exhibits unusual long-range (31)P-(31)P NMR coupling through the bridging dinitrogen ligand from the phosphines at the Fe(0) center and those at the Fe(II) center. Reaction of 4 with base under an atmosphere of argon resulted in the known dinitrogen Fe(0) complex Fe(N(2))(PP(3)) (6) and a solvent C-H activation product. Complexes 3, 4, and 5 were fully characterized by multinuclear NMR spectroscopy, and complexes 3 and 4 by X-ray crystallography.
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Affiliation(s)
- Leslie D Field
- School of Chemistry, The University of New South Wales, NSW 2052, Australia.
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14
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Gordon JC, Kubas GJ. Perspectives on How Nature Employs the Principles of Organometallic Chemistry in Dihydrogen Activation in Hydrogenases. Organometallics 2010. [DOI: 10.1021/om100436c] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- John C. Gordon
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Gregory J. Kubas
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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15
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16
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Tanaka H, Ohsako F, Seino H, Mizobe Y, Yoshizawa K. Theoretical Study on Activation and Protonation of Dinitrogen on Cubane-Type MIr3S4 Clusters (M = V, Cr, Mn, Fe, Co, Ni, Cu, Mo, Ru, and W). Inorg Chem 2010; 49:2464-70. [DOI: 10.1021/ic902414n] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hiromasa Tanaka
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Fumihiro Ohsako
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
| | - Hidetake Seino
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
| | - Yasushi Mizobe
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan
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17
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Tanaka H, Mori H, Seino H, Hidai M, Mizobe Y, Yoshizawa K. DFT Study on Chemical N2 Fixation by Using a Cubane-Type RuIr3S4 Cluster: Energy Profile for Binding and Reduction of N2 to Ammonia via Ru−N−NHx (x = 1−3) Intermediates with Unique Structures. J Am Chem Soc 2008; 130:9037-47. [DOI: 10.1021/ja8009567] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Hiromasa Tanaka
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan, and Department of Materials Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Hiroyuki Mori
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan, and Department of Materials Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Hidetake Seino
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan, and Department of Materials Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Masanobu Hidai
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan, and Department of Materials Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Yasushi Mizobe
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan, and Department of Materials Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan, and Department of Materials Science and Technology, Faculty of Industrial Science and Technology, Tokyo University of Science, Noda, Chiba 278-8510, Japan
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18
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Kubas GJ. Fundamentals of H2 Binding and Reactivity on Transition Metals Underlying Hydrogenase Function and H2 Production and Storage. Chem Rev 2007; 107:4152-205. [DOI: 10.1021/cr050197j] [Citation(s) in RCA: 796] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Gregory J. Kubas
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545
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19
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McKee ML. Modeling hydrogen evolution from the Fe4S4and Fe8S9X (X = N, C) clusters. Can a FeS high-spin cluster serve as a surrogate for the FeMo cofactor? J Comput Chem 2007; 28:1796-808. [PMID: 17285558 DOI: 10.1002/jcc.20636] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A high-spin model of nitrogenase with a Fe(8)S(9)X(+) cluster (X = nitrogen or carbon) is used to test a mechanism for molecular hydrogen production, which is known to accompany ammonia production. The reaction proceeds with a series of protonation-reduction (PR) steps which are considered to be spontaneous if the calculated hydrogen-cluster bond energy exceeds 35-40 kcal/mol. The novel features of this mechanism include the opening of the cluster when one of the bridging sulfides undergoes two PR steps and the direct participation of the central atom when it undergoes a PR step. After the sixth PR step, a cluster is formed which has a low barrier for loss of molecular hydrogen in an exothermic reaction step. The central atom (nitrogen or carbon) has only a minor effect on the reaction steps.
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Affiliation(s)
- Michael L McKee
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA.
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20
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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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21
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McKee ML. Modeling the nitrogenase FeMo cofactor with high-spin Fe8
S9
X+
(XN, C) clusters. Is the first step for N2
reduction to NH3
a concerted dihydrogen transfer? J Comput Chem 2007; 28:1342-56. [PMID: 17318945 DOI: 10.1002/jcc.20635] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A high-spin Fe(8)S(9)X(+) (X=N, C) cluster is used to model the reduction of molecular nitrogen to ammonia by the nitrogenase FeMo cofactor at the B3LYP/6-311G(d,p)/ECP(Fe,SDD) level of theory. A total of seventy-three structures were optimized (including three transition state optimizations) to explore the structure and energetic of N(2), C(2)H(2), and CO coordination to the Fe(8)S(9)X(+) cluster. After three protonation-reduction (PR) steps (modeled by addition of hydrogen atoms), N(2), C(2)H(2), and CO are predicted to bind to a Fe atom in the exo (cage does not open) position with binding energies of 7.6, 14.7, and 11.7 kcal/mol. With additional PR steps the coordination number of the core nitrogen atom is reduced from six to five and the bridging thiol group becomes a terminal SH(2) group. The fifth and sixth PR steps occur on the core nitrogen and the open Fe site. Coordination of N(2) is enhanced after six PR steps to give an intermediate ideally suited for a concerted dihydrogen transfer from the Fe and core nitrogen atoms to the coordinated N(2). The identity of the central atom (nitrogen or carbon) has only a minor effect on the reaction steps.
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Affiliation(s)
- Michael L McKee
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, USA.
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22
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Yates BF, Basch H, Musaev DG, Morokuma K. Reaction of H2 with a Binuclear Zirconium Dinitrogen Complex - Evaluation of Theoretical Models and Hybrid Approaches. J Chem Theory Comput 2006; 2:1298-316. [PMID: 26626838 DOI: 10.1021/ct050320e] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular orbital and hybrid ONIOM (both IMOMO and IMOMM) calculations have been carried out on the important reaction of H2 with a binuclear zirconium dinitrogen complex to test the efficacy of several structural models of the ancillary ligand. The complete experimental ligand, PhP(CH2SiMe2NSiMe2CH2)2PPh, in the zirconium complex has been treated at the IMOMM level, while two smaller approximations of the ligand, HP(CH2SiH2NSiH2CH2)2PH and (PH3)2(NH2)2, have received the full molecular orbital treatment. The mechanism of dihydrogen addition has been compared with our earlier study (Basch, Musaev, and Morokuma J. Am. Chem. Soc. 1999, 121, 5754-5761). We find that the substituent effects do cause some small changes in both the structures of the complexes studied and the activation energies of the transition structures. However for the most part the potential energy profiles are very similar to our earlier study and lend support to our use of simple theoretical models to represent moderately large experimental structures.
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Affiliation(s)
- Brian F Yates
- School of Chemistry, University of Tasmania, Private Bag 75, Hobart TAS 7001, Australia, Department of Chemistry, Bar Ilan University, Ramat Gan, Israel, and Cherry L Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - Harold Basch
- School of Chemistry, University of Tasmania, Private Bag 75, Hobart TAS 7001, Australia, Department of Chemistry, Bar Ilan University, Ramat Gan, Israel, and Cherry L Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - Djamaladdin G Musaev
- School of Chemistry, University of Tasmania, Private Bag 75, Hobart TAS 7001, Australia, Department of Chemistry, Bar Ilan University, Ramat Gan, Israel, and Cherry L Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322
| | - Keiji Morokuma
- School of Chemistry, University of Tasmania, Private Bag 75, Hobart TAS 7001, Australia, Department of Chemistry, Bar Ilan University, Ramat Gan, Israel, and Cherry L Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322
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23
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MacLachlan EA, Fryzuk MD. Synthesis and Reactivity of Side-On-Bound Dinitrogen Metal Complexes. Organometallics 2006. [DOI: 10.1021/om051055i] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Erin A. MacLachlan
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
| | - Michael D. Fryzuk
- Department of Chemistry, The University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, Canada V6T 1Z1
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Yoshizawa K, Kihara N, Shiota Y, Seino H, Mizobe Y. DFT Calculations of Cubane-Type Mo2Ru2S4Clusters. Stability of a Possible Dinitrogen Cluster and an Isolable Acetonitrile Cluster. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2006. [DOI: 10.1246/bcsj.79.53] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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26
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Henderson RA. Mechanistic Studies on Synthetic Fe−S-Based Clusters and Their Relevance to the Action of Nitrogenases. Chem Rev 2005; 105:2365-437. [PMID: 15941217 DOI: 10.1021/cr030706m] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Padden Metzker JK, McGrady JE. An Electronic Perspective on the Reduction of an N?N Double Bond at a Conserved Dimolybdenum Core. Chemistry 2004; 10:6447-55. [PMID: 15540264 DOI: 10.1002/chem.200400580] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Density functional theory has been used to assess the role of the bimetallic core in supporting reductive cleavage of the N=N double bond in [Cp2Mo2(mu-SMe)3(mu-eta1:eta1-HN=NPh)]+. The HOMO of the complex, the Mo-Mo delta orbital, plays a key role as a source of high-energy electrons, available for transfer into the vacant orbitals of the N=N unit. As a result, the metal centres cycle between the Mo(III) and Mo(IV) oxidation states. The symmetry of the Mo-Mo delta "buffer" orbital has a profound influence on the reaction pathway, because significant overlap with the redox-active orbital on the N=N unit (pi* or sigma*) is required for efficient electron transfer. The orthogonality of the Mo-Mo delta and N-N sigma* orbitals in the eta1:eta1 coordination mode ensures that electron transfer into the N-N sigma bond is effectively blocked, and a rate-limiting eta1:eta1-->eta1 rearrangement is a necessary precursor to cleavage of the bond.
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Sellmann D, Prakash R, Heinemann F. Reactivity of a Thiolate‐Bridged Dinuclear Ruthenium Complex with Nitrogenous Molecules: Spectroscopic Identification of a Labile Dinitrogen Complex. Eur J Inorg Chem 2004. [DOI: 10.1002/ejic.200400375] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Dieter Sellmann
- Institut für Anorganische Chemie der Universität Erlangen‐Nürnberg, Egerlandstrasse 1, 91058 Erlangen, Germany
| | - Raju Prakash
- Institut für Anorganische Chemie der Universität Erlangen‐Nürnberg, Egerlandstrasse 1, 91058 Erlangen, Germany
- Institut für Organische Chemie der Universität Erlangen‐Nürnberg, Henkestrasse 42, 91054 Erlangen, Germany, Fax: 49‐9131‐852‐1165
| | - Frank W. Heinemann
- Institut für Anorganische Chemie der Universität Erlangen‐Nürnberg, Egerlandstrasse 1, 91058 Erlangen, Germany
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29
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Noodleman L, Lovell T, Han WG, Li J, Himo F. Quantum chemical studies of intermediates and reaction pathways in selected enzymes and catalytic synthetic systems. Chem Rev 2004; 104:459-508. [PMID: 14871132 DOI: 10.1021/cr020625a] [Citation(s) in RCA: 330] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Louis Noodleman
- Department of Molecular Biology TPC-15, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
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30
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Hinnemann B, Nørskov JK. Chemical activity of the nitrogenase FeMo cofactor with a central nitrogen ligand: density functional study. J Am Chem Soc 2004; 126:3920-7. [PMID: 15038746 DOI: 10.1021/ja037792s] [Citation(s) in RCA: 111] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigate the chemical consequences of a central ligand in the nitrogenase FeMo cofactor using density functional calculations. Several studies have shown that the central ligand most probably is a nitrogen atom, but the consequences for the chemical reactivity of the cofactor are unknown. We investigate several possible routes for insertion of the central nitrogen ligand and conclude that all routes involve barriers and intermediate states, which are inaccessible at ambient conditions. On this basis we suggest that the central nitrogen ligand is present at all times during the reaction. Furthermore, we investigate how the FeMoco with the central ligand can interact with N(2) and reduce it.
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Affiliation(s)
- Berit Hinnemann
- Center for Atomic-scale Materials Physics, Department of Physics, Building 307, Technical University of Denmark, DK-2800 Lyngby, Denmark
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31
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Nava P, Han J, Ahlrichs R, Coucouvanis D. An Evaluation by Density Functional Theory of M−M Interactions in Organometallic Clusters with the [Fe 3MoS 3] 2+ Cores. Inorg Chem 2004; 43:3225-9. [PMID: 15132630 DOI: 10.1021/ic0499392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Density functional theory calculations were carried out on the structurally characterized [(Cl(4)-cat)Mo(py)Fe(3)S(3) (CO)(4)(P(n)Pr(3))(3)], A, and (Cl(4)-cat)Mo(py)Fe(3)S(3)(CO)(6)(PEt(3))(2), B, and also on A(2)(-) and B(2+) clusters. The Fe-Fe distances in these molecules depend on the total number of valence electrons (60 e(-) in A and B(2)(+) and 62 e(-) in A(2)(-) and B) and undergo great structural changes upon addition or removal of electrons. The changes are consistent with known electron-counting rules in organometallic chemistry. The weak nature of the Fe-Fe bonding interactions in these clusters is apparent in the very similar energies of states with widely different Fe-Fe distances.
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Affiliation(s)
- Paola Nava
- Departments of Chemistry, University of Karlsruhe, Karlsruhe, Germany, and University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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32
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Huniar U, Ahlrichs R, Coucouvanis D. Density Functional Theory Calculations and Exploration of a Possible Mechanism of N2 Reduction by Nitrogenase. J Am Chem Soc 2004; 126:2588-601. [PMID: 14982469 DOI: 10.1021/ja030541z] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Density functional theory (DFT) calculations have been performed on the nitrogenase cofactor, FeMoco. Issues that have been addressed concern the nature of M-M interactions and the identity and origin of the central light atom, revealed in a recent crystallographic study of the FeMo protein of nitrogenase (Einsle, O.; et al. Science 2002, 297, 871). Introduction of Se in place of the S atoms in the cofactor and energy minimization results in an optimized structure very similar to that in the native enzyme. The nearly identical, short, lengths of the Fe-Fe distances in the Se and S analogues are interpreted in terms of M-M weak bonding interactions. DFT calculations with O or N as the central atoms in the FeMoco marginally support the assignment of the central atom as N rather than O. The assumption was made that the central atom is the N atom, and steps of a catalytic cycle were calculated starting with either of two possible states for the cofactor and maintaining the same charge throughout (by addition of equal numbers of H(+) and e(-)) between steps. The states were [(Cl)Fe(II)(6)Fe(III)Mo(IV)S(9)(H(+))(3)N(3-)(Gl)(Im)](2-), [I-N-3H](2-), and [(Cl)Fe(II)(4)Fe(III)(3)Mo(IV)S(9)(H(+))(3)N(3-)(Gl)(Im)], [I-N-3H](0) (Gl = deprotonated glycol; Im = imidazole). These are the triply protonated ENDOR/ESEEM [I-N](5-) and Mössbauer [I-N](3-) models, respectively. The proposed mechanism explores the possibilities that (a) redox-induced distortions facilitate insertion of N(2) and derivative substrates into the Fe(6) central unit of the cofactor, (b) the central atom in the cofactor is an exchangeable nitrogen, and (c) the individual steps are related by H(+)/e(-) additions (and reduction of substrate) or aquation/dehydration (and distortion of the Fe(6) center). The Delta E's associated with the individual steps of the proposed mechanism are small and either positive or negative. The largest positive Delta E is +121 kJ/mol. The largest negative Delta E of -333 kJ/mol is for the FeMoco with a N(3-) in the center (the isolated form) and an intermediate in the proposed mechanism.
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Affiliation(s)
- Uwe Huniar
- Department of Chemistry, University of Karlsruhe, Karlsruhe, Germany
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33
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Sellmann D, Peters K, Heinemann F. New Pentadentate Carboxylate-Derivatized Sulfur Ligands Affording Water Soluble Iron Complexes with [Fe(NS4)] Cores that Bind Small Molecules (CO, NO, PMe3) as Co-Ligands. Eur J Inorg Chem 2004. [DOI: 10.1002/ejic.200300519] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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34
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Hinnemann B, Nørskov JK. Structure of the FeFe-cofactor of the iron-only nitrogenase and possible mechanism for dinitrogen reduction. Phys Chem Chem Phys 2004. [DOI: 10.1039/b310850c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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35
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QUANTUM CHEMICAL INVESTIGATIONS INTO THE PROBLEM OF BIOLOGICAL NITROGEN FIXATION: SELLMANN-TYPE METAL–SULFUR MODEL COMPLEXES. ADVANCES IN INORGANIC CHEMISTRY 2004. [DOI: 10.1016/s0898-8838(04)56003-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Cao Z, Zhou Z, Wan H, Zhang Q, Thiel W. Density Functional Calculations on the Binding of Dinitrogen to the FeFe Cofactor in Fe-Only Nitrogenase: FeFeco(μ6-N2) as Intermediate in Nitrogen Fixation. Inorg Chem 2003; 42:6986-8. [PMID: 14577763 DOI: 10.1021/ic034714x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The geometries and stabilities of the FeFe cofactor at different oxidation states and its complexes with N(2) have been determined by density functional calculations. These calculations support an EPR-inactive resting state of the FeFe cofactor with four Fe(2+) and four Fe(3+) sites (4Fe(2+)4Fe(3+)). FeFeco(mu(6)-N(2)) with a central dinitrogen ligand is predicted to be the most stable complex of the FeFe cofactor with N(2). It is easily formed by penetration of N(2) into the trigonal Fe(6) prism of the FeFe cofactor with an approximate barrier of 4 kcal mol(-1). The present DFT results suggest that an FeFeco(mu(6)-N(2)) entity is a plausible intermediate in dinitrogen fixation by nitrogenase. CO is calculated to bind even more strongly than N(2) to the FeFe cofactor so that CO may inhibit the reduction of nitrogen by Fe-only nitrogenase.
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Affiliation(s)
- Zexing Cao
- Department of Chemistry, State Key Laboratory for Physical Chemistry of Solid Surfaces, Center for Theoretical Chemistry, Xiamen University, Xiamen 361005, China.
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37
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Lovell T, Liu T, Case DA, Noodleman L. Structural, spectroscopic, and redox consequences of a central ligand in the FeMoco of nitrogenase: a density functional theoretical study. J Am Chem Soc 2003; 125:8377-83. [PMID: 12837110 DOI: 10.1021/ja0301572] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Broken symmetry density functional and electrostatics calculations have been used to shed light on which of three proposed atoms, C, N, or O, is most likely to be present in the center of the FeMoco, the active site of nitrogenase. At the Mo(4+)4Fe(2+)3Fe(3+) oxidation level, a central N(3-) anion results in (1) calculated Fe-N bond distances that are in very good agreement with the recent high-resolution X-ray data of Einsle et al.; (2) a calculated redox potential of 0.19 eV versus the standard hydrogen electrode (SHE) for FeMoco(oxidized) + e(-) --> FeMoco(resting), in good agreement with the measured value of -0.042 V in Azotobacter vinelandii; and (3) average Mössbauer isomer shift values (IS(av) = 0.48 mm s(-1)) compatible with experiment (IS(av) = 0.40 mm s(-1)). At the more reduced Mo(4+)6Fe(2+)1Fe(3+) level, the calculated geometry around a central N(3-) anion still correlates well with the X-ray data, but the average Mössbauer isomer shift value (IS(av) = 0.54 mm s(-1)) and the redox potential of -2.21 eV show a much poorer agreement with experiment. These calculated structural, spectroscopic, and redox data indicate the most likely iron oxidation state for the resting FeMoco of nitrogenase to be 4Fe(2+)3Fe(3+). At this favored oxidation state, oxygen or carbon coordination leads to (1) Fe-O distances in poor agreement and Fe-C distances in good agreement with experiment and (2) calculated redox potentials of +0.97 eV for O(2-) and -1.31 eV for C(4-). The calculated structural parameters and/or redox data suggest either O(2-) or C(4-) is unlikely as a central anion.
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Affiliation(s)
- Timothy Lovell
- Department of Molecular Biology TPC-15, The Scripps Research Institute, La Jolla, CA 92037, USA
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38
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Sellmann D, Peters K, Molina R, Heinemann F. A Dinuclear Iron Complex with Two Cofacial [FeS4] Cores Linked by Covalent Ligand Periphery Clamps and Dissociable Thiolate Bridges. Eur J Inorg Chem 2003. [DOI: 10.1002/ejic.200390119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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39
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40
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Lovell T, Torres RA, Han WG, Liu T, Case DA, Noodleman L. Metal substitution in the active site of nitrogenase MFe(7)S(9) (M = Mo(4+), V(3+), Fe(3+)). Inorg Chem 2002; 41:5744-53. [PMID: 12401079 DOI: 10.1021/ic020474u] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The unifying view that molybdenum is the essential component in nitrogenase has changed over the past few years with the discovery of a vanadium-containing nitrogenase and an iron-only nitrogenase. The principal question that has arisen for the alternative nitrogenases concerns the structures of their corresponding cofactors and their metal-ion valence assignments and whether there are significant differences with that of the more widely known molybdenum-iron cofactor (FeMoco). Spin-polarized broken-symmetry (BS) density functional theory (DFT) calculations are used to assess which of the two possible metal-ion valence assignments (4Fe(2+)4Fe(3+) or 6Fe(2+)2Fe(3+)) for the iron-only cofactor (FeFeco) best represents the resting state. For the 6Fe(2+)2Fe(3+) oxidation state, the spin coupling pattern for several spin state alignments compatible with S = 0 were generated and assessed by energy criteria. The most likely BS spin state is composed of a 4Fe cluster with spin S(a) = (7)/(2) antiferromagnetically coupled to a 4Fe' cluster with spin S(b) = (7)/(2). This state has the lowest DFT energy for the isolated FeFeco cluster and displays calculated Mössbauer isomer shifts consistent with experiment. Although the S = 0 resting state of FeFeco has recently been proposed to have metal-ion valencies of 4Fe(2+)4Fe(3+) (derived from experimental Mössbauer isomer shifts), our isomer shift calculations for the 4Fe(2+)4Fe(3+) oxidation state are in poorer agreement with experiment. Using the Mo(4+)6Fe(2+)Fe(3+) oxidation level of the cofactor as a starting point, the structural consequences of replacement of molybdenum (Mo(4+)) with vanadium (V(3+)) or iron (Fe(3+)) in the cofactor have been investigated. The size of the cofactor cluster shows a dependency on the nature of the heterometal and increases in the order FeMoco < FeVco < FeFeco.
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Affiliation(s)
- Timothy Lovell
- Department of Molecular Biology TPC-15, The Scripps Research Institute, La Jolla, CA 92037, USA.
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41
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Dunford AJ, Henderson RA. Substitution reactions of [Fe(4)S(4)Cl(4)](2-) with Bu(t)NC or Et(2)NCS(2)(-): trapping intermediates and detecting new pathways. Inorg Chem 2002; 41:5487-94. [PMID: 12377044 DOI: 10.1021/ic0202110] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kinetic studies on the substitution reaction between [Fe(4)S(4)Cl(4)](2-) and Bu(t)NC or Et(2)NCS(2)(-) are reported. The binding of small molecules and ions to Fe-S clusters is a fundamental step in substitution reactions but can be difficult to follow directly because these reactions are rapid and often associated with small spectroscopic changes. A novel kinetic method is reported which allows the time course of molecule and ion binding to Fe-S clusters to be followed by monitoring the lability of the cluster. Using a stopped-flow, sequential-mix apparatus, [Fe(4)S(4)Cl(4)](2-) and L (L = Et(2)NCS(2)(-) or Bu(t)NC) are rapidly mixed, and after a known time (delta) the resulting solution is mixed with a solution of PhS(-). The thiolate substitutes for the chloro ligands on the cluster, in a reaction which is easy to follow because of the large change in the visible absorption spectrum. The rate of this substitution is extremely sensitive to whether L is bound to the cluster or not. By correlation of delta with the rate of the reaction with PhS(-), the time course of the reaction between [Fe(4)S(4)Cl(4)](2-) and L can be mapped out. In studies where L = Bu(t)NC this technique has allowed the detection of an intermediate ([Fe(4)S(4)Cl(4)(CNBu(t))](2-)) which cannot be detected spectrophotometrically. In further studies, the substitution reactions of [Fe(4)S(4)Cl(4)](2-) with PhS(-), Et(2)NCS(2)(-), or Bu(t)NC are all perturbed by the addition of Cl(-). In all cases a common pathway for substitution is evident, but with Et(2)NCS(2)(-) an additional, slower pathway becomes apparent under conditions where the common pathway is completely inhibited by Cl(-).
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Affiliation(s)
- Adrian J Dunford
- Department of Chemistry, Bedson Building, University of Newcastle, Newcastle-upon-Tyne NE1 7RU, U.K
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42
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Einsle O, Tezcan FA, Andrade SLA, Schmid B, Yoshida M, Howard JB, Rees DC. Nitrogenase MoFe-protein at 1.16 A resolution: a central ligand in the FeMo-cofactor. Science 2002; 297:1696-700. [PMID: 12215645 DOI: 10.1126/science.1073877] [Citation(s) in RCA: 780] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
A high-resolution crystallographic analysis of the nitrogenase MoFe-protein reveals a previously unrecognized ligand coordinated to six iron atoms in the center of the catalytically essential FeMo-cofactor. The electron density for this ligand is masked in structures with resolutions lower than 1.55 angstroms, owing to Fourier series termination ripples from the surrounding iron and sulfur atoms in the cofactor. The central atom completes an approximate tetrahedral coordination for the six iron atoms, instead of the trigonal coordination proposed on the basis of lower resolution structures. The crystallographic refinement at 1.16 angstrom resolution is consistent with this newly detected component being a light element, most plausibly nitrogen. The presence of a nitrogen atom in the cofactor would have important implications for the mechanism of dinitrogen reduction by nitrogenase.
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Affiliation(s)
- Oliver Einsle
- Howard Hughes Medical Institute, Division of Chemistry and Chemical Engineering, California Institute of Technology, Mail Code 147-75CH, Pasadena, CA 91125, USA
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43
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Lovell T, Li J, Case DA, Noodleman L. Binding modes for the first coupled electron and proton addition to FeMoco of nitrogenase. J Am Chem Soc 2002; 124:4546-7. [PMID: 11971686 DOI: 10.1021/ja012311v] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A combined broken-symmetry density functional and electrostatics approach has been used to model the one-electron reduced and protonated state of the iron-molybdenum cofactor active site of nitrogenase. The active site of the protein contains Fe, Mo, S, N, and O atoms, and many possible sites for protonation have been examined. A novel hydridic proton asymmetrically located in the central cavity created by six Fe sites is most favored from the calculations. Under physiological turnover conditions of low electron flux, the formation of this iron-hydride intermediate may represent a first step towards cofactor liberation of dihydrogen in the absence of dinitrogen.
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Affiliation(s)
- Timothy Lovell
- The Scripps Research Institute, La Jolla California 92037, USA
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44
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Noodleman L, Lovell T, Liu T, Himo F, Torres RA. Insights into properties and energetics of iron-sulfur proteins from simple clusters to nitrogenase. Curr Opin Chem Biol 2002; 6:259-73. [PMID: 12039013 DOI: 10.1016/s1367-5931(02)00309-5] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Some of the principal physical features of iron-sulfur clusters in proteins are analyzed, including metal-ligand covalency, spin polarization, spin coupling, valence delocalization, valence interchange and small reorganization energies, with emphasis on recent spectroscopic and theoretical work. The current state of structural, spectroscopic, and computational knowledge for the iron-sulfur clusters in the nitrogenase iron and iron-molybdenum proteins is examined by comparison and contrast to 'simpler' ironclusters. The differing interactions of the nitrogenase iron and iron-molybdenum clusters compared with those of other iron-sulfur clusters with the protein and solvent environment are also explored.
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Affiliation(s)
- Louis Noodleman
- Department of Molecular Biology, TPC15, The Scripps Research Institute, La Jolla, California 92037, USA.
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45
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Siemann S, Schneider K, Dröttboom M, Müller A. The Fe-only nitrogenase and the Mo nitrogenase from Rhodobacter capsulatus: a comparative study on the redox properties of the metal clusters present in the dinitrogenase components. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:1650-61. [PMID: 11895435 DOI: 10.1046/j.1432-1327.2002.02804.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The dinitrogenase component proteins of the conventional Mo nitrogenase (MoFe protein) and of the alternative Fe-only nitrogenase (FeFe protein) were both isolated and purified from Rhodobacter capsulatus, redox-titrated according to the same procedures and subjected to an EPR spectroscopic comparison. In the course of an oxidative titration of the MoFe protein (Rc1Mo) three significant S = 1/2 EPR signals deriving from oxidized states of the P-cluster were detected: (1) a rhombic signal (g = 2.07, 1.96 and 1.83), which showed a bell-shaped redox curve with midpoint potentials (Em) of -195 mV (appearance) and -30 mV (disappearance), (2) an axial signal (g(parallel) = 2.00, g perpendicular = 1.90) with almost identical redox properties and (3) a second rhombic signal (g = 2.03, 2.00, 1.90) at higher redox potentials (> 100 mV). While the 'low-potential' rhombic signal and the axial signal have been both attributed to the one-electron-oxidized P-cluster (P1+) present in two conformationally different proteins, the 'high-potential' rhombic signal has been suggested rather to derive from the P3+ state. Upon oxidation, the FeFe protein (Rc1Fe) exhibited three significant S = 1/2 EPR signals as well. However, the Rc1Fe signals strongly deviated from the MoFe protein signals, suggesting that they cannot simply be assigned to different P-cluster states. (a) The most prominent feature is an unusually broad signal at g = 2.27 and 2.06, which proved to be fully reversible and to correlate with catalytic activity. The cluster giving rise to this signal appears to be involved in the transfer of two electrons. The midpoint potentials determined were: -80 mV (appearance) and 70 mV (disappearance). (b) Under weakly acidic conditions (pH 6.4) a slightly altered EPR signal occurred. It was characterized by a shift of the g values to 2.22 and 2.05 and by the appearance of an additional negative absorption-shaped peak at g = 1.86. (c) A very narrow rhombic EPR signal at g = 2.00, 1.98 and 1.96 appeared at positive redox potentials (Em = 80 mV, intensity maximum at 160 mV). Another novel S = 1/2 signal at g = 1.96, 1.92 and 1.77 was observed on further, enzymatic reduction of the dithionite-reduced state of Rc1Fe with the dinitrogenase reductase component (Rc2Fe) of the same enzyme system (turnover conditions in the presence of N2 and ATP). When the Rc1Mo protein was treated analogously, neither this 'turnover signal' nor any other S = 1/2 signal were detectable. All Rc1Fe-specific EPR signals detected are discussed and tentatively assigned with special consideration of the reference spectra obtained from Rc1Mo preparations.
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Affiliation(s)
- Stefan Siemann
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie der Universität Bielefeld, Bielefeld, Germany
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46
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Lovell T, Li J, Liu T, Case DA, Noodleman L. FeMo cofactor of nitrogenase: a density functional study of states M(N), M(OX), M(R), and M(I). J Am Chem Soc 2001; 123:12392-410. [PMID: 11734043 DOI: 10.1021/ja011860y] [Citation(s) in RCA: 147] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The M(N) S = (3)/(2) resting state of the FeMo cofactor of nitrogenase has been proposed to have metal-ion valencies of either Mo(4+)6Fe(2+)Fe(3+) (derived from metal hyperfine interactions) or Mo(4+)4Fe(2+)3Fe(3+) (from Mössbauer isomer shifts). Spin-polarized broken-symmetry (BS) density functional theory (DFT) calculations have been undertaken to determine which oxidation level best represents the M(N) state and to provide a framework for understanding its energetics and spectroscopy. For the Mo(4+)6Fe(2+)Fe(3+) oxidation state, the spin coupling pattern for several spin state alignments compatible with S = (3)/(2) were generated and assessed by energy and geometric criteria. The most likely BS spin state is composed of a Mo3Fe cluster with spin S(a) = 2 antiferromagnetically coupled to a 4Fe' cluster with spin S(b) = (7)/(2). This state has a low DFT energy for the isolated FeMoco cluster and the lowest energy when the interaction with the protein and solvent environment is included. This spin state also displays calculated metal hyperfine and Mössbauer isomer shifts compatible with experiment, and optimized geometries that are in excellent agreement with the protein X-ray data. Our best model for the actual spin-coupled state within FeMoco alters this BS state by a slight canting of spins and is analogous in several respects to that found in the 8Fe P-cluster in the same protein. The spin-up and spin-down components of the LUMO contain atomic contributions from Mo(4+) and the homocitrate and from the central prismane Fe sites and muS(2) atoms, respectively. This qualitative picture of the accepting orbitals for M(N) is consistent with observations from Mössbauer spectra of the one-electron reduced states. Similar calculations for the Mo(4+)4Fe(2+)3Fe(3+) oxidation state yield results that are in poorer agreement with experiment. Using the Mo(4+)6Fe(2+)Fe(3+) oxidation level as the most plausible resting state, the geometric, electronic and energetic properties of the one-electron redox transition to the oxidized state, M(OX), catalytically observed M(R) and radiolytically reduced M(I) states have also been explored.
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Affiliation(s)
- T Lovell
- Department of Molecular Biology TPC-15, The Scripps Research Institute, La Jolla, CA 92037, USA.
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47
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Solari E, Hesschenbrouck J, Scopelliti R, Floriani C, Re N. From Oligomers to Conducting Polymers of the Metal–Dinitrogen Functionality. Angew Chem Int Ed Engl 2001; 40:932-934. [DOI: 10.1002/1521-3773(20010302)40:5<932::aid-anie932>3.0.co;2-#] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2000] [Indexed: 11/11/2022]
Affiliation(s)
- Euro Solari
- Institut de Chimie Minérale et Analytique Université de Lausanne BCH, 1015 Lausanne (Switzerland) Fax: (+41) 21‐6923905
| | - Joëlle Hesschenbrouck
- Institut de Chimie Minérale et Analytique Université de Lausanne BCH, 1015 Lausanne (Switzerland) Fax: (+41) 21‐6923905
| | - Rosario Scopelliti
- Institut de Chimie Minérale et Analytique Université de Lausanne BCH, 1015 Lausanne (Switzerland) Fax: (+41) 21‐6923905
| | - Carlo Floriani
- Institut de Chimie Minérale et Analytique Université de Lausanne BCH, 1015 Lausanne (Switzerland) Fax: (+41) 21‐6923905
| | - Nazzareno Re
- Facoltà di Farmacia Università degli Studi “G. D'Annunzio” 66100 Chieti (Italy)
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48
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Solari E, Hesschenbrouck J, Scopelliti R, Floriani C, Re N. From Oligomers to Conducting Polymers of the Metal-Dinitrogen Functionality. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010302)113:5<958::aid-ange958>3.0.co;2-l] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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49
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Szilagyi RK, Musaev DG, Morokuma K. Theoretical studies of biological nitrogen fixation. I. Density functional modeling of the Mo-site of the FeMo-cofactor. Inorg Chem 2001; 40:766-75. [PMID: 11225121 DOI: 10.1021/ic000188n] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Mo-site and its ligand environment of the FeMo-cofactor (FeMo-co) were studied using the hybrid density functional method B3LYP. The structure and stability of the model complex (S-ligand)3(N-ligand)Mo[(S)-OCH(CH3)C(O)O-] along with its various protonated and reduced/oxidized forms were calculated. Several hypotheses were tested: (i) ligand environment of the Mo-site, (ii) monodentate vs bidentate coordination of the Mo-bound homocitrate ligand, (iii) substrate coordination to the Mo center, and (iv) Mo-His interaction. It was found that the decoordination of one of the homocitrate (lactate in the model) "legs", the bidentate-->monodentate rearrangement, does not occur spontaneously upon either single/double protonation or one-electron reduction. However, it could occur only upon substrate coordination to the Mo-center of the single-protonated forms of the complex. It was shown that one-electron reduction, single-protonation, and substrate coordination facilitate the bidentate<-->monodentate rearrangement of the homocitrate (lactate) ligand of FeMo-co. It was demonstrated that the smallest acceptable model of His ligand in FeMo-co is methylimidazolate (MeIm-). Our studies suggest that the epsilon-N of the FeMo-co-bound His residue is not protonated, and as a consequence the cluster is tightly bound to the protein matrix via a strong Mo-N delta bond.
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Affiliation(s)
- R K Szilagyi
- Cherry L. Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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50
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Extended Hückel calculations on functional and structural models of the FeMo-cofactor of nitrogenase. Polyhedron 2001. [DOI: 10.1016/s0277-5387(00)00532-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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