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McKee ML. A New Nitrogenase Mechanism Using a CFe8S9 Model: Does H2 Elimination Activate the Complex to N2 Addition to the Central Carbon Atom? J Phys Chem A 2016; 120:754-64. [PMID: 26821350 DOI: 10.1021/acs.jpca.5b10384] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A truncated model of the FeMo cofactor is used to explore a new mechanism for the conversion of N2 to NH3 by the nitrogenase enzyme. After four initial protonation/reduction steps, the H4CFe8S9 cluster has two hydrogen atoms attached to sulfur, one hydrogen bridging two iron centers and one hydrogen bonded to carbon. The loss of the CH and FeHFe hydrogens as molecular hydrogen activates the cluster to addition of N2 to the carbon center. This unique step takes place at a nearly planar four-coordinate carbon center and leads to an intermediate with a significantly weakened N-N bond. A hydrogen attached to a sulfur atom is then transferred to the distal nitrogen atom. Additional prontonation/reduction steps are modeled by adding a hydrogen atom to sulfur and locating the transition states for transfer to nitrogen. The first NH3 is lost in a thermal neutral step, while the second step is endothermic. The loss of H2 activates the complex by reducing the barrier for N2 addition by 3.5 kcal/mol. Since this is the most difficult step in the mechanism, reducing the barrier for this step justifies the "extra expense" of H2 production.
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Affiliation(s)
- Michael L McKee
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849, United States
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3
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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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5
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Yan L, Dapper CH, George SJ, Wang H, Mitra D, Dong W, Newton WE, Cramer SP. Photolysis of Hi-CO Nitrogenase - Observation of a Plethora of Distinct CO Species using Infrared Spectroscopy. Eur J Inorg Chem 2011; 2011:2064-2074. [PMID: 27630531 DOI: 10.1002/ejic.201100029] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Fourier transform infrared spectroscopy (FT-IR) was used to study the photochemistry of CO-inhibited Azotobacter vinelandii nitrogenase using visible light at cryogenic temperatures. The FT-IR difference spectrum of photolyzed hi-CO at 4 K comprises negative bands at 1973 cm-1 and 1679 cm-1 together with positive bands at 1711 cm-1, 2135 and 2123 cm-1. The negative bands are assigned to a hi-CO state that comprises 2 metal-bound CO ligands, one terminally bound, and one bridged and/or protonated species. The positive band at 1711 cm-1 is assigned to a lo-CO product with a single bridged and/or protonated metal-CO group. We term these species 'Hi-1' and 'Lo-1' respectively. The high-energy bands are assigned to a liberated CO trapped in the protein pocket. Warming results in CO recombination, and the temperature dependence of the recombination rate yields an activation energy of 4 kJ mol-1. Two α-H195 variant enzymes yielded additional signals. Asparagine substitution, α-H195N, gives a spectrum containing 2 negative 'Hi-2' bands at 1936 and 1858 cm-1 with a positive 'Lo-2' band at 1780 cm-1, while glutamine substitution, α-H195Q, produces a complex spectrum that includes a third CO species, with negative 'Hi-3' bands at 1938 and 1911 cm-1 and a positive feature 'Lo-3' band at 1921 cm-1. These species can be assigned to a combination of terminal, bridged, and possibly protonated CO groups bound to the FeMo-cofactor active site. The proposed structures are discussed in terms of both CO inhibition and the mechanism nitrogenase catalysis. Given the intractability of observing nitrogenase intermediates by crystallographic methods, IR-monitored photolysis appears to be a promising and information-rich probe of nitrogenase structure and chemistry.
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Affiliation(s)
- Lifen Yan
- Department of Applied Science, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - Christie H Dapper
- Department of Biochemistry, Virginia Polytechnic Institute and State University, 123 Engel Hall, Blacksburg, VA 24061, USA
| | - Simon J George
- Department of Applied Science, University of California, One Shields Avenue, Davis, CA 95616 USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS 6R2100, Berkeley, CA 94720, USA
| | - Hongxin Wang
- Department of Applied Science, University of California, One Shields Avenue, Davis, CA 95616 USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS 6R2100, Berkeley, CA 94720, USA
| | - Devrani Mitra
- Department of Applied Science, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - Weibing Dong
- Department of Applied Science, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - William E Newton
- Department of Biochemistry, Virginia Polytechnic Institute and State University, 123 Engel Hall, Blacksburg, VA 24061, USA
| | - Stephen P Cramer
- Department of Applied Science, University of California, One Shields Avenue, Davis, CA 95616 USA; Physical Biosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, MS 6R2100, Berkeley, CA 94720, USA
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6
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Harris TV, Szilagyi RK. Nitrogenase structure and function relationships by density functional theory. Methods Mol Biol 2011; 766:267-291. [PMID: 21833874 DOI: 10.1007/978-1-61779-194-9_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Modern density functional theory has tremendous potential with matching popularity in metalloenzymology to reveal the unseen atomic and molecular details of structural data, spectroscopic measurements, and biochemical experiments by providing insights into unobservable structures and states, while also offering theoretical justifications for observed trends and differences. An often untapped potential of this theoretical approach is to bring together diverse experimental structural and reactivity information and allow for these to be critically evaluated at the same level. This is particularly applicable for the tantalizingly complex problem of the structure and molecular mechanism of biological nitrogen fixation. In this chapter we provide a review with extensive practical details of the compilation and evaluation of experimental data for an unbiased and systematic density functional theory analysis that can lead to remarkable new insights about the structure-function relationships of the iron-sulfur clusters of nitrogenase.
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Affiliation(s)
- Travis V Harris
- Department of Chemistry and Biochemistry, Astrobiology Biogeochemistry Research Center, Montana State University, Bozeman, MT 59717, USA.
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7
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Dance I. Electronic Dimensions of FeMo-co, the Active Site of Nitrogenase, and Its Catalytic Intermediates. Inorg Chem 2010; 50:178-92. [DOI: 10.1021/ic1015884] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Ian Dance
- School of Chemistry, University of New South Wales, Sydney 2052, Australia
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Xie H, Wu R, Zhou Z, Cao Z. Exploring the Interstitial Atom in the FeMo Cofactor of Nitrogenase: Insights from QM and QM/MM Calculations. J Phys Chem B 2008; 112:11435-9. [DOI: 10.1021/jp803616z] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Hujun Xie
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Ruibo Wu
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zhaohui Zhou
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Zexing Cao
- Department of Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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