1
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Landaeta VR, Horsley Downie TM, Wolf R. Low-Valent Transition Metalate Anions in Synthesis, Small Molecule Activation, and Catalysis. Chem Rev 2024; 124:1323-1463. [PMID: 38354371 PMCID: PMC10906008 DOI: 10.1021/acs.chemrev.3c00121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 10/09/2023] [Accepted: 10/09/2023] [Indexed: 02/16/2024]
Abstract
This review surveys the synthesis and reactivity of low-oxidation state metalate anions of the d-block elements, with an emphasis on contributions reported between 2006 and 2022. Although the field has a long and rich history, the chemistry of transition metalate anions has been greatly enhanced in the last 15 years by the application of advanced concepts in complex synthesis and ligand design. In recent years, the potential of highly reactive metalate complexes in the fields of small molecule activation and homogeneous catalysis has become increasingly evident. Consequently, exciting applications in small molecule activation have been developed, including in catalytic transformations. This article intends to guide the reader through the fascinating world of low-valent transition metalates. The first part of the review describes the synthesis and reactivity of d-block metalates stabilized by an assortment of ligand frameworks, including carbonyls, isocyanides, alkenes and polyarenes, phosphines and phosphorus heterocycles, amides, and redox-active nitrogen-based ligands. Thereby, the reader will be familiarized with the impact of different ligand types on the physical and chemical properties of metalates. In addition, ion-pairing interactions and metal-metal bonding may have a dramatic influence on metalate structures and reactivities. The complex ramifications of these effects are examined in a separate section. The second part of the review is devoted to the reactivity of the metalates toward small inorganic molecules such as H2, N2, CO, CO2, P4 and related species. It is shown that the use of highly electron-rich and reactive metalates in small molecule activation translates into impressive catalytic properties in the hydrogenation of organic molecules and the reduction of N2, CO, and CO2. The results discussed in this review illustrate that the potential of transition metalate anions is increasingly being tapped for challenging catalytic processes with relevance to organic synthesis and energy conversion. Therefore, it is hoped that this review will serve as a useful resource to inspire further developments in this dynamic research field.
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Affiliation(s)
| | | | - Robert Wolf
- University of Regensburg, Institute
of Inorganic Chemistry, 93040 Regensburg, Germany
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2
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Barchenko M, O’Malley PJ, de Visser SP. Mechanism of Nitrogen Reduction to Ammonia in a Diiron Model of Nitrogenase. Inorg Chem 2023; 62:14715-14726. [PMID: 37650683 PMCID: PMC10498488 DOI: 10.1021/acs.inorgchem.3c02089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Indexed: 09/01/2023]
Abstract
Nitrogenase is a fascinating enzyme in biology that reduces dinitrogen from air to ammonia through stepwise reduction and protonation. Despite it being studied in detail by experimental and computational groups, there are still many unknown factors in the catalytic cycle of nitrogenase, especially related to the addition of protons and electrons and their order. A recent biomimetic study characterized a potential dinitrogen-bridged diiron cluster as a synthetic model of nitrogenase. Using strong acid and reductants, the dinitrogen was converted into ammonia molecules, but details of the mechanism remains unknown. In particular, it was unclear from the experimental studies whether the proton and electron transfer steps are sequential or alternating. Moreover, the work failed to establish what the function of the diiron core is and whether it split into mononuclear iron fragments during the reaction. To understand the structure and reactivity of the biomimetic dinitrogen-bridged diiron complex [(P2P'PhFeH)2(μ-N2)] with triphenylphosphine ligands, we performed a density functional theory study. Our computational methods were validated against experimental crystal structure coordinates, Mössbauer parameters, and vibrational frequencies and show excellent agreement. Subsequently, we investigated the alternating and consecutive addition of electrons and protons to the system. The calculations identify a number of possible reaction channels, namely, same-site protonation, alternating protonation, and complex dissociation into mononuclear iron centers. The calculations show that the overall mechanism is not a pure sequential set of electron and proton transfers but a mixture of alternating and consecutive steps. In particular, the first reaction steps will start with double proton transfer followed by an electron transfer, while thereafter, there is another proton transfer and a second electron transfer to give a complex whereby ammonia can split off with a low energetic barrier. The second channel starts with alternating protonation of the two nitrogen atoms, whereafter the initial double proton transfer, electrons and protons are added sequentially to form a hydrazine-bound complex. The latter split off ammonia spontaneously after further protonation. The various reaction channels are analyzed with valence bond and orbital diagrams. We anticipate the nitrogenase enzyme to operate with mixed alternating and consecutive protonation and electron transfer steps.
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Affiliation(s)
- Maxim Barchenko
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Patrick J. O’Malley
- Department
of Chemistry, The University of Manchester, Oxford Road, 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.
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3
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Optimization of nitrogen, water and salinity for maximizing soil organic carbon in coastal wetlands. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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4
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Kfoury J, Benedek Z, Szilvási T, Oláh J. H 2 and N 2 Binding Affinities Are Coupled in Synthetic Fe Nitrogenases Limiting N 2 Fixation. Organometallics 2022. [DOI: 10.1021/acs.organomet.1c00681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Joseph Kfoury
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rakpart 3, 1111 Budapest, Hungary
| | - Zsolt Benedek
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rakpart 3, 1111 Budapest, Hungary
- Wigner Research Centre for Physics, H-1525 Budapest, Hungary
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Tibor Szilvási
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rakpart 3, 1111 Budapest, Hungary
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5
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Barona M, Johnson SI, Mbea M, Bullock RM, Raugei S. Computational Investigations of the Reactivity of Metalloporphyrins for Ammonia Oxidation. Top Catal 2022. [DOI: 10.1007/s11244-021-01511-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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6
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Li R, Yang X, Ping H. A radical mechanism for C–H bond cross-coupling and N 2 activation catalysed by β-diketiminate iron complexes. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00564f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Density functional theory calculations and electronic structure analyses reveal a radical mechanism with spin-crossovers for C–H bond cross-coupling and N2 activation catalysed by β-diketiminate iron complexes.
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Affiliation(s)
- Rongrong Li
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xinzheng Yang
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Hongming Ping
- Department of Computer Science, University of Nottingham Ningbo China, Ningbo, 315100, China
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7
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Furan S, Molkenthin M, Winkels K, Lork E, Mebs S, Hupf E, Beckmann J. Tris(6-diphenylphosphinoacenaphth-5-yl)gallium: Z-Type Ligand and Transmetalation Reagent. Organometallics 2021. [DOI: 10.1021/acs.organomet.1c00522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sinas Furan
- Institut für Anorganische Chemie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany
| | - Martin Molkenthin
- Institut für Anorganische Chemie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany
| | - Konrad Winkels
- Institut für Anorganische Chemie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany
| | - Enno Lork
- Institut für Anorganische Chemie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany
| | - Stefan Mebs
- Institut für Experimentalphysik, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Emanuel Hupf
- Institut für Anorganische Chemie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany
| | - Jens Beckmann
- Institut für Anorganische Chemie, Universität Bremen, Leobener Straße 7, 28359 Bremen, Germany
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8
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Tanabe Y, Nishibayashi Y. Comprehensive insights into synthetic nitrogen fixation assisted by molecular catalysts under ambient or mild conditions. Chem Soc Rev 2021; 50:5201-5242. [PMID: 33651046 DOI: 10.1039/d0cs01341b] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
N2 is fixed as NH3 industrially by the Haber-Bosch process under harsh conditions, whereas biological nitrogen fixation is achieved under ambient conditions, which has prompted development of alternative methods to fix N2 catalyzed by transition metal molecular complexes. Since the early 21st century, catalytic conversion of N2 into NH3 under ambient conditions has been achieved by using molecular catalysts, and now H2O has been utilized as a proton source with turnover frequencies reaching the values found for biological nitrogen fixation. In this review, recent advances in the development of molecular catalysts for synthetic N2 fixation under ambient or mild conditions are summarized, and potential directions for future research are also discussed.
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Affiliation(s)
- Yoshiaki Tanabe
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
| | - Yoshiaki Nishibayashi
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.
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9
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Ali HS, Henchman RH, de Visser SP. What Determines the Selectivity of Arginine Dihydroxylation by the Nonheme Iron Enzyme OrfP? Chemistry 2020; 27:1795-1809. [PMID: 32965733 DOI: 10.1002/chem.202004019] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/22/2020] [Indexed: 12/13/2022]
Abstract
The nonheme iron enzyme OrfP reacts with l-Arg selectively to form the 3R,4R-dihydroxyarginine product, which in mammals can inhibit the nitric oxide synthase enzymes involved in blood pressure control. To understand the mechanisms of dioxygen activation of l-Arg by OrfP and how it enables two sequential oxidation cycles on the same substrate, we performed a density functional theory study on a large active site cluster model. We show that substrate binding and positioning in the active site guides a highly selective reaction through C3 -H hydrogen atom abstraction. This happens despite the fact that the C3 -H and C4 -H bond strengths of l-Arg are very similar. Electronic differences in the two hydrogen atom abstraction pathways drive the reaction with an initial C3 -H activation to a low-energy 5 σ-pathway, while substrate positioning destabilizes the C4 -H abstraction and sends it over the higher-lying 5 π-pathway. We show that substrate and monohydroxylated products are strongly bound in the substrate binding pocket and hence product release is difficult and consequently its lifetime will be long enough to trigger a second oxygenation cycle.
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Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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10
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Benedek Z, Papp M, Oláh J, Szilvási T. Demonstrating the Direct Relationship between Hydrogen Evolution Reaction and Catalyst Deactivation in Synthetic Fe Nitrogenases. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Zsolt Benedek
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Marcell Papp
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Tibor Szilvási
- Department of Chemical and Biological Engineering, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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11
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Jin WT, Yuan C, Deng L, An DL, Zhou ZH. Isolated Mixed-Valence Iron Vanadium Malate and Its Metal Hydrates (M = Fe 2+, Cu 2+, Zn 2+) with Reversible and Irreversible Adsorptions for Oxygen. Inorg Chem 2020; 59:12768-12777. [PMID: 32856453 DOI: 10.1021/acs.inorgchem.0c01827] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Isolated octanuclear iron-vanadium malate (NH4)3(CH3NH3)3[FeIII2VIV2VV4O11(mal)6]·7.5H2O (1; H3mal = malic acid) and its family of metal hydrates M'3n[MII(H2O)2]1.5n[FeIII2VIV2VV4O11(mal)6]n·xnH2O (2 or 2-Fe, M' = NH4+, M = Fe, x = 7.5; 3 or 3-Cu, M' = K+, M = Cu, x = 10; 4 or 4-Zn, M' = K+, M = Zn, x = 6.5) have been obtained by self-assembly in water. The cluster anion [Fe2V6O11(mal)6]6- (1a) shows an interesting iron bicapped-triangular-prismatic structure, which is bridged by M2+ hydrates (M = Fe, Cu, Zn) to construct isostructural metal organic frameworks (MOFs) 2-4. The mixed-valence vanadium systems in 1-4 were determined by theoretical bond valence calculations (BVS) and charge balance. The magnetic susceptibilities are further elucidated as high spin for Fe3+ in 1a and bridging Fe2+ in 2-Fe, respectively. A strong ferromagnetic interaction was also observed for 2-Fe at 3 K. 2-Fe, 3-Cu, and 4-Zn have similar hydrophilic channels with diameters of 6.8, 6.5, and 6.6 Å, respectively, which show obvious affinity for O2 in comparison with no adsorption of N2, H2, CO2, and CH4 at room temperature under different pressures. Moreover, 2-Fe and 4-Zn exhibit irreversible O2 absorptions, which may be attributed to charge transfer between O2 and open metal sites (OMSs) formed during vacuum heating pretreatment. UV-vis and EPR spectra show a change in electronic structure of 2-Fe after O2 adsorption. The reversible adsorption observed in 3-Cu suggests a weak interaction between O2 and Cu2+ due to the Jahn-Teller effect. The properties of gas adsorption provide an insight into the performances of small molecules in the channels constructed by synthetic octanuclear model compounds, which are related to the interactions between the gas substrate and the heterometal cluster in biology.
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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, People's Republic of China
| | - Chang Yuan
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Lan Deng
- State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
| | - Dong-Li An
- State Key Laboratory of 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 of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People's Republic of China
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12
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Gao Z, Huang H, Xu S, Li L, Yan G, Zhao M, Yang W, Zhao X. Regulating the coordination environment through doping N atoms for single-atom Mn electrocatalyst of N2 reduction with high catalytic activity and selectivity: A theoretical study. MOLECULAR CATALYSIS 2020. [DOI: 10.1016/j.mcat.2020.111091] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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13
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Chalkley MJ, Drover MW, Peters JC. Catalytic N 2-to-NH 3 (or -N 2H 4) Conversion by Well-Defined Molecular Coordination Complexes. Chem Rev 2020; 120:5582-5636. [PMID: 32352271 DOI: 10.1021/acs.chemrev.9b00638] [Citation(s) in RCA: 187] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nitrogen fixation, the six-electron/six-proton reduction of N2, to give NH3, is one of the most challenging and important chemical transformations. Notwithstanding the barriers associated with this reaction, significant progress has been made in developing molecular complexes that reduce N2 into its bioavailable form, NH3. This progress is driven by the dual aims of better understanding biological nitrogenases and improving upon industrial nitrogen fixation. In this review, we highlight both mechanistic understanding of nitrogen fixation that has been developed, as well as advances in yields, efficiencies, and rates that make molecular alternatives to nitrogen fixation increasingly appealing. We begin with a historical discussion of N2 functionalization chemistry that traverses a timeline of events leading up to the discovery of the first bona fide molecular catalyst system and follow with a comprehensive overview of d-block compounds that have been targeted as catalysts up to and including 2019. We end with a summary of lessons learned from this significant research effort and last offer a discussion of key remaining challenges in the field.
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Affiliation(s)
- Matthew J Chalkley
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Marcus W Drover
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Jonas C Peters
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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14
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Vyas N, Kumar A, Ojha AK, Grover A. Electronic structure of iron dinitrogen complex [(TPB)FeN 2] 2−/1−/0: correlation to Mössbauer parameters. RSC Adv 2020; 10:7948-7955. [PMID: 35492201 PMCID: PMC9049905 DOI: 10.1039/c9ra10481j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 01/30/2020] [Indexed: 12/29/2022] Open
Abstract
Low-valent species of iron are key intermediates in many important biological processes such as the nitrogenase enzymatic catalytic reaction. These species play a major role in activating highly stable N2 molecules. Thus, there is a clear need to establish the factors which are responsible for the reactivity of the metal–dinitrogen moiety. In this regard, we have investigated the electronic structure of low-valent iron (2−/1−/0) in a [(TPB)FeN2]2−/1−/0 complex using density functional theory (DFT). The variation in the oxidation states of iron in the nitrogenase enzyme cycle is associated with the flexibility of Fe→B bonding. Therefore, the flexibility of Fe→B bonding acts as an electron source that sustains the formation of various oxidation states, which is necessary for the key species in dinitrogen activation. AIM calculations are also performed to understand the strength of Fe→B and Fe–N2 bonds. A detailed interpretation of the contributions to the isomer shift (IS) and quadrupole splitting (ΔEQ) are discussed. The major contribution to IS comes mainly from the 3s-contribution, which differs depending on the d orbital population due to different shielding. The valence shell contribution also comes from the 4s-orbital. The Fe–N2 bond distance has a great influence on the Mössbauer parameters, which are associated with the radial distribution, i.e. the shape of the 4s-orbital and the charge density at the nucleus. A linear relationship between IS with Fe–N2 and ΔEQ with Fe–N2 is observed. We use density functional theory studies to explore the electronic structure, bonding and spectroscopic analysis of a low-valent iron (2−/1−/0) complex [(TPB)FeN2]2−/1−/0 and reveled the factor which affects the reactivity of the metal–dinitrogen moiety.![]()
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Affiliation(s)
- Nidhi Vyas
- School of Biotechnology
- Jawaharlal Nehru University
- New Delhi-110067
- India
| | - Aditya Kumar
- Department of Physics
- Motilal Nehru National Institute of Technology
- Allahabad-211004
- India
| | - Animesh K. Ojha
- Department of Physics
- Motilal Nehru National Institute of Technology
- Allahabad-211004
- India
| | - Abhinav Grover
- School of Biotechnology
- Jawaharlal Nehru University
- New Delhi-110067
- India
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15
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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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16
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Progress in Synthesizing Analogues of Nitrogenase Metalloclusters for Catalytic Reduction of Nitrogen to Ammonia. Catalysts 2019. [DOI: 10.3390/catal9110939] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Ammonia (NH3) has played an essential role in meeting the increasing demand for food and the worldwide need for nitrogen (N2) fertilizer since 1913. Unfortunately, the traditional Haber–Bosch process for producing NH3 from N2 is a high energy-consumption process with approximately 1.9 metric tons of fossil CO2 being released per metric ton of NH3 produced. As a very challenging target, any ideal NH3 production process reducing fossil energy consumption and environmental pollution would be welcomed. Catalytic NH3 synthesis is an attractive and promising alternative approach. Therefore, developing efficient catalysts for synthesizing NH3 from N2 under ambient conditions would create a significant opportunity to directly provide nitrogenous fertilizers in agricultural fields as needed in a distributed manner. In this paper, the literature on alternative, available, and sustainable NH3 production processes in terms of the scientific aspects of the spatial structures of nitrogenase metalloclusters, the mechanism of reducing N2 to NH3 catalyzed by nitrogenase, the synthetic analogues of nitrogenase metalloclusters, and the opportunities for continued research are reviewed.
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17
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Properties and reactivity of μ-nitrido-bridged dimetal porphyrinoid complexes: how does ruthenium compare to iron? J Biol Inorg Chem 2019; 24:1127-1134. [PMID: 31560098 DOI: 10.1007/s00775-019-01725-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 09/19/2019] [Indexed: 12/23/2022]
Abstract
Methane hydroxylation by metal-oxo oxidants is one of the Holy Grails in biomimetic and biotechnological chemistry. The only enzymes known to perform this reaction in Nature are iron-containing soluble methane monooxygenase and copper-containing particulate methane monooxygenase. Furthermore, few biomimetic iron-containing oxidants have been designed that can hydroxylate methane efficiently. Recent studies reported that μ-nitrido-bridged diiron(IV)-oxo porphyrin and phthalocyanine complexes hydroxylate methane to methanol efficiently. To find out whether the reaction rates are enhanced by replacing iron by ruthenium, we performed a detailed computational study. Our work shows that the μ-nitrido-bridged diruthenium(IV)-oxo reacts with methane via hydrogen atom abstraction barriers that are considerably lower in energy (by about 5 kcal mol‒1) as compared to the analogous diiron(IV)-oxo complex. An analysis of the electronic structure implicates similar spin and charge distributions for the diiron(IV)-oxo and diruthenium(IV)-oxo complexes, but the strength of the O‒H bond formed during the reaction is much stronger for the latter. As such a larger hydrogen atom abstraction driving force for the Ru complex than for the Fe complex is found, which should result in higher reactivity in the oxidation of methane.
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18
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Najafian A, Cundari TR. Computational Mechanistic Study of Electro-Oxidation of Ammonia to N 2 by Homogenous Ruthenium and Iron Complexes. J Phys Chem A 2019; 123:7973-7982. [PMID: 31454245 DOI: 10.1021/acs.jpca.9b05908] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A comprehensive DFT study of the electrocatalytic oxidation of ammonia to dinitrogen by a ruthenium polypyridyl complex, [(tpy)(bpy)RuII(NH3)]2+ (a), and its NMe2-substituted derivative (b) is presented. The thermodynamics and kinetics of electron (ET) and proton transfer (PT) steps and transition states are calculated. NMe2 substitution on bpy reduces the ET steps on average 8 kcal/mol for complex b as compared to a. The calculations indicate that N-N formation occurs by ammonia nucleophilic attack/H-transfer via a nitrene intermediate rather than a nitride intermediate. Comparison of the free energy profiles of Ru-b with its first-row Fe congener reveals that the thermodynamics are less favorable for the Fe-b model, especially for ET steps. The N-H bond dissociation free energies (BDFEs) for NH3 to form N2 show the following trend: Ru-b < Ru-a < Fe-b, indicating the lowest and most favorable BDFEs for Ru-b complex.
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Affiliation(s)
- Ahmad Najafian
- Department of Chemistry, Center of Advanced Scientific Computing and Modeling (CASCaM) , University of North Texas , 1155 Union Circle, #305070 , Denton , Texas 76203-5017 , United States
| | - Thomas R Cundari
- Department of Chemistry, Center of Advanced Scientific Computing and Modeling (CASCaM) , University of North Texas , 1155 Union Circle, #305070 , Denton , Texas 76203-5017 , United States
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19
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Colomban C, Tobing AH, Mukherjee G, Sastri CV, Sorokin AB, de Visser SP. Mechanism of Oxidative Activation of Fluorinated Aromatic Compounds by N-Bridged Diiron-Phthalocyanine: What Determines the Reactivity? Chemistry 2019; 25:14320-14331. [PMID: 31339185 DOI: 10.1002/chem.201902934] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/19/2019] [Indexed: 11/06/2022]
Abstract
The biodegradation of compounds with C-F bonds is challenging due to the fact that these bonds are stronger than the C-H bond in methane. In this work, results on the unprecedented reactivity of a biomimetic model complex that contains an N-bridged diiron-phthalocyanine are presented; this model complex is shown to react with perfluorinated arenes under addition of H2 O2 effectively. To get mechanistic insight into this unusual reactivity, detailed density functional theory calculations on the mechanism of C6 F6 activation by an iron(IV)-oxo active species of the N-bridged diiron phthalocyanine system were performed. Our studies show that the reaction proceeds through a rate-determining electrophilic C-O addition reaction followed by a 1,2-fluoride shift to give the ketone product, which can further rearrange to the phenol. A thermochemical analysis shows that the weakest C-F bond is the aliphatic C-F bond in the ketone intermediate. The oxidative defluorination of perfluoroaromatics is demonstrated to proceed through a completely different mechanism compared to that of aromatic C-H hydroxylation by iron(IV)-oxo intermediates such as cytochrome P450 Compound I.
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Affiliation(s)
- Cédric Colomban
- Institut de Recherches sur la Catalyse et l'Environnement de Lyon, IRCELYON, UMR 5256, CNRS Université Lyon 1, 2 Av. Albert Einstein, 69626, Villeurbanne Cedex, France
| | - Anthonio H Tobing
- The Manchester Institute of Biotechnology and Department of, Chemical Engineering and Analytical Science, The University of, Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Gourab Mukherjee
- The Manchester Institute of Biotechnology and Department of, Chemical Engineering and Analytical Science, The University of, Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, 781039, Assam, India
| | - Alexander B Sorokin
- Institut de Recherches sur la Catalyse et l'Environnement de Lyon, IRCELYON, UMR 5256, CNRS Université Lyon 1, 2 Av. Albert Einstein, 69626, Villeurbanne Cedex, France
| | - Sam P de Visser
- The Manchester Institute of Biotechnology and Department of, Chemical Engineering and Analytical Science, The University of, Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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20
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Davethu PA, de Visser SP. CO2 Reduction on an Iron-Porphyrin Center: A Computational Study. J Phys Chem A 2019; 123:6527-6535. [DOI: 10.1021/acs.jpca.9b05102] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Paul A. Davethu
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, the University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sam P. de Visser
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, the University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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21
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Benedek Z, Papp M, Oláh J, Szilvási T. Exploring Hydrogen Evolution Accompanying Nitrogen Reduction on Biomimetic Nitrogenase Analogs: Can Fe-N xH yIntermediates Be Active Under Turnover Conditions? Inorg Chem 2019; 58:7969-7977. [PMID: 31125218 DOI: 10.1021/acs.inorgchem.9b00719] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Nitrogen reduction reaction (N2RR) carried out on biomimetic catalytic systems is considered to be a promising alternative for the traditional Haber-Bosch ammonia synthesis. Unfortunately, the selectivity of the currently known biomimetic catalysts is poor, as they also catalyze the unproductive hydrogen evolution reaction (HER). In the present computational study, we examine the HER activity of early N2RR intermediates in EP3 (E = B, Si) ligated single-site biomimetic iron complexes by calculating and comparing the activation Gibbs free energies of HER and N2RR elementary steps. We find that, in contrast to previous suggestions, early N2RR intermediates are not likely sources of HER under turnover conditions, as the barriers of the competing N2RR steps are significantly lower. Consequently, future research should focus on preventing other potential HER mechanisms, e.g., hydride formation, rather than accelerating the consumption of early N2RR intermediates as proposed earlier to design more efficient biomimetic catalysts.
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Affiliation(s)
- Zsolt Benedek
- Department of Inorganic and Analytical Chemistry , Budapest University of Technology and Economics , Szent Gellért tér 4 , 1111 Budapest , Hungary
| | - Marcell Papp
- Department of Inorganic and Analytical Chemistry , Budapest University of Technology and Economics , Szent Gellért tér 4 , 1111 Budapest , Hungary
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry , Budapest University of Technology and Economics , Szent Gellért tér 4 , 1111 Budapest , Hungary
| | - Tibor Szilvási
- Department of Chemical and Biological Engineering , University of Wisconsin-Madison , 1415 Engineering Drive , Madison , Wisconsin 53706 , United States
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22
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Song L, Liu P, Jiang W, Guo Q, Zhang C, Basit A, Li Y, Li J. α-Lys 424 Participates in Insertion of FeMoco to MoFe Protein and Maintains Nitrogenase Activity in Klebsiella oxytoca M5al. Front Microbiol 2019; 10:802. [PMID: 31057512 PMCID: PMC6477116 DOI: 10.3389/fmicb.2019.00802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 03/28/2019] [Indexed: 11/13/2022] Open
Abstract
Our previous investigation of substrates reduction catalyzed by nitrogenase suggested that α-Ile423 of MoFe protein possibly functions as an electron transfer gate to Mo site of active center-"FeMoco". Amino acid residue α-Lys424 connects directly to α-Ile423, and they are located in the same α-helix (α423-431). In the present study, function of α-Lys424 was investigated by replacing it with Arg (alkaline, like Lys), Gln (neutral), Glu (acidic), and Ala (neutral) through site-directed mutagenesis and homologous recombination. The mutants were, respectively, termed 424R, 424Q, 424E, and 424A. Studies of diazotrophic cell growth, cytological, and enzymatic properties indicated that none of the substitutions altered the secondary structure of MoFe protein, or normal expression of nifA, nifL, and nifD. Substitution of alkaline amino acid (i.e., 424R) maintained acetylene (C2H2) and proton (H+) reduction activities at normal levels similar to that of wild-type (WT), because its FeMoco content did not reduce. In contrast, substitution of acidic or neutral amino acid (i.e., 424Q, 424E, 424A) impaired the catalytic activity of nitrogenase to varying degrees. Combination of MoFe protein structural simulation and the results of a series of experiments, the function of α-Lys424 in ensuring insertion of FeMoco to MoFe protein was further confirmed, and the contribution of α-Lys424 in maintaining low potential of the microenvironment causing efficient catalytic activity of nitrogenase was demonstrated.
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Affiliation(s)
- Lina Song
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Pengxi Liu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Wei Jiang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Qingjuan Guo
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Chunxi Zhang
- Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Abdul Basit
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Ying Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Jilun Li
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
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23
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Pickl M, Kurakin S, Cantú Reinhard FG, Schmid P, Pöcheim A, Winkler CK, Kroutil W, de Visser SP, Faber K. Mechanistic Studies of Fatty Acid Activation by CYP152 Peroxygenases Reveal Unexpected Desaturase Activity. ACS Catal 2019; 9:565-577. [PMID: 30637174 PMCID: PMC6323616 DOI: 10.1021/acscatal.8b03733] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/04/2018] [Indexed: 02/05/2023]
Abstract
![]()
The
majority of cytochrome P450 enzymes (CYPs) predominantly operate
as monooxygenases, but recently a class of P450 enzymes was discovered,
that can act as peroxygenases (CYP152). These enzymes convert fatty
acids through oxidative decarboxylation, yielding terminal alkenes,
and through α- and β-hydroxylation to yield hydroxy-fatty
acids. Bioderived olefins may serve as biofuels, and hence understanding
the mechanism and substrate scope of this class of enzymes is important.
In this work, we report on the substrate scope and catalytic promiscuity
of CYP OleTJE and two of its orthologues from the CYP152
family, utilizing α-monosubstituted branched carboxylic acids.
We identify α,β-desaturation as an unexpected dominant
pathway for CYP OleTJE with 2-methylbutyric acid. To rationalize
product distributions arising from α/β-hydroxylation,
oxidative decarboxylation, and desaturation depending on the substrate’s
structure and binding pattern, a computational study was performed
based on an active site complex of CYP OleTJE containing
the heme cofactor in the substrate binding pocket and 2-methylbutyric
acid as substrate. It is shown that substrate positioning determines
the accessibility of the oxidizing species (Compound I) to the substrate
and hence the regio- and chemoselectivity of the reaction. Furthermore,
the results show that, for 2-methylbutyric acid, α,β-desaturation
is favorable because of a rate-determining α-hydrogen atom abstraction,
which cannot proceed to decarboxylation. Moreover, substrate hydroxylation
is energetically impeded due to the tight shape and size of the substrate
binding pocket.
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Affiliation(s)
- Mathias Pickl
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - Sara Kurakin
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - Fabián G. Cantú Reinhard
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Philipp Schmid
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - Alexander Pöcheim
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - Christoph K. Winkler
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Petersgasse 14, A-8010 Graz, Austria
| | - Wolfgang Kroutil
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - Sam P. de Visser
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Kurt Faber
- Department of Chemistry, Organic & Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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24
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Timmins A, Fowler NJ, Warwicker J, Straganz GD, de Visser SP. Does Substrate Positioning Affect the Selectivity and Reactivity in the Hectochlorin Biosynthesis Halogenase? Front Chem 2018; 6:513. [PMID: 30425979 PMCID: PMC6218459 DOI: 10.3389/fchem.2018.00513] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 10/04/2018] [Indexed: 12/17/2022] Open
Abstract
In this work we present the first computational study on the hectochlorin biosynthesis enzyme HctB, which is a unique three-domain halogenase that activates non-amino acid moieties tethered to an acyl-carrier, and as such may have biotechnological relevance beyond other halogenases. We use a combination of small cluster models and full enzyme structures calculated with quantum mechanics/molecular mechanics methods. Our work reveals that the reaction is initiated with a rate-determining hydrogen atom abstraction from substrate by an iron (IV)-oxo species, which creates an iron (III)-hydroxo intermediate. In a subsequent step the reaction can bifurcate to either halogenation or hydroxylation of substrate, but substrate binding and positioning drives the reaction to optimal substrate halogenation. Furthermore, several key residues in the protein have been identified for their involvement in charge-dipole interactions and induced electric field effects. In particular, two charged second coordination sphere amino acid residues (Glu223 and Arg245) appear to influence the charge density on the Cl ligand and push the mechanism toward halogenation. Our studies, therefore, conclude that nonheme iron halogenases have a chemical structure that induces an electric field on the active site that affects the halide and iron charge distributions and enable efficient halogenation. As such, HctB is intricately designed for a substrate halogenation and operates distinctly different from other nonheme iron halogenases.
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Affiliation(s)
- Amy Timmins
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
| | - Nicholas J. Fowler
- The Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Jim Warwicker
- The Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, United Kingdom
| | - Grit D. Straganz
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
- Institute of Molecular Biosciences, Graz University, Graz, Austria
| | - Sam P. de Visser
- The Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, University of Manchester, Manchester, United Kingdom
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25
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A Comparative Review on the Catalytic Mechanism of Nonheme Iron Hydroxylases and Halogenases. Catalysts 2018. [DOI: 10.3390/catal8080314] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Enzymatic halogenation and haloperoxidation are unusual processes in biology; however, a range of halogenases and haloperoxidases exist that are able to transfer an aliphatic or aromatic C–H bond into C–Cl/C–Br. Haloperoxidases utilize hydrogen peroxide, and in a reaction with halides (Cl−/Br−), they react to form hypohalides (OCl−/OBr−) that subsequently react with substrate by halide transfer. There are three types of haloperoxidases, namely the iron-heme, nonheme vanadium, and flavin-dependent haloperoxidases that are reviewed here. In addition, there are the nonheme iron halogenases that show structural and functional similarity to the nonheme iron hydroxylases and form an iron(IV)-oxo active species from a reaction of molecular oxygen with α-ketoglutarate on an iron(II) center. They subsequently transfer a halide (Cl−/Br−) to an aliphatic C–H bond. We review the mechanism and function of nonheme iron halogenases and hydroxylases and show recent computational modelling studies of our group on the hectochlorin biosynthesis enzyme and prolyl-4-hydroxylase as examples of nonheme iron halogenases and hydroxylases. These studies have established the catalytic mechanism of these enzymes and show the importance of substrate and oxidant positioning on the stereo-, chemo- and regioselectivity of the reaction that takes place.
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26
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Postils V, Saint-André M, Timmins A, Li XX, Wang Y, Luis JM, Solà M, de Visser SP. Quantum Mechanics/Molecular Mechanics Studies on the Relative Reactivities of Compound I and II in Cytochrome P450 Enzymes. Int J Mol Sci 2018; 19:E1974. [PMID: 29986417 PMCID: PMC6073316 DOI: 10.3390/ijms19071974] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/28/2018] [Accepted: 07/02/2018] [Indexed: 02/03/2023] Open
Abstract
The cytochromes P450 are drug metabolizing enzymes in the body that typically react with substrates through a monoxygenation reaction. During the catalytic cycle two reduction and protonation steps generate a high-valent iron (IV)-oxo heme cation radical species called Compound I. However, with sufficient reduction equivalents present, the catalytic cycle should be able to continue to the reduced species of Compound I, called Compound II, rather than a reaction of Compound I with substrate. In particular, since electron transfer is usually on faster timescales than atom transfer, we considered this process feasible and decided to investigate the reaction computationally. In this work we present a computational study using density functional theory methods on active site model complexes alongside quantum mechanics/molecular mechanics calculations on full enzyme structures of cytochrome P450 enzymes. Specifically, we focus on the relative reactivity of Compound I and II with a model substrate for O⁻H bond activation. We show that generally the barrier heights for hydrogen atom abstraction are higher in energy for Compound II than Compound I for O⁻H bond activation. Nevertheless, for the activation of such bonds, Compound II should still be an active oxidant under enzymatic conditions. As such, our computational modelling predicts that under high-reduction environments the cytochromes P450 can react with substrates via Compound II but the rates will be much slower.
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Affiliation(s)
- Verònica Postils
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany i Farnés, 69, 17003 Girona, Catalonia, Spain.
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Maud Saint-André
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Amy Timmins
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Xiao-Xi Li
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Suzhou Research Institute of LICP, Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences, Lanzhou 730000, China.
| | - Yong Wang
- State Key Laboratory for Oxo Synthesis and Selective Oxidation, Suzhou Research Institute of LICP, Lanzhou Institute of Chemical Physics (LICP), Chinese Academy of Sciences, Lanzhou 730000, China.
| | - Josep M Luis
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany i Farnés, 69, 17003 Girona, Catalonia, Spain.
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Maria Aurèlia Capmany i Farnés, 69, 17003 Girona, Catalonia, Spain.
| | - Sam P de Visser
- Manchester Institute of Biotechnology, School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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27
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Benedek Z, Papp M, Oláh J, Szilvási T. Identifying the Rate-Limiting Elementary Steps of Nitrogen Fixation with Single-Site Fe Model Complexes. Inorg Chem 2018; 57:8499-8508. [DOI: 10.1021/acs.inorgchem.8b01183] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zsolt Benedek
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Marcell Papp
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Julianna Oláh
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Tibor Szilvási
- Department of Chemical and Biological Engineering, University of Wisconsin—Madison, 1415 Engineering Drive, Madison, Wisconsin 53706, United States
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28
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de Visser SP. Mechanistic Insight on the Activity and Substrate Selectivity of Nonheme Iron Dioxygenases. CHEM REC 2018; 18:1501-1516. [PMID: 29878456 DOI: 10.1002/tcr.201800033] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 05/18/2018] [Indexed: 01/05/2023]
Abstract
Nonheme iron dioxygenases catalyze vital reactions for human health particularly related to aging processes. They are involved in the biosynthesis of amino acids, but also the biodegradation of toxic compounds. Typically they react with their substrate(s) through oxygen atom transfer, although often with the assistance of a co-substrate like α-ketoglutarate that is converted to succinate and CO2 . Many reaction processes catalyzed by the nonheme iron dioxygenases are stereoselective or regiospecific and hence understanding the mechanism and protein involvement in the selectivity is important for the design of biotechnological applications of these enzymes. To this end, I will review recent work of our group on nonheme iron dioxygenases and include background information on their general structure and catalytic cycle. Examples of stereoselective and regiospecific reaction mechanisms we elucidated are for the AlkB repair enzyme, prolyl-4-hydroxylase and the ergothioneine biosynthesis enzyme. Finally, I cover an example where we bioengineered S-p-hydroxymandelate synthase into the R-p-hydroxymandelate synthase.
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Affiliation(s)
- Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
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29
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Lu JB, Ma XL, Wang JQ, Liu JC, Xiao H, Li J. Efficient Nitrogen Fixation via a Redox-Flexible Single-Iron Site with Reverse-Dative Iron → Boron σ Bonding. J Phys Chem A 2018; 122:4530-4537. [PMID: 29648830 DOI: 10.1021/acs.jpca.8b02089] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Model systems of the FeMo cofactor of nitrogenase have been explored extensively in catalysis to gain insights into their ability for nitrogen fixation that is of vital importance to the human society. Here we investigate the trigonal pyramidal borane-ligand Fe complex by first-principles calculations, and find that the variation of oxidation state of Fe along the reaction path correlates with that of the reverse-dative Fe → B bonding. The redox-flexibility of the reverse-dative Fe → B bonding helps to provide an electron reservoir that buffers and stabilizes the evolution of Fe oxidation state, which is essential for forming the key intermediates of N2 activation. Our work provides insights for understanding and optimizing homogeneous and surface single-atom catalysts with reverse-dative donating ligands for efficient dinitrogen fixation. The extension of this kind of molecular catalytic active center to heterogeneous catalysts with surface single-clusters is also discussed.
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Affiliation(s)
- Jun-Bo Lu
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education , Tsinghua University , Beijing 100084 , China
| | - Xue-Lu Ma
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education , Tsinghua University , Beijing 100084 , China
| | - Jia-Qi Wang
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education , Tsinghua University , Beijing 100084 , China
| | - Jin-Cheng Liu
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education , Tsinghua University , Beijing 100084 , China
| | - Hai Xiao
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education , Tsinghua University , Beijing 100084 , China
| | - Jun Li
- Department of Chemistry and Key Laboratory of Organic Optoelectronics & Molecular Engineering of the Ministry of Education , Tsinghua University , Beijing 100084 , China.,Institute for Interfacial Catalysis and Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , P.O. Box 999 , Richland , Washington 99352 , United States
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30
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Mukherjee G, Lee CWZ, Nag SS, Alili A, Cantú Reinhard FG, Kumar D, Sastri CV, de Visser SP. Dramatic rate-enhancement of oxygen atom transfer by an iron(iv)-oxo species by equatorial ligand field perturbations. Dalton Trans 2018; 47:14945-14957. [DOI: 10.1039/c8dt02142b] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The reactivity and characterization of a novel iron(iv)-oxo species is reported that gives enhanced reactivity as a result of second-coordination sphere perturbations of the ligand system.
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Affiliation(s)
- Gourab Mukherjee
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
| | - Calvin W. Z. Lee
- The Manchester Institute of Biotechnology and the School of Chemical Engineering and Analytical Science
- The University of Manchester
- Manchester M1 7DN
- UK
| | | | - Aligulu Alili
- The Manchester Institute of Biotechnology and the School of Chemical Engineering and Analytical Science
- The University of Manchester
- Manchester M1 7DN
- UK
| | - Fabián G. Cantú Reinhard
- The Manchester Institute of Biotechnology and the School of Chemical Engineering and Analytical Science
- The University of Manchester
- Manchester M1 7DN
- UK
| | - Devesh Kumar
- Department of Applied Physics
- School for Physical Sciences
- Babasaheb Bhimrao Ambedkar University
- Lucknow 226025
- India
| | | | - Sam P. de Visser
- The Manchester Institute of Biotechnology and the School of Chemical Engineering and Analytical Science
- The University of Manchester
- Manchester M1 7DN
- UK
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Kaczmarek MA, Malhotra A, Balan GA, Timmins A, de Visser SP. Nitrogen Reduction to Ammonia on a Biomimetic Mononuclear Iron Centre: Insights into the Nitrogenase Enzyme. Chemistry 2017; 24:5293-5302. [PMID: 29165842 PMCID: PMC5915742 DOI: 10.1002/chem.201704688] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Indexed: 11/05/2022]
Abstract
Nitrogenases catalyse nitrogen fixation to ammonia on a multinuclear Fe‐Mo centre, but their mechanism and particularly the order of proton and electron transfer processes that happen during the catalytic cycle is still unresolved. Recently, a unique biomimetic mononuclear iron model was developed using tris(phosphine)borate (TPB) ligands that was shown to convert N2 into NH3. Herein, we present a computational study on the [(TPB)FeN2]− complex and describe its conversion into ammonia through the addition of electrons and protons. In particular, we tested the consecutive proton transfer on only the distal nitrogen atom or alternated protonation of the distal/proximal nitrogen. It is found that the lowest energy pathway is consecutive addition of three protons to the same site, which forms ammonia and an iron‐nitrido complex. In addition, the proton transfer step of complexes with the metal in various oxidation and spin states were tested and show that the pKa values of biomimetic mononuclear nitrogenase intermediates vary little with iron oxidation states. As such, the model gives several possible NH3 formation pathways depending on the order of electron/proton transfer, and all should be physically accessible in the natural system. These results may have implications for enzymatic nitrogenases and give insight into the catalytic properties of mononuclear iron centres.
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Affiliation(s)
- Monika A Kaczmarek
- Manchester Institute of Biotechnology and School of Chemical, Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemistry, University of Warsaw, Ludwika Pasteura 1, 02-093, Warsaw, Poland
| | - Abheek Malhotra
- Manchester Institute of Biotechnology and School of Chemical, Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - G Alex Balan
- Manchester Institute of Biotechnology and School of Chemical, Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Amy Timmins
- Manchester Institute of Biotechnology and School of Chemical, Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical, Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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