1
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Kass D, Yao S, Krause KB, Corona T, Richter L, Braun T, Mebs S, Haumann M, Dau H, Lohmiller T, Limberg C, Drieß M, Ray K. Spectroscopic Properties of a Biologically Relevant [Fe 2 (μ-O) 2 ] Diamond Core Motif with a Short Iron-Iron Distance. Angew Chem Int Ed Engl 2023; 62:e202209437. [PMID: 36541062 DOI: 10.1002/anie.202209437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 12/05/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Diiron cofactors in enzymes perform diverse challenging transformations. The structures of high valent intermediates (Q in methane monooxygenase and X in ribonucleotide reductase) are debated since Fe-Fe distances of 2.5-3.4 Å were attributed to "open" or "closed" cores with bridging or terminal oxido groups. We report the crystallographic and spectroscopic characterization of a FeIII 2 (μ-O)2 complex (2) with tetrahedral (4C) centres and short Fe-Fe distance (2.52 Å), persisting in organic solutions. 2 shows a large Fe K-pre-edge intensity, which is caused by the pronounced asymmetry at the TD FeIII centres due to the short Fe-μ-O bonds. A ≈2.5 Å Fe-Fe distance is unlikely for six-coordinate sites in Q or X, but for a Fe2 (μ-O)2 core containing four-coordinate (or by possible extension five-coordinate) iron centres there may be enough flexibility to accommodate a particularly short Fe-Fe separation with intense pre-edge transition. This finding may broaden the scope of models considered for the structure of high-valent diiron intermediates formed upon O2 activation in biology.
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Affiliation(s)
- Dustin Kass
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Shenglai Yao
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, 10623, Berlin, Germany
| | - Konstantin B Krause
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Teresa Corona
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Liza Richter
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Thomas Braun
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Stefan Mebs
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Michael Haumann
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Holger Dau
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Thomas Lohmiller
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany.,EPR4Energy Joint Lab, Department Spins in Energy Conversion and Quantum Information Science, Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Straße 16, 12489, Berlin, Germany
| | - Christian Limberg
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Matthias Drieß
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, 10623, Berlin, Germany
| | - Kallol Ray
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
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2
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Liu J, Wu P, Yan S, Li Y, Cao Z, Wang B. Spin-Regulated Inner-Sphere Electron Transfer Enables Efficient O—O Bond Activation in Nonheme Diiron Monooxygenase MIOX. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jia Liu
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Peng Wu
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Shengheng Yan
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Yuanyuan Li
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China
| | - Zexing Cao
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
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3
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Schulz CE, Castillo RG, Pantazis DA, DeBeer S, Neese F. Structure-Spectroscopy Correlations for Intermediate Q of Soluble Methane Monooxygenase: Insights from QM/MM Calculations. J Am Chem Soc 2021; 143:6560-6577. [PMID: 33884874 PMCID: PMC8154522 DOI: 10.1021/jacs.1c01180] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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The determination
of the diiron core intermediate structures involved
in the catalytic cycle of soluble methane monooxygenase (sMMO), the
enzyme that selectively catalyzes the conversion of methane to methanol,
has been a subject of intense interest within the bioinorganic scientific
community. Particularly, the specific geometry and electronic structure
of the intermediate that precedes methane binding, known as intermediate
Q (or MMOHQ), has been debated for over 30 years. Some
reported studies support a bis-μ-oxo-bridged Fe(IV)2O2 closed-core conformation Fe(IV)2O2 core, whereas others favor an open-core geometry, with a longer
Fe–Fe distance. The lack of consensus calls for a thorough
re-examination and reinterpretation of the spectroscopic data available
on the MMOHQ intermediate. Herein, we report extensive
simulations based on a hybrid quantum mechanics/molecular mechanics
approach (QM/MM) approach that takes into account the complete enzyme
to explore possible conformations for intermediates MMOHox and MMOHQ of the sMMOH catalytic cycle. High-level quantum
chemical approaches are used to correlate specific structural motifs
with geometric parameters for comparison with crystallographic and
EXAFS data, as well as with spectroscopic data from Mössbauer
spectroscopy, Fe K-edge high-energy resolution X-ray absorption spectroscopy
(HERFD XAS), and resonance Raman 16O–18O difference spectroscopy. The results provide strong support for
an open-core-type configuration in MMOHQ, with the most
likely topology involving mono-oxo-bridged Fe ions and alternate terminal
Fe-oxo and Fe-hydroxo groups that interact via intramolecular hydrogen
bonding. The implications of an open-core intermediate Q on the reaction
mechanism of sMMO are discussed.
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Affiliation(s)
- Christine E Schulz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Rebeca G Castillo
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A Pantazis
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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4
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Bím D, Chalupský J, Culka M, Solomon EI, Rulíšek L, Srnec M. Proton-Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ 9-Desaturase. J Am Chem Soc 2020; 142:10412-10423. [PMID: 32406236 DOI: 10.1021/jacs.0c01786] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A full understanding of the catalytic action of non-heme iron (NHFe) and non-heme diiron (NHFe2) enzymes is still beyond the grasp of contemporary computational and experimental techniques. Many of these enzymes exhibit fascinating chemo-, regio-, and stereoselectivity, in spite of employing highly reactive intermediates which are necessary for activations of most stable chemical bonds. Herein, we study in detail one intriguing representative of the NHFe2 family of enzymes: soluble Δ9 desaturase (Δ9D), which desaturates rather than performing the thermodynamically favorable hydroxylation of substrate. Its catalytic mechanism has been explored in great detail by using QM(DFT)/MM and multireference wave function methods. Starting from the spectroscopically observed 1,2-μ-peroxo diferric P intermediate, the proton-electron uptake by P is the favored mechanism for catalytic activation, since it allows a significant reduction of the barrier of the initial (and rate-determining) H-atom abstraction from the stearoyl substrate as compared to the "proton-only activated" pathway. Also, we ruled out that a Q-like intermediate (high-valent diamond-core bis-μ-oxo-[FeIV]2 unit) is involved in the reaction mechanism. Our mechanistic picture is consistent with the experimental data available for Δ9D and satisfies fairly stringent conditions required by Nature: the chemo-, stereo-, and regioselectivity of the desaturation of stearic acid. Finally, the mechanisms evaluated are placed into a broader context of NHFe2 chemistry, provided by an amino acid sequence analysis through the families of the NHFe2 enzymes. Our study thus represents an important contribution toward understanding the catalytic action of the NHFe2 enzymes and may inspire further work in NHFe(2) biomimetic chemistry.
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Affiliation(s)
- Daniel Bím
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, Prague 8 182 23, Czech Republic.,Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Jakub Chalupský
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Edward I Solomon
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305-5080, United States
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, Prague 8 182 23, Czech Republic
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5
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Pokutsa A, Tkach S, Zaborovsky A, Bloniarz P, Paczeŝniak T, Muzart J. Sustainable Oxidation of Cyclohexane and Toluene in the Presence of Affordable Catalysts: Impact of the Tandem of Promoter/Oxidant on Process Efficiency. ACS Omega 2020; 5:7613-7626. [PMID: 32280905 PMCID: PMC7144162 DOI: 10.1021/acsomega.0c00447] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/17/2020] [Indexed: 06/11/2023]
Abstract
The oxygenation of cyclohexane and toluene by O2 and H2O2 catalyzed by VO(acac)2 and Co(acac)2 was studied at 40-100 °C and 1-10 atm. Upon such conditions, the process can be remarkably (30× times) enhanced by the minute (6-15 mM) additives of oxalic acid (OxalH) or N-hydroxyphthalimide (NHPI). The revealed effect of OxalH on H2O2-piloted oxidation is closely associated with the nature of the catalyst cation and boosted by VO(acac)2. Whereas the effectiveness of Co(acac)2-based systems was curbed by the addition of OxalH and remained much below the one displayed with the previous system. The observed conspicuous difference in activity was attributed to the substantially higher solubility of in situ formed VO(IV)oxalate compared to that of Co(II)oxalate. The exploration of H2O2 for the NHPI-promoted process leads to the decisively lower (5-7 times) yield in comparison to the O2-driven reaction. Similarly, for the O2-operated protocol, the yield cannot be improved by addition of OxalH either to VO(acac)2 + NHPI or to Co(acac)2 + NHPI mixture. By contrast, the combination of NHPI with VO(acac)2 or Co(acac)2 and particularly with the above two mixtures in O2-piloted oxidation enhances the yield of the aimed products 3-6 times regardless of the substrate used. The revealed significant synergetic effect of the cobalt + vanadyl bicomponent catalyst was due to the participation of each of its moiety in the different stages of the process mechanism. Only benzyl alcohol and benzaldehyde were identified in VO(acac)2- or Co(acac)2-catalyzed toluene oxidation, while cyclohexane oxidation yields cyclohexylhydroperoxide in line with cyclohexanol and cyclohexanone. The putative mechanism of investigated processes is highlighted and discussed.
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Affiliation(s)
- Alexander Pokutsa
- Department
of Physical Chemistry of Fuel Fossils NAS of Ukraine, Institute of Physical Organic Chemistry and Chemistry of Coal NAS
of Ukraine, Naukova Str.,
3A, Lviv 79060, Ukraine
| | - Sergiy Tkach
- Yuriya-Farm
Corp., Narodnogo Opolchennya
Str., 19, Kyiv 03151, Ukraine
| | - Andriy Zaborovsky
- Department
of Physical Chemistry of Fuel Fossils NAS of Ukraine, Institute of Physical Organic Chemistry and Chemistry of Coal NAS
of Ukraine, Naukova Str.,
3A, Lviv 79060, Ukraine
| | - Pawel Bloniarz
- Chemistry
Department, Rzeszow University of Technology, P.O. Box 85, Rzeszow 35-959, Poland
| | - Tomasz Paczeŝniak
- Chemistry
Department, Rzeszow University of Technology, P.O. Box 85, Rzeszow 35-959, Poland
| | - Jacques Muzart
- CNRS—Université
de Reims Champagne-Ardenne, Institut de Chimie Moléculaire
de Reims, UMR 7312, UFR des Sciences Exactes et Naturelles, BP 1039, Reims 51687, Cedex 2, France
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6
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Pokutsa A, Bloniarz P, Fliunt O, Kubaj Y, Zaborovskyi A, Paczeŝniak T. Sustainable oxidation of cyclohexane catalyzed by a VO(acac) 2-oxalic acid tandem: the electrochemical motive of the process efficiency. RSC Adv 2020; 10:10959-10971. [PMID: 35492932 PMCID: PMC9050442 DOI: 10.1039/d0ra00495b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/27/2020] [Indexed: 11/21/2022] Open
Abstract
Cyclohexane oxidation by H2O2 to cyclohexanol, cyclohexanone, and cyclohexylhydroperoxide under mild (40 °C, 1 atm) conditions is significantly enhanced in the system composed of VO(acac)2 (starting catalyst) and small additives of oxalic acid (process promoter). In corroboration of this, several times higher yield of the desired products was obtained compared to that obtained in the acid-free process. The revealed advantage was addressed to elevate the electrical conductance G (or vice versa, decreasing the resistance, 1/G) of the reaction medium. On the other hand, the content of oxalic acid (20–30 mM) was compulsory to optimize the process parameters. The last value of concentration affords, besides the lowest 1/G, the utmost impact on pH, redox potential, and current–voltage relationships. Exceeding this level leads to an increase in 1/G of the reaction solution, ceases the impact on pH, ORP, and CV profiles, and is detrimental for the product yield. The putative mechanism of the revealed effects has been envisaged. Cyclohexane oxidation by H2O2 to cyclohexanol, cyclohexanone, and cyclohexylhydroperoxide under mild (40 °C, 1 atm) conditions is significantly enhanced in the system composed of VO(acac)2 (starting catalyst) and small additives of oxalic acid (process promoter).![]()
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Affiliation(s)
- Alexander Pokutsa
- Department of Physical Chemistry of Fossil Fuels, Institute of Physical Organic Chemistry and Chemistry of Coal NAS of Ukraine Naukova Str., 3A Lviv 79060 Ukraine +38 032 263 51 74 +38 032 263 51 74
| | - Pawel Bloniarz
- Rzeszow University of Technology P. O. Box 85 35-959 Rzeszow Poland
| | - Orest Fliunt
- Ivan Franko National University of Lviv, Faculty of Electronics and Computer Technologies Dragomanov Str., 50 Lviv 79005 Ukraine
| | - Yuliya Kubaj
- Department of Physical Chemistry of Fossil Fuels, Institute of Physical Organic Chemistry and Chemistry of Coal NAS of Ukraine Naukova Str., 3A Lviv 79060 Ukraine +38 032 263 51 74 +38 032 263 51 74
| | - Andriy Zaborovskyi
- Department of Physical Chemistry of Fossil Fuels, Institute of Physical Organic Chemistry and Chemistry of Coal NAS of Ukraine Naukova Str., 3A Lviv 79060 Ukraine +38 032 263 51 74 +38 032 263 51 74
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7
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Pietra F. A New Route for Dioxygen Activation Uncovered from Quantum Mechanics Investigations of X‐Ray‐Diffraction‐Captured Intermediates of the Ferroxidase Reaction of Ferritins from Gram‐Negative Bacteria. Adv Theory Simul 2020. [DOI: 10.1002/adts.201900253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Francesco Pietra
- Accademia Lucchese di Scienze Lettere e ArtiClasse di Scienze, Palazzo Pretorio Via Vittorio Veneto 1 I‐55100 Lucca Italy
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8
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Wang J, Ma Y, Wang X, Zhang Y, Tan H, Li X, Chen G. Theoretical study on the catalytic mechanism of human deoxyhypusine hydroxylase. Phys Chem Chem Phys 2020; 22:22736-22745. [DOI: 10.1039/d0cp03598j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Deoxyhypusine hydroxylase is a critical enzyme for hypusination of eukaryotic translation initiation factor 5A.
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Affiliation(s)
- Junkai Wang
- Key Laboratory of Theoretical and Computational Photochemistry
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Yan Ma
- Key Laboratory of Theoretical and Computational Photochemistry
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Xixi Wang
- Key Laboratory of Theoretical and Computational Photochemistry
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Ying Zhang
- Key Laboratory of Theoretical and Computational Photochemistry
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Hongwei Tan
- Key Laboratory of Theoretical and Computational Photochemistry
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Xichen Li
- Key Laboratory of Theoretical and Computational Photochemistry
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
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9
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Abstract
Aerobic life is possible because the molecular structure of oxygen (O2) makes direct reaction with most organic materials at ambient temperatures an exceptionally slow process. Of course, these reactions are inherently very favorable, and they occur rapidly with the release of a great deal of energy at high temperature. Nature has been able to tap this sequestered reservoir of energy with great spatial and temporal selectivity at ambient temperatures through the evolution of oxidase and oxygenase enzymes. One mechanism used by these enzymes for O2 activation has been studied in detail for the soluble form of the enzyme methane monooxygenase. These studies have revealed the step-by-step process of O2 activation and insertion into the ultimately stable C-H bond of methane. Additionally, an elegant regulatory mechanism has been defined that enlists size selection and quantum tunneling to allow methane oxidation to occur specifically in the presence of more easily oxidized substrates.
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Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA; , ,
| | - Jason C Jones
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA; , ,
| | - John D Lipscomb
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA; , ,
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10
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Xu K, Hirao H. Revisiting the catalytic mechanism of Mo-Cu carbon monoxide dehydrogenase using QM/MM and DFT calculations. Phys Chem Chem Phys 2018; 20:18938-18948. [PMID: 29744484 DOI: 10.1039/c8cp00858b] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Previous density functional theory (DFT) studies have shown that the release of the produced carbon dioxide (CO2) from an active-site cluster is a thermodynamically or kinetically difficult step in the enzymatic carbon monoxide (CO) oxidation catalyzed by Mo-Cu carbon monoxide dehydrogenase (Mo-Cu CODH). To better understand the effect of the protein environment on this difficult CO2 release step as well as other reaction steps, we applied hybrid quantum mechanics and molecular mechanics (QM/MM) calculations to the Mo-Cu CODH enzyme. The results show that in the first step, the equatorial Mo[double bond, length as m-dash]O group in the active-site cluster attacks the nearby CO molecule bound to the Cu site. Afterward, a stable thiocarbonate intermediate is formed in which the CO2 molecule is embedded and the copper-S(μ-sulfido) bond is broken. A free CO2 molecule, i.e., the final product, is then released from the active-site cluster, not directly from the thiocarbonate intermediate but via a previously formed intermediate that also contains CO2 but retains the Cu-S(μ-sulfido) bond. In contrast to the previous DFT results, the calculated barrier for this process was low in our QM/MM calculations. An additional QM/MM analysis of the barrier height showed that the effect of the protein environment on this barrier lowering is not very large. We found that the reason for the low barrier obtained by QM/MM is that the barrier for CO2 release is already not high at the DFT level. These results allow us to conclude that the CO oxidation reaction passes through the formation of a thiocarbonate intermediate, and that the subsequent CO2 release is kinetically not difficult. Nevertheless, the protein environment has an important role to play in making the latter process thermodynamically favored. No low-barrier pathway for the product release could be obtained for the reaction of n-butylisocyanide, which is consistent with the experimental fact that n-butylisocyanide inhibits Mo-Cu CODH.
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Affiliation(s)
- Kai Xu
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, China.
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11
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Abstract
A growing subset of metalloenzymes activates dioxygen with nonheme diiron active sites to effect substrate oxidations that range from the hydroxylation of methane and the desaturation of fatty acids to the deformylation of fatty aldehydes to produce alkanes and the six-electron oxidation of aminoarenes to nitroarenes in the biosynthesis of antibiotics. A common feature of their reaction mechanisms is the formation of O2 adducts that evolve into more reactive derivatives such as diiron(II,III)-superoxo, diiron(III)-peroxo, diiron(III,IV)-oxo, and diiron(IV)-oxo species, which carry out particular substrate oxidation tasks. In this review, we survey the various enzymes belonging to this unique subset and the mechanisms by which substrate oxidation is carried out. We examine the nature of the reactive intermediates, as revealed by X-ray crystallography and the application of various spectroscopic methods and their associated reactivity. We also discuss the structural and electronic properties of the model complexes that have been found to mimic salient aspects of these enzyme active sites. Much has been learned in the past 25 years, but key questions remain to be answered.
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Affiliation(s)
- Andrew J. Jasniewski
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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12
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Castillo RG, Banerjee R, Allpress CJ, Rohde GT, Bill E, Que L, Lipscomb JD, DeBeer S. High-Energy-Resolution Fluorescence-Detected X-ray Absorption of the Q Intermediate of Soluble Methane Monooxygenase. J Am Chem Soc 2017; 139:18024-18033. [PMID: 29136468 PMCID: PMC5729100 DOI: 10.1021/jacs.7b09560] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Kα high-energy-resolution fluorescence detected X-ray absorption spectroscopy (HERFD XAS) provides a powerful tool for overcoming the limitations of conventional XAS to identify the electronic structure and coordination environment of metalloprotein active sites. Herein, Fe Kα HERFD XAS is applied to the diiron active site of soluble methane monooxygenase (sMMO) and to a series of high-valent diiron model complexes, including diamond-core [FeIV2(μ-O)2(L)2](ClO4)4] (3) and open-core [(O═FeIV-O-FeIV(OH)(L)2](ClO4)3 (4) models (where, L = tris(3,5-dimethyl-4-methoxypyridyl-2-methyl)amine) (TPA*)). Pronounced differences in the HERFD XAS pre-edge energies and intensities are observed for the open versus closed Fe2O2 cores in the model compounds. These differences are reproduced by time-dependent density functional theory (TDDFT) calculations and allow for the pre-edge energies and intensity to be directly correlated with the local active site geometric and electronic structure. A comparison of the model complex HERFD XAS data to that of MMOHQ (the key intermediate in methane oxidation) is supportive of an open-core structure. Specifically, the large pre-edge area observed for MMOHQ may be rationalized by invoking an open-core structure with a terminal FeIV═O motif, though further modulations of the core structure due to the protein environment cannot be ruled out. The present study thus motivates the need for additional experimental and theoretical studies to unambiguously assess the active site conformation of MMOHQ.
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Affiliation(s)
- Rebeca G. Castillo
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34, D-45470 Mülheim an der Ruhr, Germany
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, 321 Church St. SE, Minneapolis, MN 55455
| | - Caleb J. Allpress
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455
| | - Gregory T. Rohde
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34, D-45470 Mülheim an der Ruhr, Germany
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, 321 Church St. SE, Minneapolis, MN 55455
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34, D-45470 Mülheim an der Ruhr, Germany
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13
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Abstract
Isotope effects of four broad and overlapping categories have been applied to the study of the mechanisms of chemical reaction and regulation of nonheme diiron cluster-containing oxygenases. The categories are: (a) mass properties that allow substrate-to-product conversions to be tracked, (b) atomic properties that allow specialized spectroscopies, (c) mass properties that impact primarily vibrational spectroscopies, and (d) bond dissociation energy shifts that permit dynamic isotope effect studies of many types. The application of these categories of isotope effects is illustrated using the soluble methane monooxygenase system and CmlI, which catalyzes the multistep arylamine to arylnitro conversion in the biosynthetic pathway for chloramphenicol.
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Affiliation(s)
| | - Anna J Komor
- University of Minnesota, Minneapolis, MN, United States
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15
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Martinie RJ, Blaesi EJ, Krebs C, Bollinger JM, Silakov A, Pollock CJ. Evidence for a Di-μ-oxo Diamond Core in the Mn(IV)/Fe(IV) Activation Intermediate of Ribonucleotide Reductase from Chlamydia trachomatis. J Am Chem Soc 2017; 139:1950-1957. [PMID: 28075562 DOI: 10.1021/jacs.6b11563] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
High-valent iron and manganese complexes effect some of the most challenging biochemical reactions known, including hydrocarbon and water oxidations associated with the global carbon cycle and oxygenic photosynthesis, respectively. Their extreme reactivity presents an impediment to structural characterization, but their biological importance and potential chemical utility have, nevertheless, motivated extensive efforts toward that end. Several such intermediates accumulate during activation of class I ribonucleotide reductase (RNR) β subunits, which self-assemble dimetal cofactors with stable one-electron oxidants that serve to initiate the enzyme's free-radical mechanism. In the class I-c β subunit from Chlamydia trachomatis, a heterodinuclear Mn(II)/Fe(II) complex reacts with dioxygen to form a Mn(IV)/Fe(IV) intermediate, which undergoes reduction of the iron site to produce the active Mn(IV)/Fe(III) cofactor. Herein, we assess the structure of the Mn(IV)/Fe(IV) activation intermediate using Fe- and Mn-edge extended X-ray absorption fine structure (EXAFS) analysis and multifrequency pulse electron paramagnetic resonance (EPR) spectroscopy. The EXAFS results reveal a metal-metal vector of 2.74-2.75 Å and an intense light-atom (C/N/O) scattering interaction 1.8 Å from the Fe. Pulse EPR data reveal an exchangeable deuterium hyperfine coupling of strength |T| = 0.7 MHz, but no stronger couplings. The results suggest that the intermediate possesses a di-μ-oxo diamond core structure with a terminal hydroxide ligand to the Mn(IV).
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Affiliation(s)
- Ryan J Martinie
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Elizabeth J Blaesi
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - J Martin Bollinger
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Alexey Silakov
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Christopher J Pollock
- Department of Chemistry and ‡Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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Rokob TA. Pathways for Arene Oxidation in Non-Heme Diiron Enzymes: Lessons from Computational Studies on Benzoyl Coenzyme A Epoxidase. J Am Chem Soc 2016; 138:14623-14638. [PMID: 27682344 DOI: 10.1021/jacs.6b06987] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oxygenation of aromatic rings using O2 is catalyzed by several non-heme carboxylate-bridged diiron enzymes. In order to provide a general mechanistic description for these reactions, computational studies were carried out at the ONIOM(B3LYP/BP86/Amber) level on the non-heme diiron enzyme benzoyl coenzyme A epoxidase, BoxB. The calculations revealed four possible pathways for attacking the aromatic ring: (a) electrophilic (2e-) attack by a bis(μ-oxo)-diiron(IV) species (Q pathway); (b) electrophilic (2e-) attack via the σ* orbital of a μ-η2:η2-peroxo-diiron(III) intermediate (Pσ* pathway); (c) radical (1e-) attack via the π*-orbital of a superoxo-diiron(II,III) species (Pπ* pathway); (d) radical (1e-) attack of a partially quenched bis(μ-oxo)-diiron(IV) intermediate (Q' pathway). The results allowed earlier work of de Visser on olefin epoxidation by diiron complexes and QM-cluster studies of Liao and Siegbahn on BoxB to be put into a broader perspective. Parallels with epoxidation using organic peracids were also examined. Specifically for the BoxB enzyme, the Q pathway was found to be the most preferred, but the corresponding bis(μ-oxo)-diiron(IV) species is significantly destabilized and not expected to be directly observable. Epoxidation via the Pσ* pathway represents an energetically somewhat higher lying alternative; possible strategies for experimental discrimination are discussed. The selectivity toward epoxidation is shown to stem from a combination of inherent electronic properties of the thioacyl substituent and enzymatic constraints. Possible implications of the results for toluene monooxygenases are considered as well.
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Affiliation(s)
- Tibor András Rokob
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences , Magyar Tudósok körútja 2, 1117 Budapest, Hungary
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Groenenboom MC, Keith JA. Explicitly Unraveling the Roles of Counterions, Solvent Molecules, and Electron Correlation in Solution Phase Reaction Pathways. J Phys Chem B 2016; 120:10797-10807. [DOI: 10.1021/acs.jpcb.6b07606] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mitchell C. Groenenboom
- Department
of Chemical and
Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - John A. Keith
- Department
of Chemical and
Petroleum Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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Trehoux A, Mahy J, Avenier F. A growing family of O2 activating dinuclear iron enzymes with key catalytic diiron(III)-peroxo intermediates: Biological systems and chemical models. Coord Chem Rev 2016; 322:142-58. [DOI: 10.1016/j.ccr.2016.05.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Jasniewski AJ, Engstrom LM, Vu VV, Park MH, Que L. X-ray absorption spectroscopic characterization of the diferric-peroxo intermediate of human deoxyhypusine hydroxylase in the presence of its substrate eIF5a. J Biol Inorg Chem 2016; 21:605-18. [PMID: 27380180 PMCID: PMC4990465 DOI: 10.1007/s00775-016-1373-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 06/16/2016] [Indexed: 11/29/2022]
Abstract
Human deoxyhypusine hydroxylase (hDOHH) is an enzyme that is involved in the critical post-translational modification of the eukaryotic translation initiation factor 5A (eIF5A). Following the conversion of a lysine residue on eIF5A to deoxyhypusine (Dhp) by deoxyhypusine synthase, hDOHH hydroxylates Dhp to yield the unusual amino acid residue hypusine (Hpu), a modification that is essential for eIF5A to promote peptide synthesis at the ribosome, among other functions. Purification of hDOHH overexpressed in E. coli affords enzyme that is blue in color, a feature that has been associated with the presence of a peroxo-bridged diiron(III) active site. To gain further insight into the nature of the diiron site and how it may change as hDOHH goes through the catalytic cycle, we have conducted X-ray absorption spectroscopic studies of hDOHH on five samples that represent different species along its reaction pathway. Structural analysis of each species has been carried out, starting with the reduced diferrous state, proceeding through its O2 adduct, and ending with a diferric decay product. Our results show that the Fe⋯Fe distances found for the five samples fall within a narrow range of 3.4-3.5 Å, suggesting that hDOHH has a fairly constrained active site. This pattern differs significantly from what has been associated with canonical dioxygen activating nonheme diiron enzymes, such as soluble methane monooxygenase and Class 1A ribonucleotide reductases, for which the Fe⋯Fe distance can change by as much as 1 Å during the redox cycle. These results suggest that the O2 activation mechanism for hDOHH deviates somewhat from that associated with the canonical nonheme diiron enzymes, opening the door to new mechanistic possibilities for this intriguing family of enzymes.
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Affiliation(s)
- Andrew J Jasniewski
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA
| | - Lisa M Engstrom
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA
| | - Van V Vu
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, 298-300A Nguyen Tat Thanh Street, Ward 13, District 4, Ho Chi Minh City, Vietnam
| | - Myung Hee Park
- National Institute of Dental and Craniofacial Research, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD, 20892, USA
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN, 55455, USA.
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Abstract
We introduce and discuss a hybrid quantum-mechanics molecular-mechanics (QM-MM) approach for Car-Parrinello DFT simulations with pseudopotentials and planewaves basis, designed for the treatment of periodic systems. In this implementation the MM atoms are considered as additional QM ions having fractional charges of either sign, which provides conceptual and computational simplicity by exploiting the machinery already existing in planewave codes to deal with electrostatics in periodic boundary conditions. With this strategy, both the QM and MM regions are contained in the same supercell, which determines the periodicity for the whole system. Thus, while this method is not meant to compete with non-periodic QM-MM schemes able to handle extremely large but finite MM regions, it is shown that for periodic systems of a few hundred atoms, our approach provides substantial savings in computational times by treating classically a fraction of the particles. The performance and accuracy of the method is assessed through the study of energetic, structural, and dynamical aspects of the water dimer and of the aqueous bulk phase. Finally, the QM-MM scheme is applied to the computation of the vibrational spectra of water layers adsorbed at the TiO2 anatase (1 0 1) solid-liquid interface. This investigation suggests that the inclusion of a second monolayer of H2O molecules is sufficient to induce on the first adsorbed layer, a vibrational dynamics similar to that taking place in the presence of an aqueous environment. The present QM-MM scheme appears as a very interesting tool to efficiently perform molecular dynamics simulations of complex condensed matter systems, from solutions to nanoconfined fluids to different kind of interfaces.
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Affiliation(s)
- Diego Hunt
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires (C1428EHA) Argentina
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21
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Proos Vedin N, Lundberg M. Protein effects in non-heme iron enzyme catalysis: insights from multiscale models. J Biol Inorg Chem 2016; 21:645-57. [DOI: 10.1007/s00775-016-1374-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 06/20/2016] [Indexed: 01/09/2023]
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Jayapal P, Ansari A, Rajaraman G. Computational Examination on the Active Site Structure of a (Peroxo)diiron(III) Intermediate in the Amine Oxygenase AurF. Inorg Chem 2015; 54:11077-82. [PMID: 26588098 DOI: 10.1021/acs.inorgchem.5b00872] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In this work, we report the first computational investigation on the structure and properties of the (peroxo)diiron(III) intermediate of the AurF enzyme. Our calculations predict that, in the oxidized state of the AurF enzyme, the peroxo ligand is depicted in a μ-1,1-coordination mode with a protonated bridging ligand and is not in a μ-η(2):η(2) or μ-1,2 mode. Computed spectral data for the μ-1,1-coordination mode correlate well with experimental observations and unravel the potential of the energetics-spectroscopic approach adapted here.
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Affiliation(s)
- Prabha Jayapal
- Department of Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India
| | - Azaj Ansari
- Department of Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay , Mumbai 400076, India
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Das B, Al-Hunaiti A, Haukka M, Demeshko S, Meyer S, Shteinman AA, Meyer F, Repo T, Nordlander E. Catalytic Oxidation of Alkanes and Alkenes by H2O2with a μ-Oxido Diiron(III) Complex as Catalyst/Catalyst Precursor. Eur J Inorg Chem 2015. [DOI: 10.1002/ejic.201500576] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Abdel-Azeim S, Jedidi A, Eppinger J, Cavallo L. Mechanistic insights into the reductive dehydroxylation pathway for the biosynthesis of isoprenoids promoted by the IspH enzyme. Chem Sci 2015; 6:5643-5651. [PMID: 28757951 PMCID: PMC5511988 DOI: 10.1039/c5sc01693b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 06/22/2015] [Indexed: 11/21/2022] Open
Abstract
Here, we report an integrated quantum mechanics/molecular mechanics (QM/MM) study of the bio-organometallic reaction pathway of the 2H+/2e- reduction of (E)-4-hydroxy-3-methylbut-2-enyl pyrophosphate (HMBPP) into the so called universal terpenoid precursors isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP), promoted by the IspH enzyme. Our results support the viability of the bio-organometallic pathway through rotation of the OH group of HMBPP away from the [Fe4S4] cluster at the core of the catalytic site, to become engaged in a H-bond with Glu126. This rotation is synchronous with π-coordination of the C2 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 1111111111111111111111111111111111 1111111111111111111111111111111111 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 0000000000000000000000000000000000 C3 double bond of HMBPP to the apical Fe atom of the [Fe4S4] cluster. Dehydroxylation of HMBPP is triggered by a proton transfer from Glu126 to the OH group of HMBPP. The reaction pathway is completed by competitive proton transfer from the terminal phosphate group to the C2 or C4 atom of HMBPP.
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Affiliation(s)
- Safwat Abdel-Azeim
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
| | - Abdesslem Jedidi
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
| | - Jorg Eppinger
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
| | - Luigi Cavallo
- King Abdullah University of Science and Technology , KAUST Catalysis Research Center , Physical Sciences and Engineering Division , Thuwal 23955-6900 , Saudi Arabia .
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25
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Abstract
Methane monooxygenases (MMOs) are enzymes that catalyze the oxidation of methane to methanol in methanotrophic bacteria. As potential targets for new gas-to-liquid methane bioconversion processes, MMOs have attracted intense attention in recent years. There are two distinct types of MMO, a soluble, cytoplasmic MMO (sMMO) and a membrane-bound, particulate MMO (pMMO). Both oxidize methane at metal centers within a complex, multisubunit scaffold, but the structures, active sites, and chemical mechanisms are completely different. This Current Topic review article focuses on the overall architectures, active site structures, substrate reactivities, protein-protein interactions, and chemical mechanisms of both MMOs, with an emphasis on fundamental aspects. In addition, recent advances, including new details of interactions between the sMMO components, characterization of sMMO intermediates, and progress toward understanding the pMMO metal centers are highlighted. The work summarized here provides a guide for those interested in exploiting MMOs for biotechnological applications.
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Affiliation(s)
- Sarah Sirajuddin
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy C. Rosenzweig
- Departments of Molecular Biosciences and of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
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26
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Fohlmeister L, Vignesh KR, Winter F, Moubaraki B, Rajaraman G, Pöttgen R, Murray KS, Jones C. Neutral diiron(iii) complexes with Fe2(μ-E)2 (E = O, S, Se) core structures: reactivity of an iron(i) dimer towards chalcogens. Dalton Trans 2015; 44:1700-8. [DOI: 10.1039/c4dt03081h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Three neutral guanidinato bis(μ-chalcogenido)diiron(iii) complexes (e.g. see picture) have been prepared from reactions of an iron(i) dimer with elemental chalcogens.
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Affiliation(s)
| | - Kuduva R. Vignesh
- Department of Chemistry
- Indian Institute of Technology Bombay Powai
- Mumbai 400076
- India
- IITB-Monash Research Academy
| | - Florian Winter
- Institut für Anorganische und Analytische Chemie
- D-48149 Münster
- Germany
| | | | - Gopalan Rajaraman
- Department of Chemistry
- Indian Institute of Technology Bombay Powai
- Mumbai 400076
- India
| | - Rainer Pöttgen
- Institut für Anorganische und Analytische Chemie
- D-48149 Münster
- Germany
| | | | - Cameron Jones
- School of Chemistry
- Monash University
- Melbourne
- Australia
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Pandelia ME, Li N, Nørgaard H, Warui DM, Rajakovich LJ, Chang WC, Booker SJ, Krebs C, Bollinger JM. Substrate-triggered addition of dioxygen to the diferrous cofactor of aldehyde-deformylating oxygenase to form a diferric-peroxide intermediate. J Am Chem Soc 2013; 135:15801-12. [PMID: 23987523 PMCID: PMC3869994 DOI: 10.1021/ja405047b] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cyanobacterial aldehyde-deformylating oxygenases (ADOs) belong to the ferritin-like diiron-carboxylate superfamily of dioxygen-activating proteins. They catalyze conversion of saturated or monounsaturated C(n) fatty aldehydes to formate and the corresponding C(n-1) alkanes or alkenes, respectively. This unusual, apparently redox-neutral transformation actually requires four electrons per turnover to reduce the O2 cosubstrate to the oxidation state of water and incorporates one O-atom from O2 into the formate coproduct. We show here that the complex of the diiron(II/II) form of ADO from Nostoc punctiforme (Np) with an aldehyde substrate reacts with O2 to form a colored intermediate with spectroscopic properties suggestive of a Fe2(III/III) complex with a bound peroxide. Its Mössbauer spectra reveal that the intermediate possesses an antiferromagnetically (AF) coupled Fe2(III/III) center with resolved subsites. The intermediate is long-lived in the absence of a reducing system, decaying slowly (t(1/2) ~ 400 s at 5 °C) to produce a very modest yield of formate (<0.15 enzyme equivalents), but reacts rapidly with the fully reduced form of 1-methoxy-5-methylphenazinium methylsulfate ((MeO)PMS) to yield product, albeit at only ~50% of the maximum theoretical yield (owing to competition from one or more unproductive pathway). The results represent the most definitive evidence to date that ADO can use a diiron cofactor (rather than a homo- or heterodinuclear cluster involving another transition metal) and provide support for a mechanism involving attack on the carbonyl of the bound substrate by the reduced O2 moiety to form a Fe2(III/III)-peroxyhemiacetal complex, which undergoes reductive O-O-bond cleavage, leading to C1-C2 radical fragmentation and formation of the alk(a/e)ne and formate products.
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Affiliation(s)
- Maria E. Pandelia
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Ning Li
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Hanne Nørgaard
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Douglas M. Warui
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Lauren J. Rajakovich
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Wei-chen Chang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Squire J. Booker
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
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Abstract
During a single turnover of the hydroxylase component (MMOH) of soluble methane monooxygenase from Methylosinus trichosporium OB3b, several discrete intermediates are formed. The diiron cluster of MMOH is first reduced to the Fe(II)Fe(II) state (H(red)). O₂ binds rapidly at a site away from the cluster to form the Fe(II)Fe(II) intermediate O, which converts to an Fe(III)Fe(III)-peroxo intermediate P and finally to the Fe(IV)Fe(IV) intermediate Q. Q binds and reacts with methane to yield methanol and water. The rate constants for these steps are increased by a regulatory protein, MMOB. Previously reported transient kinetic studies have suggested that an intermediate P* forms between O and P in which the g = 16 EPR signal characteristic of the reduced diiron cluster of H(red) and O is lost. This was interpreted as signaling oxidation of the cluster, but a low level of accumulation of P* prevented further characterization. In this study, three methods for directly detecting and trapping P* are applied together to allow its spectroscopic and kinetic characterization. First, the MMOB mutant His33Ala is used to specifically slow the decay of P* without affecting its formation rate, leading to its nearly quantitative accumulation. Second, spectra-kinetic data collection is used to provide a sensitive measure of the formation and decay rate constants of intermediates as well as their optical spectra. Finally, the substrate furan is included to react with Q and quench its strong chromophore. The optical spectrum of P* closely mimics those of H(red) and O, but it is distinctly different from that of P. The reaction cycle rate constants allowed prediction of the times for maximal accumulation of the intermediates. Mössbauer spectra of rapid freeze-quench samples at these times show that the intermediates are formed at almost exactly the predicted levels. The Mössbauer spectra show that the diiron cluster of P*, quite unexpectedly, is in the Fe(II)Fe(II) state. Thus, the loss of the g = 16 EPR signal results from a change in the electronic structure of the Fe(II)Fe(II) center rather than oxidation. The similarity of the optical and Mössbauer spectra of H(red), O, and P* suggests that only subtle changes occur in the electronic and physical structure of the diiron cluster as P* forms. Nevertheless, the changes that do occur are necessary for O₂ to be activated for hydrocarbon oxidation.
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Affiliation(s)
- Rahul Banerjee
- Department of Biochemistry, Molecular Biology, and Biophysics and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Uehara K, Taketsugu T, Yonehara K, Mizuno N. Effects of Isolobal Heteroatoms in Divanadium-Substituted γ-Keggin-type Polyoxometalates on (OV)2(μ-OH)2 Diamond and (OV)2(μ-O) Core Structures and the Transformation. Inorg Chem 2013; 52:1133-40. [DOI: 10.1021/ic302508c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Kazuhiro Uehara
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tatsuya Taketsugu
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kazuhiro Yonehara
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Noritaka Mizuno
- Department of Applied Chemistry, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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Cranswick MA, Meier KK, Shan X, Stubna A, Kaizer J, Mehn MP, Münck E, Que L. Protonation of a peroxodiiron(III) complex and conversion to a diiron(III/IV) intermediate: implications for proton-assisted O-O bond cleavage in nonheme diiron enzymes. Inorg Chem 2012; 51:10417-26. [PMID: 22971084 PMCID: PMC3462276 DOI: 10.1021/ic301642w] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Oxygenation of a diiron(II) complex, [Fe(II)(2)(μ-OH)(2)(BnBQA)(2)(NCMe)(2)](2+) [2, where BnBQA is N-benzyl-N,N-bis(2-quinolinylmethyl)amine], results in the formation of a metastable peroxodiferric intermediate, 3. The treatment of 3 with strong acid affords its conjugate acid, 4, in which the (μ-oxo)(μ-1,2-peroxo)diiron(III) core of 3 is protonated at the oxo bridge. The core structures of 3 and 4 are characterized in detail by UV-vis, Mössbauer, resonance Raman, and X-ray absorption spectroscopies. Complex 4 is shorter-lived than 3 and decays to generate in ~20% yield of a diiron(III/IV) species 5, which can be identified by electron paramagnetic resonance and Mössbauer spectroscopies. This reaction sequence demonstrates for the first time that protonation of the oxo bridge of a (μ-oxo)(μ-1,2-peroxo)diiron(III) complex leads to cleavage of the peroxo O-O bond and formation of a high-valent diiron complex, thereby mimicking the steps involved in the formation of intermediate X in the activation cycle of ribonucleotide reductase.
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Affiliation(s)
- Matthew A. Cranswick
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - Katlyn K. Meier
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Xiaopeng Shan
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - Audria Stubna
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Jószef Kaizer
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - Mark P. Mehn
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
| | - Eckard Münck
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA 15213
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, MN 55455
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Affiliation(s)
- Likai Du
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Jun Gao
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
- Key Laboratory of Theoretical and Computational Chemistry in Universities of Shandong (Shandong University), Jinan, 250100, P. R. China
| | - Yongjun Liu
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
- Key Laboratory of Theoretical and Computational Chemistry in Universities of Shandong (Shandong University), Jinan, 250100, P. R. China
| | - Chengbu Liu
- Key Laboratory of Colloid and Interface Chemistry, Ministry of Education, Institute of Theoretical Chemistry, School of Chemistry & Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
- Key Laboratory of Theoretical and Computational Chemistry in Universities of Shandong (Shandong University), Jinan, 250100, P. R. China
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Fu G, Liu H, Doerksen RJ. Molecular modeling to provide insight into the substrate binding and catalytic mechanism of human biliverdin-IXα reductase. J Phys Chem B 2012; 116:9580-94. [PMID: 22823425 DOI: 10.1021/jp301456j] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Human biliverdin-IXα reductase (hBVR-A) catalyzes the conversion of biliverdin-IXα to bilirubin-IXα in the last step of heme degradation and is a key enzyme in regulating a wide range of cellular responses. Though the X-ray structure of hBVR-A is available including cofactor, a crystal structure with a bound substrate would be even more useful as a starting point for protein-structure-based inhibitor design, but none have been reported. The present study employed induced fit docking (IFD) to study the substrate binding modes to hBVR-A of biliverdin-IXα and four analogues. The proposed substrate binding modes were examined further by performing molecular dynamics (MD) simulations followed by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations. The predicted binding free energies for the five biliverdin-IXα analogues match well with the relative potency of their reported experimental binding affinities, supporting that the proposed binding modes are reasonable. Furthermore, the ternary complex structure of hBVR-A binding with biliverdin-IXα and the electron donor cofactor NADPH obtained from MD simulations was exploited to investigate the catalytic mechanism, by calculating the reaction energy profile using the quantum mechanics/molecular mechanics (QM/MM) method. On the basis of our calculations, the energetically preferred pathway consists of an initial protonation of the pyrrolic nitrogen on the biliverdin substrate followed by hydride transfer to yield the reduction product. This conclusion is consistent with a previous mechanistic study on human biliverdin IXβ reductase (hBVR-B).
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Affiliation(s)
- Gang Fu
- Department of Medicinal Chemistry, School of Pharmacy, University of Mississippi, University, Mississippi 38677, United States
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Turitsyna EA, Trukhan VM, Shteinman AA. Synthesis and structure of binuclear iron(ii) complex with the cage-like ligand as a model of methane monooxygenase. Russ Chem Bull 2011; 60:2088-93. [DOI: 10.1007/s11172-011-0319-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Abstract
Iron-catalyzed reactions are receiving a surge of interest owing to the natural abundance and biocompatibility of Fe and the urge to develop practically useful sustainable catalysis for fine chemical industries. This article is a brief account of our studies on the C–O and C–N bond formation reactions catalyzed by Fe complexes supported by oligopyridine, macrocyclic tetraaza, and fluorinated porphyrin ligands. The working principle is the in situ generation of reactive Fe=O and Fe=NR intermediates supported by these oxidatively robust N-donor ligands for oxygen atom/nitrogen group transfer and insertion reactions. The catalytic reactions include C–H bond oxidation of saturated hydrocarbons (up to 87 % yield), epoxidation of alkenes (up to 96 % yield), cis-dihydroxylation of alkenes (up to 99 % yield), epoxidation–isomerization (E–I) reaction of aryl alkenes (up to 94 % yield), amination of C–H bonds (up to 95 % yield), aziridination of alkenes (up to 95 % yield), sulfimidation of sulfides (up to 96 % yield), and amide formation from aldehydes (up to 89 % yield). Many of these catalytic reactions feature high regio- and diastereoselectivity and/or high product yields and substrate conversions, and recyclability of the catalyst, demonstrating the applicability of Fe-catalyzed oxidative organic transformation reactions in practical organic synthesis.
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Srnec M, Rokob TA, Schwartz JK, Kwak Y, Rulíšek L, Solomon EI. Structural and Spectroscopic Properties of the Peroxodiferric Intermediate of Ricinus communis Soluble Δ9 Desaturase. Inorg Chem 2012; 51:2806-20. [DOI: 10.1021/ic2018067] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Martin Srnec
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences & IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Tibor András Rokob
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences & IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Jennifer K. Schwartz
- Department of Chemistry, Stanford University, Stanford, California 94305-5080,
United States
| | - Yeonju Kwak
- Department of Chemistry, Stanford University, Stanford, California 94305-5080,
United States
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences & IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94305-5080,
United States
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Hughes TF, Friesner RA. Development of Accurate DFT Methods for Computing Redox Potentials of Transition Metal Complexes: Results for Model Complexes and Application to Cytochrome P450. J Chem Theory Comput 2012; 8:442-59. [DOI: 10.1021/ct2006693] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas F. Hughes
- Department of Chemistry,
Columbia University, New York,
New York 10027, United States
| | - Richard A. Friesner
- Department of Chemistry,
Columbia University, New York,
New York 10027, United States
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Kundu S, Matito E, Walleck S, Pfaff FF, Heims F, Rábay B, Luis JM, Company A, Braun B, Glaser T, Ray K. O-O bond formation mediated by a hexanuclear iron complex supported on a stannoxane core. Chemistry 2012; 18:2787-91. [PMID: 22262528 DOI: 10.1002/chem.201102326] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Indexed: 11/10/2022]
Affiliation(s)
- Subrata Kundu
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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Rokob TA, Srnec M, Rulíšek L. Theoretical calculations of physico-chemical and spectroscopic properties of bioinorganic systems: current limits and perspectives. Dalton Trans 2012; 41:5754-68. [DOI: 10.1039/c2dt12423h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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41
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Do LH, Lippard SJ. Evolution of strategies to prepare synthetic mimics of carboxylate-bridged diiron protein active sites. J Inorg Biochem 2011; 105:1774-85. [PMID: 22113107 PMCID: PMC3232320 DOI: 10.1016/j.jinorgbio.2011.08.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Revised: 08/08/2011] [Accepted: 08/11/2011] [Indexed: 10/17/2022]
Abstract
We present a comprehensive review of research conducted in our laboratory in pursuit of the long-term goal of reproducing the structures and reactivity of carboxylate-bridged diiron centers used in biology to activate dioxygen for the conversion of hydrocarbons to alcohols and related products. This article describes the evolution of strategies devised to achieve these goals and illustrates the challenges in getting there. Particular emphasis is placed on controlling the geometry and coordination environment of the diiron core, preventing formation of polynuclear iron clusters, maintaining the structural integrity of model complexes during reactions with dioxygen, and tuning the ligand framework to stabilize desired oxygenated diiron species. Studies of the various model systems have improved our understanding of the electronic and physical characteristics of carboxylate-bridged diiron units and their reactivity toward molecular oxygen and organic moieties. The principles and lessons that have emerged from these investigations will guide future efforts to develop more sophisticated diiron protein model complexes.
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Affiliation(s)
- Loi H. Do
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139. U.S.A
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139. U.S.A
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XU JIAN, YANG HUAQING, QIN SONG, HU CHANGWEI. THEORETICAL STUDY ON METHANE HYDROXYLATION BY MIMIC METHANE MONOOXYGENASE WITH bis(μ-OXO)DIMANGANESE CORE. J Theor Comput Chem 2011. [DOI: 10.1142/s0219633610005633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The reaction mechanism for methane hydroxylation catalyzed by mimic methane monooxygenase (MMO) with bis(μ-oxo)dimanganese core has been investigated on the septet and nonet potential energy surfaces by hybrid density functional method B3LYP. The key reactive compound Q of MMO was modeled by trans- (H2CNH)(COOH) Mn(μ-O)2(μ-HCOO)2Mn(H2CNH)(COOH) . The ground state of Q is located on the septet state, which has a diamond-core structure with two Mn(IV) atoms. It is shown that the reaction proceeds via a radical-rebound mechanism, in which the step of C–H cleavage is the rate-determining step both in the gas phase and solution. Furthermore, the reaction may proceed more easily as the polarity of solution is larger. On the other hand, the kinetic isotope effects (KIEs) for H atom abstraction from methane are taken into account on the basis of transition state theory with Wigner tunneling corrections. The mimic MMO with bis(μ-oxo)dimanganese core might be an effective mimic catalyst for methane hydroxylation.
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Affiliation(s)
- JIAN XU
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China
- College of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - HUA-QING YANG
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China
- College of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - SONG QIN
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - CHANG-WEI HU
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China
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Abstract
An [Fe(IV)(2)(μ-O)(2)] diamond core structure has been postulated for intermediate Q of soluble methane monooxygenase (sMMO-Q), the oxidant responsible for cleaving the strong C-H bond of methane and its hydroxylation. By extension, analogous species may be involved in the mechanisms of related diiron hydroxylases and desaturases. Because of the paucity of well-defined synthetic examples, there are few, if any, mechanistic studies on the oxidation of hydrocarbon substrates by complexes with high-valent [Fe(2)(μ-O)(2)] cores. We report here that water or alcohol substrates can activate synthetic [Fe(III)Fe(IV)(μ-O)(2)] complexes supported by tetradentate tris(pyridyl-2-methyl)amine ligands (1 and 2) by several orders of magnitude for C-H bond oxidation. On the basis of detailed kinetic studies, it is postulated that the activation results from Lewis base attack on the [Fe(III)Fe(IV)(μ-O)(2)] core, resulting in the formation of a more reactive species with a [X-Fe(III)-O-Fe(IV)═O] ring-opened structure (1-X, 2-X, X = OH(-) or OR(-)). Treatment of 2 with methoxide at -80 °C forms the 2-methoxide adduct in high yield, which is characterized by an S = 1/2 EPR signal indicative of an antiferromagnetically coupled [S = 5/2 Fe(III)/S = 2 Fe(IV)] pair. Even at this low temperature, the complex undergoes facile intramolecular C-H bond cleavage to generate formaldehyde, showing that the terminal high-spin Fe(IV)═O unit is capable of oxidizing a C-H bond as strong as 96 kcal mol(-1). This intramolecular oxidation of the methoxide ligand can in fact be competitive with intermolecular oxidation of triphenylmethane, which has a much weaker C-H bond (D(C-H) 81 kcal mol(-1)). The activation of the [Fe(III)Fe(IV)(μ-O)(2)] core is dramatically illustrated by the oxidation of 9,10-dihydroanthracene by 2-methoxide, which has a second-order rate constant that is 3.6 × 10(7)-fold larger than that for the parent diamond core complex 2. These observations provide strong support for the DFT-based notion that an S = 2 Fe(IV)═O unit is much more reactive at H-atom abstraction than its S = 1 counterpart and suggest that core isomerization could be a viable strategy for the [Fe(IV)(2)(μ-O)(2)] diamond core of sMMO-Q to selectively attack the strong C-H bond of methane in the presence of weaker C-H bonds of amino acid residues that define the diiron active site pocket.
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Affiliation(s)
- Genqiang Xue
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, USA
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Do LH, Wang H, Tinberg CE, Dowty E, Yoda Y, Cramer SP, Lippard SJ. Characterization of a synthetic peroxodiiron(III) protein model complex by nuclear resonance vibrational spectroscopy. Chem Commun (Camb) 2011; 47:10945-7. [PMID: 21897991 DOI: 10.1039/c1cc13836g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The vibrational spectrum of an η(1),η(1)-1,2-peroxodiiron(III) complex was measured by nuclear resonance vibrational spectroscopy and fit using an empirical force field analysis. Isotopic (18)O(2) labelling studies revealed a feature involving motion of the {Fe(2)(O(2))}(4+) core that was not previously observed by resonance Raman spectroscopy.
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Affiliation(s)
- Loi H Do
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
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Dillard BD, Demick JM, Adams MWW, Lanzilotta WN. A cryo-crystallographic time course for peroxide reduction by rubrerythrin from Pyrococcus furiosus. J Biol Inorg Chem 2011; 16:949-59. [PMID: 21647777 DOI: 10.1007/s00775-011-0795-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2011] [Accepted: 05/16/2011] [Indexed: 11/28/2022]
Abstract
High-resolution crystal structures of Pyrococcus furiosus rubrerythrin (PfRbr) in the resting (all-ferrous) state and at time points following exposure of the crystals to hydrogen peroxide are reported. This approach was possible because of the relativity slow turnover of PfRbr at room temperature. To this end, we were able to perform time-dependent peroxide treatment of the fully reduced enzyme, under strictly anaerobic conditions, in the crystalline state. In this work we demonstrate, for the first time, that turnover of a thermophilic rubrerythrin results in approximately 2-Å movement of one iron atom in the diiron site from a histidine to a carboxylate ligand. These results confirm that, despite the domain-swapped architecture, the hyperthermophilic rubrerythrins also utilize the classic combination of iron sites together with redox-dependent iron toggling to selectively reduce hydrogen peroxide over dioxygen. In addition, we have identified previously unobserved intermediates in the reaction cycle and observed structural changes that may explain the enzyme precipitation observed for the all-iron form of PfRbr upon oxidation to the all-ferric state.
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Affiliation(s)
- Bret D Dillard
- Department of Biochemistry and Molecular Biology, The Center for Metalloenzyme Studies, University of Georgia, Athens, GA 30602, USA
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46
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Assary RS, Broadbelt LJ. Computational screening of novel thiamine-catalyzed decarboxylation reactions of 2-keto acids. Bioprocess Biosyst Eng 2011; 34:375-88. [PMID: 21061135 DOI: 10.1007/s00449-010-0481-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Accepted: 10/18/2010] [Indexed: 01/02/2023]
Abstract
A molecular modeling strategy to screen the capacity of known enzymes to catalyze the reactions of non-native substrates is presented. The binding of pyruvic acid and non-native ketoacids in the active site of pyruvate ferredoxin oxidoreductase was examined using docking analysis, and our results suggest that enzyme-non-native ketoacid-bound species are feasible. Quantum mechanics/molecular mechanics methods were then used to study the geometry of the covalent intermediate formed from the enzyme and the various ketoacids. Finally, quantum mechanical methods were used to study the decarboxylation reaction of 2-keto acids at the mechanistic level. This hierarchical screening ranked the substrates from those that cannot be accommodated by the enzyme (phenyl pyruvate) to those whose conversion rate would most closely approach that of the native substrate (2-ketobutanoic acid and 2-ketovaleric acid). Most notably, our investigation suggests that novel pathways generated using generalized enzyme actions may be screened using the hierarchical approach employed here.
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Affiliation(s)
- Rajeev S Assary
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL 60208, USA
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Rather LJ, Weinert T, Demmer U, Bill E, Ismail W, Fuchs G, Ermler U. Structure and mechanism of the diiron benzoyl-coenzyme A epoxidase BoxB. J Biol Chem 2011; 286:29241-29248. [PMID: 21632537 DOI: 10.1074/jbc.m111.236893] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The coenzyme A (CoA)-dependent aerobic benzoate metabolic pathway uses an unprecedented chemical strategy to overcome the high aromatic resonance energy by forming the non-aromatic 2,3-epoxybenzoyl-CoA. The crucial dearomatizing reaction is catalyzed by three enzymes, BoxABC, where BoxA is an NADPH-dependent reductase, BoxB is a benzoyl-CoA 2,3-epoxidase, and BoxC is an epoxide ring hydrolase. We characterized the key enzyme BoxB from Azoarcus evansii by structural and Mössbauer spectroscopic methods as a new member of class I diiron enzymes. Several family members were structurally studied with respect to the diiron center architecture, but no structure of an intact diiron enzyme with its natural substrate has been reported. X-ray structures between 1.9 and 2.5 Å resolution were determined for BoxB in the diferric state and with bound substrate benzoyl-CoA in the reduced state. The substrate-bound reduced state is distinguished from the diferric state by increased iron-ligand distances and the absence of directly bridging groups between them. The position of benzoyl-CoA inside a 20 Å long channel and the position of the phenyl ring relative to the diiron center are accurately defined. The C2 and C3 atoms of the phenyl ring are closer to one of the irons. Therefore, one oxygen of activated O(2) must be ligated predominantly to this proximate iron to be in a geometrically suitable position to attack the phenyl ring. Consistent with the observed iron/phenyl geometry, BoxB stereoselectively should form the 2S,3R-epoxide. We postulate a reaction cycle that allows a charge delocalization because of the phenyl ring and the electron-withdrawing CoA thioester.
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Affiliation(s)
- Liv J Rather
- Mikrobiologie, Institut für Biologie II, Universität Freiburg, Schänzlestrasse 1, D-79104 Freiburg
| | - Tobias Weinert
- Max-Planck-Institut für Biophysik, Max-von-Laue-Strasse 3, D-60438 Frankfurt am Main, and
| | - Ulrike Demmer
- Max-Planck-Institut für Biophysik, Max-von-Laue-Strasse 3, D-60438 Frankfurt am Main, and
| | - Eckhard Bill
- Max-Planck-Institut für Bioanorganische Chemie, Stiftstrasse 34-36, D-45470 Mülheim an der Ruhr, Germany
| | - Wael Ismail
- Mikrobiologie, Institut für Biologie II, Universität Freiburg, Schänzlestrasse 1, D-79104 Freiburg
| | - Georg Fuchs
- Mikrobiologie, Institut für Biologie II, Universität Freiburg, Schänzlestrasse 1, D-79104 Freiburg
| | - Ulrich Ermler
- Max-Planck-Institut für Biophysik, Max-von-Laue-Strasse 3, D-60438 Frankfurt am Main, and.
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Bochevarov AD, Li J, Song WJ, Friesner RA, Lippard SJ. Insights into the different dioxygen activation pathways of methane and toluene monooxygenase hydroxylases. J Am Chem Soc 2011; 133:7384-97. [PMID: 21517016 PMCID: PMC3092846 DOI: 10.1021/ja110287y] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The methane and toluene monooxygenase hydroxylases (MMOH and TMOH, respectively) have almost identical active sites, yet the physical and chemical properties of their oxygenated intermediates, designated P*, H(peroxo), Q, and Q* in MMOH and ToMOH(peroxo) in a subclass of TMOH, ToMOH, are substantially different. We review and compare the structural differences in the vicinity of the active sites of these enzymes and discuss which changes could give rise to the different behavior of H(peroxo) and Q. In particular, analysis of multiple crystal structures reveals that T213 in MMOH and the analogous T201 in TMOH, located in the immediate vicinity of the active site, have different rotatory configurations. We study the rotational energy profiles of these threonine residues with the use of molecular mechanics (MM) and quantum mechanics/molecular mechanics (QM/MM) computational methods and put forward a hypothesis according to which T213 and T201 play an important role in the formation of different types of peroxodiiron(III) species in MMOH and ToMOH. The hypothesis is indirectly supported by the QM/MM calculations of the peroxodiiron(III) models of ToMOH and the theoretically computed Mössbauer spectra. It also helps explain the formation of two distinct peroxodiiron(III) species in the T201S mutant of ToMOH. Additionally, a role for the ToMOD regulatory protein, which is essential for intermediate formation and protein functioning in the ToMO system, is advanced. We find that the low quadrupole splitting parameter in the Mössbauer spectrum observed for a ToMOH(peroxo) intermediate can be explained by protonation of the peroxo moiety, possibly stabilized by the T201 residue. Finally, similarities between the oxygen activation mechanisms of the monooxygenases and cytochrome P450 are discussed.
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Abstract
X-ray absorption and resonance Raman spectroscopies show that CmlA, the β-hydroxylase of the chloramphenicol biosynthetic pathway, contains a (μ-oxo)-(μ-1,3-carboxylato)diiron(III) cluster with 6-coordinate iron centers and 3 - 4 His ligands. This active site is found within a unique β-lactamase fold and is distinct from those of soluble methane monooxygenase and related enzymes that utilize a highly conserved diiron cluster with a 2-His-4-carboxylate ligand set within a 4-helix bundle motif. These structural differences may have an impact on the nature of the activated oxygen species of the reaction cycle.
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Affiliation(s)
- Van V Vu
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, USA
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50
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Abstract
The controlled oxidation of methane to methanol is a chemical transformation of great value, particularly in the pursuit of alternative fuels, but the reaction remains underutilized industrially because of inefficient and costly synthetic procedures. In contrast, methane monooxygenase enzymes (MMOs) from methanotrophic bacteria achieve this chemistry efficiently under ambient conditions. In this Account, we discuss the first observable step in the oxidation of methane at the carboxylate-bridged diiron active site of the soluble MMO (sMMO), namely, the reductive activation of atmospheric O(2). The results provide benchmarks against which the dioxygen activation mechanisms of other bacterial multicomponent monooxygenases can be measured. Molecular oxygen reacts rapidly with the reduced diiron(II) cen-ter of the hydroxylase component of sMMO (MMOH). The first spectroscopically characterized intermediate that results from this process is a peroxodiiron(III) species, P*, in which the iron atoms have identical environments. P* converts to a second peroxodiiron(III) unit, H(peroxo), in a process accompanied by the transfer of a proton, probably with the assistance of a residue near the active site. Proton-promoted O-O bond scission and rearrangement of the diiron core then leads to a diiron(IV) unit, termed Q, that is directly responsible for the oxidation of methane to methanol. In one section of this Account, we provide a detailed discussion of these processes, with particular emphasis on possible structures of the intermediates. The geometries of P* and H(peroxo) are currently unknown, and recent synthetic modeling chemistry has highlighted the need for further structural characterization of Q, currently assigned as a di(μ-oxo)diiron(IV) "diamond core." In another section of the Account, we discuss in detail proton transfer during the O(2) activation events. The role of protons in promoting O-O bond cleavage, thereby initiating the conversion of H(peroxo) to Q, was previously a controversial topic. Recent studies of the mechanism, covering a range of pH values and in D(2)O instead of H(2)O, confirmed conclusively that the transfer of protons, possibly at or near the active site, is necessary for both P*-to-H(peroxo) and H(peroxo)-to-Q conversions. Specific mechanistic insights into these processes are provided. In the final section of the Account, we present our view of experiments that need to be done to further define crucial aspects of sMMO chemistry. Here our goal is to detail the challenges that we and others face in this research, particularly with respect to some long-standing questions about the system, as well as approaches that might be used to solve them.
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Affiliation(s)
- Christine E. Tinberg
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Stephen J. Lippard
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
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