151
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Visser SP. Second‐Coordination Sphere Effects on Selectivity and Specificity of Heme and Nonheme Iron Enzymes. Chemistry 2020; 26:5308-5327. [DOI: 10.1002/chem.201905119] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/04/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Sam P. Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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152
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Singh B, Das RS. Studies on the oxidative degradation of paracetamol by a μ-oxo-diiron(III) complex. CAN J CHEM 2020. [DOI: 10.1139/cjc-2019-0193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In higher organisms, metalloenzymes like cytochrome P450, containing a Fe(III) metal center, play an active role in metabolism of paracetamol (APAP). Here, we have chosen a mimicking μ-oxo-diiron complex, [Fe(III)2(μ-O)(phen)4(H2O)2]4+(1, phen = 1,10-phenanthroline), to study spectrophotometrically the kinetics of the redox interactions with APAP. In acidic buffer media (pH = 3.4–5.1), APAP quantitatively reduces 1 following first-order reaction kinetics. Each molecule of 1 accepts two electrons from APAP and is reduced to ferroin [Fe(phen)3]2+. On oxidation, APAP produces N-acetyl-p-benzoquinone imine (NAPQI), which on hydrolysis results in a mixture of benzoquinone, quinone oxime, acetamide, and acetic acid. In reaction media due to successive deprotonations, 1 exists in equilibrium with the species [Fe(III)2(μ-O)(phen)4(H2O)(OH)]3+(1a) and [Fe(III)2(μ-O)(phen)4(OH)2]2+(1b) (pKa= 3.71 and 5.28, respectively). The kinetic analyses suggest for an unusual reactivity order as 1 < 1a ≫ 1b. The mechanistic possibilities suggest that although 1 is reduced by concerted electron transfer (ET) – proton transfer (PT) mechanism, 1a and 1b may be reduced by a concerted PT–ET mechanism where a slow proton-abstraction step is followed by a rapid ET process. It seems that the initial activation of the bridging μ-oxo group by a proton-abstraction results in the higher reactivity of 1a.
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Affiliation(s)
- Bula Singh
- Department of Chemistry, Visva-Bharati, Santiniketan 731235, India
| | - Ranendu Sekhar Das
- Department of Chemistry, Ranaghat College, Nadia, West Bengal 741201, India
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153
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Walleck S, Glaser T. A Dinucleating Ligand System with Varying Terminal Donors to Mimic Diiron Active Sites. Isr J Chem 2020. [DOI: 10.1002/ijch.201900097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Stephan Walleck
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie Universität Bielefeld Universitätsstrasse 25 D-33615 Bielefeld Germany
| | - Thorsten Glaser
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie Universität Bielefeld Universitätsstrasse 25 D-33615 Bielefeld Germany
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154
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Wang Y, Li Z, Li C, Qi Y, Li Q, Zhang P. [FeIV(O )(TMC)(Lax)]n+ for O-transfer reaction: Insight into the steric hindrance effect of the equatorial ligand. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2019.136858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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155
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Monika, Ansari A. Mechanistic insights into the allylic oxidation of aliphatic compounds by tetraamido iron( v) species: A C–H vs. O–H bond activation. NEW J CHEM 2020. [DOI: 10.1039/d0nj03095c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work is based on a deep insight into a comparative study of C–H vs. O–H bond activation of allylic compound by the high valent iron complex. Our theoretical findings can help to design catalysts with better efficiency for catalytic reactions.
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Affiliation(s)
- Monika
- Department of Chemistry
- Central University of Haryana
- Mahendergarh-123031
- India
| | - Azaj Ansari
- Department of Chemistry
- Central University of Haryana
- Mahendergarh-123031
- India
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156
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Comba P, Faltermeier D, Krieg S, Martin B, Rajaraman G. Spin state and reactivity of iron(iv)oxido complexes with tetradentate bispidine ligands. Dalton Trans 2020; 49:2888-2894. [DOI: 10.1039/c9dt04578c] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The iron(iv)oxido complex [(bispidine)FeIVO(Cl)]+is shown by experiment and high-level DLPNO-CCSD(T) quantum-chemical calculations to be an extremely short-lived and very reactive intermediate-spin (S= 1) species.
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Affiliation(s)
- Peter Comba
- Universität Heidelberg
- Anorganisch-Chemisches Institut
- D-69120 Heidelberg
- Germany
- Interdisziplinäres Zentrum für Wissenschaftliches Rechnen (IWR)
| | - Dieter Faltermeier
- Universität Heidelberg
- Anorganisch-Chemisches Institut
- D-69120 Heidelberg
- Germany
- Interdisziplinäres Zentrum für Wissenschaftliches Rechnen (IWR)
| | - Saskia Krieg
- Universität Heidelberg
- Anorganisch-Chemisches Institut
- D-69120 Heidelberg
- Germany
| | - Bodo Martin
- Universität Heidelberg
- Anorganisch-Chemisches Institut
- D-69120 Heidelberg
- Germany
- Interdisziplinäres Zentrum für Wissenschaftliches Rechnen (IWR)
| | - Gopalan Rajaraman
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai-400076
- India
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157
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Feldt M, Martín-Fernández C, Harvey JN. Energetics of non-heme iron reactivity: can ab initio calculations provide the right answer? Phys Chem Chem Phys 2020; 22:23908-23919. [DOI: 10.1039/d0cp04401f] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
We use a variety of computational methods to characterize and compare the hydrogen atom transfer (HAT) and epoxidation reaction pathways for oxidation of cyclohexene by an iron(iv)-oxo complex.
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Affiliation(s)
- Milica Feldt
- Division of Quantum Chemistry and Physical Chemistry
- Department of Chemistry
- Katholieke Universiteit Leuven
- 3001 Leuven
- Belgium
| | - Carlos Martín-Fernández
- Division of Quantum Chemistry and Physical Chemistry
- Department of Chemistry
- Katholieke Universiteit Leuven
- 3001 Leuven
- Belgium
| | - Jeremy N. Harvey
- Division of Quantum Chemistry and Physical Chemistry
- Department of Chemistry
- Katholieke Universiteit Leuven
- 3001 Leuven
- Belgium
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158
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Mukherjee G, Reinhard FGC, Bagha UK, Sastri CV, de Visser SP. Sluggish reactivity by a nonheme iron(iv)-tosylimido complex as compared to its oxo analogue. Dalton Trans 2020; 49:5921-5931. [DOI: 10.1039/d0dt00018c] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A comparative spectroscopic and computational study of reactivity between ferryl-tosylimido and ferryl-oxo complexes of two biomimetic model systems. The Fe(iv)-tosylimido complex was found to be sluggish in comparison to its fellow oxo counterpart.
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Affiliation(s)
- Gourab Mukherjee
- Department of Chemistry
- Indian Institute of Technology Guwahati
- India
| | - Fabián G. Cantú Reinhard
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science
- The University of Manchester
- Manchester M1 7DN
- UK
| | | | | | - Sam P. de Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science
- The University of Manchester
- Manchester M1 7DN
- UK
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159
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Modeling succinate dehydrogenase loss disorders in C. elegans through effects on hypoxia-inducible factor. PLoS One 2019; 14:e0227033. [PMID: 31887185 PMCID: PMC6936837 DOI: 10.1371/journal.pone.0227033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 12/10/2019] [Indexed: 12/03/2022] Open
Abstract
Mitochondrial disorders arise from defects in nuclear genes encoding enzymes of oxidative metabolism. Mutations of metabolic enzymes in somatic tissues can cause cancers due to oncometabolite accumulation. Paraganglioma and pheochromocytoma are examples, whose etiology and therapy are complicated by the absence of representative cell lines or animal models. These tumors can be driven by loss of the tricarboxylic acid cycle enzyme succinate dehydrogenase. We exploit the relationship between succinate accumulation, hypoxic signaling, egg-laying behavior, and morphology in C. elegans to create genetic and pharmacological models of succinate dehydrogenase loss disorders. With optimization, these models may enable future high-throughput screening efforts.
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160
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Li H, Zhu W, Liu Y. Mechanism of Uncoupled Carbocyclization and Epimerization Catalyzed by Two Non-Heme Iron/α-Ketoglutarate Dependent Enzymes. J Chem Inf Model 2019; 59:5086-5098. [PMID: 31790238 DOI: 10.1021/acs.jcim.9b00837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The non-heme iron/α-ketoglutarate dependent enzymes SnoK and SnoN from Streptomyces nogalater are involved in the biosynthesis of anthracycline nogalamycin. Although they have similar active sites, SnoK is responsible for carbocyclization whereas SnoN solely catalyzes the hydroxyl epimerization. Herein, we performed docking, molecular simulations, and a series of combined quantum mechanics and molecular mechanics (QM/MM) calculations to illuminate the mechanisms of two enzymes. The catalytic reactions of two enzymes occur on the quintet state surface. For SnoK, the whole reaction includes two separated hydrogen-abstraction steps and one radical addition, and the latter step is calculated to be rate limiting with an energy barrier of 21.7 kcal/mol. Residue D106 is confirmed to participate in the construction of the hydrogen bond network, which plays a crucial role in positioning the bulky substrate in a specific orientation. Moreover, it is found that SnoN is only responsible for the hydrogen abstraction of the intermediate, and no residue was suggested to be suitable for donating a hydrogen atom to the substrate radical, which further confirms the suggestion based on experiments that either a cellular reductant or another enzyme protein could donate a hydrogen atom to the substrate. Our docking results coincide with the previous structural study that the different roles of two enzymes are achieved by minor changes in the alignment of the substrates in front of the reactive ferryl-oxo species. This work highlights the reaction mechanisms catalyzed by SnoK and SnoN, which is helpful for engineering the enzymes for the biosynthesis of anthracycline nogalamycin.
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Affiliation(s)
- Hong Li
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , Shandong 250100 , China
| | - Wenyou Zhu
- College of Chemistry and Chemical Engineering , Xuzhou Institute of Technology , Xuzhou , Jiangsu 221111 , China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , Shandong 250100 , China
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161
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Ghafoor S, Mansha A, de Visser SP. Selective Hydrogen Atom Abstraction from Dihydroflavonol by a Nonheme Iron Center Is the Key Step in the Enzymatic Flavonol Synthesis and Avoids Byproducts. J Am Chem Soc 2019; 141:20278-20292. [PMID: 31749356 DOI: 10.1021/jacs.9b10526] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The plant non-heme iron dioxygenase flavonol synthase performs a regioselective desaturation reaction as part of the biosynthesis of the signaling molecule flavonol that triggers the growing of leaves and flowers. These compounds also have health benefits for humans. Desaturation of aliphatic compounds generally proceeds through two consecutive hydrogen atom abstraction steps from two adjacent carbon atoms and in nature often is performed by a high-valent iron(IV)-oxo species. We show that the order of the hydrogen atom abstraction steps, however, is opposite of those expected from the C-H bond strengths in the substrate and determines the product distributions. As such, flavonol synthase follows a negative catalysis mechanism. Using density functional theory methods on large active-site model complexes, we investigated pathways for desaturation and hydroxylation by an iron(IV)-oxo active-site model. Contrary to thermochemical predictions, we find that the oxidant abstracts the hydrogen atom from the strong C2-H bond rather than the weaker C3-H bond of the substrate first. We analyze the origin of this unexpected selective hydrogen atom abstraction pathway and find that the alternative C3-H hydrogen atom abstraction would be followed by a low-energy and competitive substrate hydroxylation mechanism hence, should give considerable amount of byproducts. Our computational modeling studies show that substrate positioning in flavonol synthase is essential, as it guides the reactivity to a chemo- and regioselective substrate desaturation from the C2-H group, leading to desaturation products efficiently.
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Affiliation(s)
- Sidra Ghafoor
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science , The University of Manchester , 131 Princess Street , Manchester M1 7DN , United Kingdom.,Department of Chemistry , Government College University Faisalabad , New Campus, Jhang Road , Faisalabad 38000 , Pakistan
| | - Asim Mansha
- Department of Chemistry , Government College University Faisalabad , New Campus, Jhang Road , Faisalabad 38000 , Pakistan
| | - Sam P de Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science , The University of Manchester , 131 Princess Street , Manchester M1 7DN , United Kingdom
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162
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Lin Y, Stańczak A, Manchev Y, Straganz GD, Visser SP. Can a Mononuclear Iron(III)‐Superoxo Active Site Catalyze the Decarboxylation of Dodecanoic Acid in UndA to Produce Biofuels? Chemistry 2019; 26:2233-2242. [DOI: 10.1002/chem.201903783] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 09/24/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Yen‐Ting Lin
- The Manchester Institute of Biotechnology and Department of, Chemical Engineering and Analytical ScienceThe University of, Manchester 131 Princess Street Manchester M1 7DN UK
| | - Agnieszka Stańczak
- The Manchester Institute of Biotechnology and Department of, Chemical Engineering and Analytical ScienceThe University of, Manchester 131 Princess Street Manchester M1 7DN UK
- Faculty of ChemistrySilesian University of Technology ks. Marcina Strzody 9 44-100 Gliwice Poland
- Tunneling Group, Biotechnology CentreSilesian University of Technology ul. Krzywoustego 8 44–100 Gliwice Poland
| | - Yulian Manchev
- The Manchester Institute of Biotechnology and Department of, Chemical Engineering and Analytical ScienceThe University of, Manchester 131 Princess Street Manchester M1 7DN UK
| | - Grit D. Straganz
- Graz University of TechnologyInstitute of Biochemistry Petergasse 12 8010 Graz Austria
| | - Sam P. Visser
- The Manchester Institute of Biotechnology and Department of, Chemical Engineering and Analytical ScienceThe University of, Manchester 131 Princess Street Manchester M1 7DN UK
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163
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Mubarak MQE, de Visser SP. Second-Coordination Sphere Effect on the Reactivity of Vanadium–Peroxo Complexes: A Computational Study. Inorg Chem 2019; 58:15741-15750. [DOI: 10.1021/acs.inorgchem.9b01778] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. Qadri E. Mubarak
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sam P. de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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164
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Wind M, Braun‐Cula B, Schax F, Herwig C, Limberg C. A Polysiloxide Complex with two Chromium(III) η
2
‐Superoxo Moieties. Isr J Chem 2019. [DOI: 10.1002/ijch.201900119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Marie‐Louise Wind
- Humboldt-Universität zu Berlin Department of Chemistry Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Beatrice Braun‐Cula
- Humboldt-Universität zu Berlin Department of Chemistry Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Fabian Schax
- Humboldt-Universität zu Berlin Department of Chemistry Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Christian Herwig
- Humboldt-Universität zu Berlin Department of Chemistry Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Christian Limberg
- Humboldt-Universität zu Berlin Department of Chemistry Brook-Taylor-Strasse 2 12489 Berlin Germany
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165
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DFT studies on the structure and stability of tetraaza macrocyclic nickel(II) complexes containing dicarbinolamine ligand moiety. J CHEM SCI 2019. [DOI: 10.1007/s12039-019-1688-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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166
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High-resolution iron X-ray absorption spectroscopic and computational studies of non-heme diiron peroxo intermediates. J Inorg Biochem 2019; 203:110877. [PMID: 31710865 DOI: 10.1016/j.jinorgbio.2019.110877] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/05/2019] [Accepted: 10/01/2019] [Indexed: 11/20/2022]
Abstract
Ferritin-like carboxylate-bridged non-heme diiron enzymes activate O2 for a variety of difficult reactions throughout nature. These reactions often begin by abstraction of hydrogen from strong CH bonds. The enzymes activate O2 at their diferrous cofactors to form canonical diferric peroxo intermediates, with a range of possible coordination modes. Herein, we explore the ability of high-energy resolution fluorescence detected X-ray absorption spectroscopy (HERFD XAS) to provide insight into the nature of peroxo level intermediates in non-heme diiron proteins. Freeze quenched (FQ) peroxo intermediates from p-aminobenzoate N-oxygenase (AurF), aldehyde-deformylating oxygenase (ADO), and the β subunit of class Ia ribonucleotide reductase from Escherichia coli (Ecβ) are investigated. All three intermediates are proposed to adopt different peroxo binding modes, and each exhibit different Fe Kα HERFD XAS pre-edge features and intensities. As these FQ-trapped samples consist of multiple species, deconvolution of HERFD XAS spectra based on speciation, as determined by Mössbauer spectroscopy, is also necessitated - yielding 'pure' diferric peroxo HERFD XAS spectra from dilute protein samples. Finally, the impact of a given peroxo coordination mode on the HERFD XAS pre-edge energy and intensity is evaluated through time-dependent density functional theory (TDDFT) calculations of the XAS spectra on a series of hypothetical model complexes, which span a full range of possible peroxo coordination modes to a diferric core. The utility of HERFD XAS for future studies of enzymatic intermediates is discussed.
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167
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Jingwen Ran, Yu Y, Li L. Synthesis, Crystal Structure, and Photocatalytic Properties of Two Novel Fe-Complexes Based on Oxalato Ligands. RUSS J INORG CHEM+ 2019. [DOI: 10.1134/s003602361909016x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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168
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Yan L, Liu Y. Insights into the Mechanism and Enantioselectivity in the Biosynthesis of Ergot Alkaloid Cycloclavine Catalyzed by Aj_EasH from Aspergillus japonicus. Inorg Chem 2019; 58:13771-13781. [PMID: 31560525 DOI: 10.1021/acs.inorgchem.9b01168] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Cycloclavine is a complex ergot alkaloid containing an unusual cyclopropyl moiety, which has a wide range of biological activities and pharmaceutical applications. The biosynthesis of cycloclavine requires a series of enzymes, one of which is a nonheme FeII/α-ketoglutarate-dependent (aKG) oxidase (Aj_EasH). According to the previous proposal, the cyclopropyl ring formation catalyzed by Aj_EasH follows an unprecedented oxidative mechanism; however, the reaction details are unknown. In this article, on the basis of the recently obtained crystal structure of Aj_EasH (EasH from Aspergillus japonicas), the reactant models were built, and the reaction details were investigated by performing QM-only and combined QM and MM calculations. Our calculation results reveal that the biosynthesis of cyclopropyl moiety involves a radical intermediate rather than a carbocationic or carbanionic intermediate as in the biosynthesis of terpenoid family. The iron(IV)-oxo first abstracts a hydrogen atom from the substrate to trigger the reaction, and then the generated radical intermediate undergoes ring rearrangement to form the fused 5-3 ring system of cycloclavine. On the basis of our calculations, the absolute configuration of the cycloclavine catalyzed by Aj_EasH from Aspergillus japonicus should be (5R,8R,10R), which is different from the product isolated from Ipomoea hildebrandtii (5R,8S,10S). Residues at the active site play an important role in substrate binding, ring rearrangement, and enantioselectivity.
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Affiliation(s)
- Lijuan Yan
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , Shandong 250100 , China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering , Shandong University , Jinan , Shandong 250100 , China
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169
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Song H, Naowarojna N, Cheng R, Lopez J, Liu P. Non-heme iron enzyme-catalyzed complex transformations: Endoperoxidation, cyclopropanation, orthoester, oxidative C-C and C-S bond formation reactions in natural product biosynthesis. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 117:1-61. [PMID: 31564305 DOI: 10.1016/bs.apcsb.2019.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Non-heme iron enzymes catalyze a wide range of chemical transformations, serving as one of the key types of tailoring enzymes in the biosynthesis of natural products. Hydroxylation reaction is the most common type of reactions catalyzed by these enzymes and hydroxylation reactions have been extensively investigated mechanistically. However, the mechanistic details for other types of transformations remain largely unknown or unexplored. In this paper, we present some of the most recently discovered transformations, including endoperoxidation, orthoester formation, cyclopropanation, oxidative C-C and C-S bond formation reactions. In addition, many of them are multi-functional enzymes, which further complicate their mechanistic investigations. In this work, we summarize their biosynthetic pathways, with special emphasis on the mechanistic details available for these newly discovered enzymes.
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Affiliation(s)
- Heng Song
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, People's Republic of China
| | | | - Ronghai Cheng
- Department of Chemistry, Boston University, Boston, MA, United States
| | - Juan Lopez
- Department of Chemistry, Boston University, Boston, MA, United States
| | - Pinghua Liu
- Department of Chemistry, Boston University, Boston, MA, United States
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170
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Singh W, Quinn D, Moody TS, Huang M. Reaction Mechanism of Histone Demethylation in αKG-dependent Non-Heme Iron Enzymes. J Phys Chem B 2019; 123:7801-7811. [PMID: 31469562 DOI: 10.1021/acs.jpcb.9b06064] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Histone demethylases (KDMs) catalyze histone lysine demethylation, an important epigenetic process that controls gene expression in eukaryotes, and represent important cancer drug targets for cancer treatment. Demethylation of histone is comprised of sequential reaction steps including oxygen activation, decarboxylation, and demethylation. The initial oxygen binding and activation steps have been studied. However, the information on the complete catalytic reaction cycle is limited, which has impeded the structure-based design of inhibitors targeting KDMs. Here we report the mechanism of the complete reaction steps catalyzed by a representative nonheme iron αKG-dependent KDM, PHF8 using QM/MM approaches. The atomic-level understanding on the complete reaction mechanism of PHF8 would shed light on the structure-based design of selective inhibitors targeting KDMs to intervene in cancer epigenetics.
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Affiliation(s)
- Warispreet Singh
- School of Chemistry & Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast BT9 5AG , Northern Ireland , United Kingdom.,Department of Biocatalysis and Isotope Chemistry , Almac Sciences , Almac House, 20 Seagoe Industrial Estate , Craigavon BT63 5QD , Northern Ireland , United Kingdom
| | - Derek Quinn
- Department of Biocatalysis and Isotope Chemistry , Almac Sciences , Almac House, 20 Seagoe Industrial Estate , Craigavon BT63 5QD , Northern Ireland , United Kingdom
| | - Thomas S Moody
- Department of Biocatalysis and Isotope Chemistry , Almac Sciences , Almac House, 20 Seagoe Industrial Estate , Craigavon BT63 5QD , Northern Ireland , United Kingdom.,Arran Chemical Company Limited , Unit 1 Monksland Industrial Estate , Athlone , Co. Roscommon , Ireland
| | - Meilan Huang
- School of Chemistry & Chemical Engineering , Queen's University Belfast , David Keir Building, Stranmillis Road , Belfast BT9 5AG , Northern Ireland , United Kingdom
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171
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Wind ML, Hoof S, Braun-Cula B, Herwig C, Limberg C. Switching from a Chromium(IV) Peroxide to a Chromium(III) Superoxide upon Coordination of a Donor in the trans Position. J Am Chem Soc 2019; 141:14068-14072. [PMID: 31461282 DOI: 10.1021/jacs.9b06826] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
O2 activation at a chromium(II) siloxide complex in propionitrile leads to a chromium(III) complex with an end-on bound superoxide ligand, while the reaction in tetrahydrofuran leads to a side-on peroxo chromium(IV) compound. The superoxide reacts faster with (2,2,6,6-tetramethylpiperidin-1-yl)oxyl hydroxylamine while the peroxide, unlike the superoxide, proved capable of deformylating aldehydes. The system was found to represent a unique case, where even a switching between the two structures can be achieved via the solvent; its ability to coordinate at the position trans to the O2 ligand is decisive, as supported by density functional theory studies. Altogether, the results show that subtle changes can determine for an initially formed metal-dioxygen adduct, whether it exists as a superoxide or a peroxide, which thus merits consideration in discussions on mechanisms and possible reaction routes.
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Affiliation(s)
- Marie-Louise Wind
- Department of Chemistry , Humboldt-Universität zu Berlin , Brook-Taylor-Straße 2 , 12489 Berlin , Germany
| | - Santina Hoof
- Department of Chemistry , Humboldt-Universität zu Berlin , Brook-Taylor-Straße 2 , 12489 Berlin , Germany
| | - Beatrice Braun-Cula
- Department of Chemistry , Humboldt-Universität zu Berlin , Brook-Taylor-Straße 2 , 12489 Berlin , Germany
| | - Christian Herwig
- Department of Chemistry , Humboldt-Universität zu Berlin , Brook-Taylor-Straße 2 , 12489 Berlin , Germany
| | - Christian Limberg
- Department of Chemistry , Humboldt-Universität zu Berlin , Brook-Taylor-Straße 2 , 12489 Berlin , Germany
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172
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Indira S, Vinoth G, Bharathi M, Bharathi S, Kalilur Rahiman A, Shanmuga Bharathi K. Catechol oxidase and phenoxazinone synthase mimicking activities of mononuclear Fe(III) and Co(III) complexes of amino-bis(phenolate)-based mixed ligands: Synthesis, spectral and electrochemical studies. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.118988] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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173
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Narwane M, Chang YL, Ching WM, Tsai ML, Hsu SC. Investigation on the coordination behaviors of tris(2-pyridyl)pyrazolyl borates iron(II) complexes. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2019.118966] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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174
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New Artificial Biomimetic Enzyme Analogues based on Iron(II/III) Schiff Base Complexes: An Effect of (Benz)imidazole Organic Moieties on Phenoxazinone Synthase and DNA Recognition. Molecules 2019; 24:molecules24173173. [PMID: 31480486 PMCID: PMC6749401 DOI: 10.3390/molecules24173173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 02/03/2023] Open
Abstract
Elucidation of the structure and function of biomolecules provides us knowledge that can be transferred into the generation of new materials and eventually applications in e.g., catalysis or bioassays. The main problems, however, concern the complexity of the natural systems and their limited availability, which necessitates utilization of simple biomimetic analogues that are, to a certain degree, similar in terms of structure and thus behaviour. We have, therefore, devised a small library of six tridentate N-heterocyclic coordinating agents (L1-L6), which, upon complexation, form two groups of artificial, monometallic non-heme iron species. Utilization of iron(III) chloride leads to the formation of the 1:1 (Fe:Ln) 'open' complexes, whereas iron(II) trifluoromethanosulfonate allows for the synthesis of 1:2 (M:Ln) 'closed' systems. The structural differences between the individual complexes are a result of the information encoded within the metallic centre and the chosen counterion, whereas the organic scaffold influences the observed properties. Indeed, the number and nature of the external hydrogen bond donors coming from the presence of (benz)imidazole moieties in the ligand framework are responsible for the observed biological behaviour in terms of mimicking phenoxazinone synthase activity and interaction with DNA.
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175
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Azarkh M, Gast P, Mason AB, Groenen EJJ, Mathies G. Analysis of the EPR spectra of transferrin: the importance of a zero-field-splitting distribution and 4 th-order terms. Phys Chem Chem Phys 2019; 21:16937-16948. [PMID: 31339131 DOI: 10.1039/c9cp02626f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Multi-frequency EPR spectroscopy can provide high-level structural information on high-spin Fe3+ sites in proteins and enzymes. Unfortunately, analysis of the EPR spectra of these spin systems is hindered by the presence of broad distributions in the zero-field-splitting (ZFS) parameters, which reflect conformational heterogeneity of the iron sites. We present the analysis of EPR spectra of high-spin Fe3+ bound to human serum transferrin. We apply a method termed the grid-of-errors to extract the distributions of the individual ZFS parameters from EPR spectra recorded in the high-field limit at a microwave frequency of 275 GHz. Study of a series of transferrin variants shows that the ZFS distributions are as characteristic of the structure of a high-spin Fe3+ site as the ZFS parameters themselves. Simulations based on the extracted ZFS distributions reproduce spectra recorded at 34 GHz (Q band) and 9.7 GHz (X band), including subtle variations that were previously difficult to quantify. The X-band spectrum of transferrin shows a characteristic double peak, which has puzzled researchers for decades. We show that the double peak is uniquely related to the term B4-3O4-3(S) in the spin Hamiltonian. Our method is generally applicable in the analysis of spectra that arise from a broad distribution of parameters.
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Affiliation(s)
- Mykhailo Azarkh
- Department of Chemistry, University of Konstanz, 78464 Konstanz, Germany.
| | - Peter Gast
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Anne B Mason
- Department of Biochemistry, University of Vermont College of Medicine, Burlington, VT 05405, USA
| | - Edgar J J Groenen
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, PO Box 9504, 2300 RA Leiden, The Netherlands
| | - Guinevere Mathies
- Department of Chemistry, University of Konstanz, 78464 Konstanz, Germany.
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176
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Roatsch M, Hoffmann I, Abboud MI, Hancock RL, Tarhonskaya H, Hsu KF, Wilkins SE, Yeh TL, Lippl K, Serrer K, Moneke I, Ahrens TD, Robaa D, Wenzler S, Barthes NPF, Franz H, Sippl W, Lassmann S, Diederichs S, Schleicher E, Schofield CJ, Kawamura A, Schüle R, Jung M. The Clinically Used Iron Chelator Deferasirox Is an Inhibitor of Epigenetic JumonjiC Domain-Containing Histone Demethylases. ACS Chem Biol 2019; 14:1737-1750. [PMID: 31287655 DOI: 10.1021/acschembio.9b00289] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Fe(II)- and 2-oxoglutarate (2OG)-dependent JumonjiC domain-containing histone demethylases (JmjC KDMs) are "epigenetic eraser" enzymes involved in the regulation of gene expression and are emerging drug targets in oncology. We screened a set of clinically used iron chelators and report that they potently inhibit JMJD2A (KDM4A) in vitro. Mode of action investigations revealed that one compound, deferasirox, is a bona fide active site-binding inhibitor as shown by kinetic and spectroscopic studies. Synthesis of derivatives with improved cell permeability resulted in significant upregulation of histone trimethylation and potent cancer cell growth inhibition. Deferasirox was also found to inhibit human 2OG-dependent hypoxia inducible factor prolyl hydroxylase activity. Therapeutic effects of clinically used deferasirox may thus involve transcriptional regulation through 2OG oxygenase inhibition. Deferasirox might provide a useful starting point for the development of novel anticancer drugs targeting 2OG oxygenases and a valuable tool compound for investigations of KDM function.
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Affiliation(s)
- Martin Roatsch
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
| | - Inga Hoffmann
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
| | - Martine I Abboud
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Rebecca L Hancock
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Hanna Tarhonskaya
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Kuo-Feng Hsu
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Sarah E Wilkins
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Tzu-Lan Yeh
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Kerstin Lippl
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Kerstin Serrer
- Institute of Physical Chemistry , Albert-Ludwigs-Universität Freiburg , Albertstraße 21 , 79104 Freiburg i.Br. , Germany
| | - Isabelle Moneke
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine , University of Freiburg , German Cancer Consortium (DKTK)-Partner Site Freiburg, Breisacher Straße 115 , 79106 Freiburg i.Br. , Germany
| | - Theresa D Ahrens
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine , University of Freiburg , Breisacher Straße 115a , 79106 Freiburg i.Br. , Germany
| | - Dina Robaa
- Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , Wolfgang-Langenbeck-Straße 4 , 06120 Halle (Saale) , Germany
| | - Sandra Wenzler
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
| | - Nicolas P F Barthes
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
| | - Henriette Franz
- Central Clinical Research, Medical Center and Faculty of Medicine , University of Freiburg , Breisacher Straße 66 , 79106 Freiburg i.Br. , Germany
| | - Wolfgang Sippl
- Institute of Pharmacy , Martin-Luther-University Halle-Wittenberg , Wolfgang-Langenbeck-Straße 4 , 06120 Halle (Saale) , Germany
| | - Silke Lassmann
- Institute for Surgical Pathology, Medical Center and Faculty of Medicine , University of Freiburg , Breisacher Straße 115a , 79106 Freiburg i.Br. , Germany
| | - Sven Diederichs
- Division of Cancer Research, Department of Thoracic Surgery, Medical Center-University of Freiburg, Faculty of Medicine , University of Freiburg , German Cancer Consortium (DKTK)-Partner Site Freiburg, Breisacher Straße 115 , 79106 Freiburg i.Br. , Germany
- Division of RNA Biology & Cancer , German Cancer Research Center (DKFZ) , Im Neuenheimer Feld 280 , 69120 Heidelberg , Germany
| | - Erik Schleicher
- Institute of Physical Chemistry , Albert-Ludwigs-Universität Freiburg , Albertstraße 21 , 79104 Freiburg i.Br. , Germany
| | - Christopher J Schofield
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Akane Kawamura
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , United Kingdom
| | - Roland Schüle
- Central Clinical Research, Medical Center and Faculty of Medicine , University of Freiburg , Breisacher Straße 66 , 79106 Freiburg i.Br. , Germany
| | - Manfred Jung
- Institute of Pharmaceutical Sciences , Albert-Ludwigs-Universität Freiburg , Albertstraße 25 , 79104 Freiburg i.Br. , Germany
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177
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Chakraborty A, Chakraborty T, Menendez MI, Chattopadhyay T. Surfactant-Mediated Solubilization of Magnetically Separable Nanocatalysts for the Oxidation of Alcohols. ACS OMEGA 2019; 4:11558-11565. [PMID: 31460262 PMCID: PMC6682040 DOI: 10.1021/acsomega.9b01143] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 06/21/2019] [Indexed: 06/10/2023]
Abstract
Cetrimonium bromide (CTAB)-coated water disperse magnetically separable nanocatalysts CTAB/Fe3O4@dopa@ML (M = Fe or Mn, L = cyclohexane-1,2-diylbis(azanylylidene)bis(methanylylidene)bis(2,4-diXphenol; X = Cl, Br, and I) have been synthesized using a simple synthetic strategy. This approach provides a new fruitful strategy to reduce the leaching of the active metal complex from the catalyst surface to the aqueous media. The synthesized catalysts have been found to be excellent for oxidation of alcohols in aqueous medium at room temperature. A probable catalytic pathway involving the generation of hydroperoxo intermediates has been assumed, and these intermediates have been characterized using density functional theory and several spectroscopic techniques. It is worthy of mention that the synthesized CTAB-coated magnetically separable nanocatalysts can be magnetically recovered from the aqueous reaction mixture after more than five cycles, which renders this approach as a sustainable and accessible one.
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Affiliation(s)
- Aratrika Chakraborty
- Department
of Chemistry, University of Calcutta, 92, A. P. C. Road, Kolkata 700009, India
| | - Tonmoy Chakraborty
- Department
of Chemistry, University of Calcutta, 92, A. P. C. Road, Kolkata 700009, India
| | - Maria Isabel Menendez
- Departamento
de Química Física y Analítica, Universidad de Oviedo, C/ Julián Clavería 8, 33006 Oviedo, Spain
| | - Tanmay Chattopadhyay
- Department
of Chemistry, Diamond Harbour Women’s
University, Diamond Harbour
Road, Sarisha, South 24 Pgs (S) 743368, India
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178
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Lin YH, Cramer HH, van Gastel M, Tsai YH, Chu CY, Kuo TS, Lee IR, Ye S, Bill E, Lee WZ. Mononuclear Manganese(III) Superoxo Complexes: Synthesis, Characterization, and Reactivity. Inorg Chem 2019; 58:9756-9765. [PMID: 31328507 PMCID: PMC6685055 DOI: 10.1021/acs.inorgchem.9b00767] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metal-superoxo species are typically proposed as key intermediates in the catalytic cycle of dioxygen activation by metalloenzymes involving different transition metal cofactors. In this regard, while a series of Fe-, Co-, and Ni-superoxo complexes have been reported to date, well-defined Mn-superoxo complexes remain rather rare. Herein, we report two mononuclear MnIII-superoxo species, Mn(BDPP)(O2•-) (2, H2BDPP = 2,6-bis((2-(S)-diphenylhydroxylmethyl-1-pyrrolidinyl)methyl)pyridine) and Mn(BDPBrP)(O2•-) (2', H2BDPBrP = 2,6-bis((2-(S)-di(4-bromo)phenylhydroxyl-methyl-1-pyrrolidinyl)methyl)pyridine), synthesized by bubbling O2 into solutions of their MnII precursors, Mn(BDPP) (1) and Mn(BDPBrP) (1'), at -80 °C. A combined spectroscopic (resonance Raman and electron paramagnetic resonance (EPR) spectroscopy) and computational study evidence that both complexes contain a high-spin MnIII center (SMn = 2) antiferromagnetically coupled to a superoxo radical ligand (SOO• = 1/2), yielding an overall S = 3/2 ground state. Complexes 2 and 2' were shown to be capable of abstracting a H atom from 2,2,6,6-tetramethyl-1-hydroxypiperidine (TEMPO-H) to form MnIII-hydroperoxo species, Mn(BDPP)(OOH) (5) and Mn(BDPBrP)(OOH) (5'). Complexes 5 and 5' can be independently prepared by the reactions of the isolated MnIII-aqua complexes, [Mn(BDPP)(H2O)]OTf (6) and [Mn(BDPBrP)(H2O)]OTf (6'), with H2O2 in the presence of NEt3. The parallel-mode EPR measurements established a high-spin S = 2 ground state for 5 and 5'.
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Affiliation(s)
| | - Hanna Hinrika Cramer
- Max-Planck-Institut für Chemische Energiekonversion , Mülheim an der Ruhr D-45470 , Germany
| | - Maurice van Gastel
- Max-Planck-Institut für Kohlenforschung , Mülheim an der Ruhr D-45470 , Germany
| | | | | | | | | | - Shengfa Ye
- Max-Planck-Institut für Kohlenforschung , Mülheim an der Ruhr D-45470 , Germany
| | - Eckhard Bill
- Max-Planck-Institut für Chemische Energiekonversion , Mülheim an der Ruhr D-45470 , Germany
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179
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Andris E, Navrátil R, Jašík J, Srnec M, Rodríguez M, Costas M, Roithová J. M-O Bonding Beyond the Oxo Wall: Spectroscopy and Reactivity of Cobalt(III)-Oxyl and Cobalt(III)-Oxo Complexes. Angew Chem Int Ed Engl 2019; 58:9619-9624. [PMID: 31083766 PMCID: PMC6618258 DOI: 10.1002/anie.201904546] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/13/2019] [Indexed: 01/05/2023]
Abstract
Terminal oxo complexes of late transition metals are frequently proposed reactive intermediates. However, they are scarcely known beyond Group 8. Using mass spectrometry, we prepared and characterized two such complexes: [(N4Py)CoIII (O)]+ (1) and [(N4Py)CoIV (O)]2+ (2). Infrared photodissociation spectroscopy revealed that the Co-O bond in 1 is rather strong, in accordance with its lack of chemical reactivity. On the contrary, 2 has a very weak Co-O bond characterized by a stretching frequency of ≤659 cm-1 . Accordingly, 2 can abstract hydrogen atoms from non-activated secondary alkanes. Previously, this reactivity has only been observed in the gas phase for small, coordinatively unsaturated metal complexes. Multireference ab-initio calculations suggest that 2, formally a cobalt(IV)-oxo complex, is best described as cobalt(III)-oxyl. Our results provide important data on changes to metal-oxo bonding behind the oxo wall and show that cobalt-oxo complexes are promising targets for developing highly active C-H oxidation catalysts.
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Affiliation(s)
- Erik Andris
- Department of Organic ChemistryFaculty of ScienceCharles UniversityHlavova 2030/8128 43Prague 2Czech Republic
| | - Rafael Navrátil
- Department of Organic ChemistryFaculty of ScienceCharles UniversityHlavova 2030/8128 43Prague 2Czech Republic
| | - Juraj Jašík
- Department of Organic ChemistryFaculty of ScienceCharles UniversityHlavova 2030/8128 43Prague 2Czech Republic
| | - Martin Srnec
- J. Heyrovsky Institute of Physical Chemistry of the CASv. v. i., Dolejškova 2155/31822 3Prague 8Czech Republic
| | - Mònica Rodríguez
- Departament de Quimica and Institute of Computational Chemistry and Catalysis (IQCC)University of GironaCampus MontiliviGirona17071Spain
| | - Miquel Costas
- Departament de Quimica and Institute of Computational Chemistry and Catalysis (IQCC)University of GironaCampus MontiliviGirona17071Spain
| | - Jana Roithová
- Department of Organic ChemistryFaculty of ScienceCharles UniversityHlavova 2030/8128 43Prague 2Czech Republic
- Radboud University NijmegenInstitute for Molecules and MaterialsHeyendaalseweg 1356525 AJNijmegenThe Netherlands
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180
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Lin HY, Chen X, Chen JN, Wang DW, Wu FX, Lin SY, Zhan CG, Wu JW, Yang WC, Yang GF. Crystal Structure of 4-Hydroxyphenylpyruvate Dioxygenase in Complex with Substrate Reveals a New Starting Point for Herbicide Discovery. RESEARCH 2019; 2019:2602414. [PMID: 31549053 PMCID: PMC6750108 DOI: 10.34133/2019/2602414] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/10/2019] [Indexed: 01/09/2023]
Abstract
4-Hydroxyphenylpyruvate dioxygenase (HPPD) is a promising target for drug and pesticide discovery. The unknown binding mode of substrate is still a big challenge for the understanding of enzymatic reaction mechanism and novel HPPD inhibitor design. Herein, we determined the first crystal structure of Arabidopsis thaliana HPPD (AtHPPD) in complex with its natural substrate (HPPA) at a resolution of 2.80 Å. Then, combination of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations confirmed that HPPA takes keto rather than enol form inside the HPPD active pocket. Subsequent site-directed mutagenesis and kinetic analysis further showed that residues (Phe424, Asn423, Glu394, Gln307, Asn282, and Ser267) played important roles in substrate binding and catalytic cycle. Structural comparison between HPPA-AtHPPD and holo-AtHPPD revealed that Gln293 underwent a remarkable rotation upon the HPPA binding and formed H-bond network of Ser267-Asn282-Gln307-Gln293, resulting in the transformation of HPPD from an inactive state to active state. Finally, taking the conformation change of Gln293 as a target, we proposed a new strategy of blocking the transformation of HPPD from inactive state to active state to design a novel inhibitor with Ki value of 24.10 nM towards AtHPPD. The inhibitor has entered into industry development as the first selective herbicide used for the weed control in sorghum field. The crystal structure of AtHPPD in complex with the inhibitor (2.40 Å) confirmed the rationality of the design strategy. We believe that the present work provides a new starting point for the understanding of enzymatic reaction mechanism and the design of next generation HPPD inhibitors.
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Affiliation(s)
- Hong-Yan Lin
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, China.,MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xi Chen
- College of Chemistry and Material Science, South-Central University for Nationalities, Wuhan 430074, China
| | - Jia-Nan Chen
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, China
| | - Da-Wei Wang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, China
| | - Feng-Xu Wu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, China
| | - Song-Yun Lin
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Chang-Guo Zhan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 South Limestone Street, Lexington, KY 40536, USA
| | - Jia-Wei Wu
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wen-Chao Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Chemical Biology Center, Central China Normal University, Wuhan 430079, China.,Collaborative Innovation Center of Chemical Science and Engineering, Tianjin 30071, China
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181
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Johnson EJ, Kleinlein C, Musgrave RA, Betley TA. Diiron oxo reactivity in a weak-field environment. Chem Sci 2019; 10:6304-6310. [PMID: 31341583 PMCID: PMC6598509 DOI: 10.1039/c9sc00605b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 05/08/2019] [Indexed: 11/21/2022] Open
Abstract
Concomitant deprotonation and metalation of a dinucleating cofacial Pacman dipyrrin ligand platform tBudmxH2 with Fe2(Mes)4 results in formation of a diiron complex ( tBudmx)Fe2(Mes)2. Treatment of ( tBudmx)Fe2(Mes)2 with one equivalent of water yields the diiron μ-oxo complex ( tBudmx)Fe2(μ-O) and free mesitylene. A two-electron oxidation of ( tBudmx)Fe2(μ-O) gives rise to the diferric complex ( tBudmx)Fe2(μ-O)Cl2, and one-electron reduction from this FeIIIFeIII state allows for isolation of a mixed-valent species [Cp2Co][( tBudmx)Fe2(μ-O)Cl2]. Both ( tBudmx)Fe2(μ-O) and [Cp2Co][( tBudmx)Fe2(μ-O)Cl2] exhibit basic character at the bridging oxygen atom and can be protonated using weak acids to form bridging diferrous hydroxide species. The basicity of the diferrous oxo ( tBudmx)Fe2(μ-O) is quantified through studies of the pK a of its conjugate acid, [( tBudmx)Fe2(μ-OH)]+, which is determined to be 15.3(6); interestingly, upon coordination of neutral solvent ligands to yield ( tBudmx)Fe2(μ-O)(thf)2, the basicity is increased as observed through an increase in the pK a of the conjugate acid [( tBudmx)Fe2(μ-OH)(thf)2]+ to 26.8(6). In contrast, attempts to synthesize a diferric bridging hydroxide by two-electron oxidation of [( tBudmx)Fe2(μ-OH)(thf)2]+ resulted in isolation of ( tBudmx)Fe2(μ-O)Cl2 with concomitant loss of a proton, consistent with the pK a of the conjugate acid [( tBudmx)Fe2(μ-OH)Cl2]+ determined computationally to be -1.8(6). The foregoing results highlight the intricate interplay between oxidation state and reactivity in diiron μ-oxo units.
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Affiliation(s)
- Elizabeth J Johnson
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , MA 02138 , USA .
| | - Claudia Kleinlein
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , MA 02138 , USA .
| | - Rebecca A Musgrave
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , MA 02138 , USA .
| | - Theodore A Betley
- Department of Chemistry and Chemical Biology , Harvard University , Cambridge , MA 02138 , USA .
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182
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Structural characterization of an isopenicillin N synthase family oxygenase from Pseudomonas aeruginosa PAO1. Biochem Biophys Res Commun 2019; 514:1031-1036. [PMID: 31097228 DOI: 10.1016/j.bbrc.2019.05.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 05/07/2019] [Indexed: 11/22/2022]
Abstract
Isopenicillin N synthase (IPNS) is a nonheme-Fe2+-dependent enzyme that mediates a key step in penicillin biosynthesis. It catalyses the conversion of the tripeptide δ-(l-α-aminoadipoyl)-l-cysteine-d-valine (ACV) to isopenicillin N, which is a key precursor to β-lactam antibiotics. The pa4191 gene in Pseudomonas aeruginosa PAO1 has provisionally been annotated as a member of the IPNS family. In this work, we report the crystal structure of PA4191 from P. aeruginosa (PaIPNS hereafter). The 1.65 Å resolution PaIPNS structure forms a jelly roll fold and is confirmed to be a member of the IPNS family based on structural homology. A metal centre within the jelly roll consists of the strictly conserved His201, Asp203 and His257 residues. MicroScale Thermophoresis binding analysis confirms that PaIPNS is a metal-binding protein with a strong preference for iron, but that it does not bind the tripeptide ACV. Structural comparison of PaIPNS with a previously reported IPNS-ACV complex structure reveals a restricted binding pocket that is unable to accommodate ACV.
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183
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Chekan JR, Ongpipattanakul C, Wright TR, Zhang B, Bollinger JM, Rajakovich LJ, Krebs C, Cicchillo RM, Nair SK. Molecular basis for enantioselective herbicide degradation imparted by aryloxyalkanoate dioxygenases in transgenic plants. Proc Natl Acad Sci U S A 2019; 116:13299-13304. [PMID: 31209034 PMCID: PMC6613135 DOI: 10.1073/pnas.1900711116] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The synthetic auxin 2,4-dichlorophenoxyacetic acid (2,4-D) is an active ingredient of thousands of commercial herbicides. Multiple species of bacteria degrade 2,4-D via a pathway initiated by the Fe(II) and α-ketoglutarate (Fe/αKG)-dependent aryloxyalkanoate dioxygenases (AADs). Recently, genes encoding 2 AADs have been deployed commercially in herbicide-tolerant crops. Some AADs can also inactivate chiral phenoxypropionate and aryloxyphenoxypropionate (AOPP) herbicides, albeit with varying substrate enantioselectivities. Certain AAD enzymes, such as AAD-1, have expanded utility in weed control systems by enabling the use of diverse modes of action with a single trait. Here, we report 1) the use of a genomic context-based approach to identify 59 additional members of the AAD class, 2) the biochemical characterization of AAD-2 from Bradyrhizobium diazoefficiens USDA 110 as a catalyst to degrade (S)-stereoisomers of chiral synthetic auxins and AOPP herbicides, 3) spectroscopic data that demonstrate the canonical ferryl complex in the AAD-1 reaction, and 4) crystal structures of representatives of the AAD class. Structures of AAD-1, an (R)-enantiomer substrate-specific enzyme, in complexes with a phenoxypropionate synthetic auxin or with AOPP herbicides and of AAD-2, which has the opposite (S)-enantiomeric substrate specificity, reveal the structural basis for stereoselectivity and provide insights into a common catalytic mechanism.
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Affiliation(s)
- Jonathan R Chekan
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | | | - Terry R Wright
- Corteva Agriscience, Agriculture Division of DowDuPont, Indianapolis, IN 46268
| | - Bo Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
| | - J Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Lauren J Rajakovich
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802
| | - Robert M Cicchillo
- Corteva Agriscience, Agriculture Division of DowDuPont, Indianapolis, IN 46268
| | - Satish K Nair
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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184
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Phung QM, Martín-Fernández C, Harvey JN, Feldt M. Ab Initio Calculations for Spin-Gaps of Non-Heme Iron Complexes. J Chem Theory Comput 2019; 15:4297-4304. [DOI: 10.1021/acs.jctc.9b00370] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Quan Manh Phung
- Department of Chemistry, KU Leuven, Celestijnenlaan 200f, Box 2404, 3001 Leuven, Belgium
| | | | - Jeremy N. Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200f, Box 2404, 3001 Leuven, Belgium
| | - Milica Feldt
- Department of Chemistry, KU Leuven, Celestijnenlaan 200f, Box 2404, 3001 Leuven, Belgium
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185
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Andris E, Navrátil R, Jašík J, Srnec M, Rodríguez M, Costas M, Roithová J. M−O Bonding Beyond the Oxo Wall: Spectroscopy and Reactivity of Cobalt(III)‐Oxyl and Cobalt(III)‐Oxo Complexes. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201904546] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Erik Andris
- Department of Organic ChemistryFaculty of ScienceCharles University Hlavova 2030/8 128 43 Prague 2 Czech Republic
| | - Rafael Navrátil
- Department of Organic ChemistryFaculty of ScienceCharles University Hlavova 2030/8 128 43 Prague 2 Czech Republic
| | - Juraj Jašík
- Department of Organic ChemistryFaculty of ScienceCharles University Hlavova 2030/8 128 43 Prague 2 Czech Republic
| | - Martin Srnec
- J. Heyrovsky Institute of Physical Chemistry of the CAS v. v. i., Dolejškova 2155/3 1822 3 Prague 8 Czech Republic
| | - Mònica Rodríguez
- Departament de Quimica and Institute of Computational Chemistry and Catalysis (IQCC)University of Girona Campus Montilivi Girona 17071 Spain
| | - Miquel Costas
- Departament de Quimica and Institute of Computational Chemistry and Catalysis (IQCC)University of Girona Campus Montilivi Girona 17071 Spain
| | - Jana Roithová
- Department of Organic ChemistryFaculty of ScienceCharles University Hlavova 2030/8 128 43 Prague 2 Czech Republic
- Radboud University NijmegenInstitute for Molecules and Materials Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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186
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Jiang H, Lai W, Chen H. Generation of Carbon Radical from Iron-Hydride/Alkene: Exchange-Enhanced Reactivity Selects the Reactive Spin State. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01691] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Hao Jiang
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- Department of Chemistry, Renmin University of China, Beijing 100872, P. R. China
| | - Wenzhen Lai
- Department of Chemistry, Renmin University of China, Beijing 100872, P. R. China
| | - Hui Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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187
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Zeb N, Rashid MH, Mubarak MQE, Ghafoor S, de Visser SP. Flavonol biosynthesis by nonheme iron dioxygenases: A computational study into the structure and mechanism. J Inorg Biochem 2019; 198:110728. [PMID: 31203088 DOI: 10.1016/j.jinorgbio.2019.110728] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/13/2019] [Accepted: 05/29/2019] [Indexed: 12/20/2022]
Abstract
Plants produce flavonol compounds for vital functions regarding plant growth, fruit and flower colouring as well as fruit ripening processes. Several of these biosynthesis steps are stereo- and regioselective and are being carried out by nonheme iron enzymes. Using density functional theory calculations on a large active site model complex of flavanone-3β-hydroxylase (FHT), we established the mechanism for conversion of naringenin to its dihydroflavonol, which is a key step in the mechanism of flavonol biosynthesis. The reaction starts with dioxygen binding to the iron(II) centre and a reaction with α-ketoglutarate co-substrate gives succinate, an iron(IV)-oxo species and CO2 with large exothermicity and small reaction barriers. The rate-determining reaction step in the mechanism; however, is hydrogen atom abstraction of an aliphatic CH bond by the iron(IV)-oxo species. We identify a large kinetic isotope effect for the replacement of the transferring hydrogen atom by deuterium. In a final step the OH and substrate radicals combine to form the alcohol product with a barrier of several kcal mol-1. We show that the latter is the result of geometric constraints in the active site pocket. Furthermore, the calculations show that a weak tertiary CH bond is shielded from the iron(IV)-oxo species in the substrate binding position and therefore the enzyme is able to activate a stronger CH bond. As such, the flavanone-3β-hydroxylase enzyme reacts regioselectively with one specific CH bond of naringenin by avoiding activation of weaker bonds through tight substrate and oxidant positioning.
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Affiliation(s)
- Neelam Zeb
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom; National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Muhammad H Rashid
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Jhang Road, P.O. Box 577, Faisalabad, Pakistan; Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - M Qadri E Mubarak
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Sidra Ghafoor
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom; Department of Chemistry, Government College University Faisalabad, Jhang Road, 3800 Faisalabad, Pakistan
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.
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188
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Karmakar M, Chattopadhyay S. A comprehensive overview of the orientation of tetradentate N2O2 donor Schiff base ligands in octahedral complexes of trivalent 3d metals. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.02.091] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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189
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Solomon EI, Iyer SR. Geometric and Electronic Structural Contributions to Fe/O 2 Reactivity. ACTA ACUST UNITED AC 2019; 73:3-14. [PMID: 32391114 DOI: 10.4019/bjscc.73.3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
While two classes of non-heme iron enzymes use ferric centers to activate singlet organic substrates for the spin forbidden reaction with 3O2, most classes use high spin ferrous sites to activate dioxygen. These FeII active sites do not exhibit intense absorption bands and have an integer spin ground state thus are mostly EPR inactive. We have developed new spectroscopic methodologies that provide geometric and electronic structural insight into the ferrous centers and their interactions with cosubstrates for dioxygen activation and into the nature of the intermediates generated in these reactions. First, we present our variable-temperature variable-field magnetic circular dichroism (VTVH MCD) methodology to experimentally define the geometric and electronic structure of the high spin ferrous active site. Then, we focus on using Nuclear Resonance Vibrational Spectroscopy (NRVS, performed at SPring-8) to define geometric structure and VTVH MCD to define the electronic structure of the FeIII-OOH and FeIV=O intermediates generated in O2 activation and the spin state dependence of their frontier molecular orbitals (FMOs) in controlling reactivity. Experimentally validated reaction coordinates are derived for the anticancer drug bleomycin in its cleavage of DNA and for an alpha- ketoglutarate dependent dioxygenase in its selective halogenation over the thermodynamically favored hydroxylation of substrate.
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190
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Barman SK, Cano J, Lloret F, Mukherjee R. Single-Molecule-Magnet FeII4FeIII2 and Antiferromagnetic FeIII4 Coordination Clusters. Inorg Chem 2019; 58:8086-8099. [DOI: 10.1021/acs.inorgchem.9b00828] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Suman K. Barman
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, India
| | - Joan Cano
- Departament de Química, Inorgànica/Instituto de Ciencia Molecular (ICMOL), Universitat de València, Polígono de
la Coma, s/n, 46980 Paterna (València), Spain
| | - Francesc Lloret
- Departament de Química, Inorgànica/Instituto de Ciencia Molecular (ICMOL), Universitat de València, Polígono de
la Coma, s/n, 46980 Paterna (València), Spain
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191
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Xue J, Lu J, Lai W. Mechanistic insights into a non-heme 2-oxoglutarate-dependent ethylene-forming enzyme: selectivity of ethylene-formation versusl-Arg hydroxylation. Phys Chem Chem Phys 2019; 21:9957-9968. [PMID: 31041955 DOI: 10.1039/c9cp00794f] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The ethylene-forming enzyme (EFE) is a unique member of the Fe(ii)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenases. It converts 2OG into ethylene plus three CO2 molecules (ethylene-forming reaction) and also catalyzes the C5 hydroxylation of l-arginine coupled to the oxidative decarboxylation of 2OG (l-Arg hydroxylation reaction). To uncover the mechanisms of the dual transformations by EFE, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out. Based on the results, a branched mechanism was proposed. An FeII-peroxysuccinate complex with a dissociated CO2 generated through the nucleophilic attack of the superoxo moiety of the Fe-O2 species on the keto carbon of 2OG is the key common intermediate in both reactions. A competition between the subsequent CO2 insertion (a key step in the ethylene-forming pathway) and the O-O bond cleavage (leading to the formation of succinate) governs the product selectivity. The calculated reaction barriers suggested that the CO2 insertion is favored over the O-O bond cleavage. This is consistent with the product preference observed in experiments. By comparison with the results of AsqJ (an Fe/2OG oxygenase that leads to substrate oxidation exclusively), the protein environment was found to be crucial for the selectivity. Further calculations demonstrated that the local electric field of the protein environment in EFE promotes ethylene formation by acting as a charge template, exemplifying the importance of the electrostatic interaction in enzyme catalysis. These findings offer mechanistic insights into the EFE catalysis and provide important clues for better understanding the unique ethylene-forming capability of EFE compared with other Fe/2OG oxygenases.
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Affiliation(s)
- Junqin Xue
- Department of Chemistry, Renmin University of China, Beijing, 100872, China.
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192
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Pattanayak S, Cantú Reinhard FG, Rana A, Gupta SS, de Visser SP. The Equatorial Ligand Effect on the Properties and Reactivity of Iron(V) Oxo Intermediates. Chemistry 2019; 25:8092-8104. [DOI: 10.1002/chem.201900708] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Santanu Pattanayak
- Department of Chemical SciencesIndian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246 India
| | - Fabián G. Cantú Reinhard
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Atanu Rana
- Indian Association for the Cultivation of Sciences 2A Raja S. C. Mullick Road Kolkata 700032 India
| | - Sayam Sen Gupta
- Department of Chemical SciencesIndian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246 India
| | - Sam P. de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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193
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Jana NC, Patra M, Brandão P, Panja A. Synthesis, structure and diverse coordination chemistry of cobalt(III) complexes derived from a Schiff base ligand and their biomimetic catalytic oxidation of o-aminophenols. Polyhedron 2019. [DOI: 10.1016/j.poly.2019.02.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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194
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Mehmood R, Qi HW, Steeves AH, Kulik HJ. The Protein’s Role in Substrate Positioning and Reactivity for Biosynthetic Enzyme Complexes: The Case of SyrB2/SyrB1. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00865] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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195
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Quesne MG, Silveri F, de Leeuw NH, Catlow CRA. Advances in Sustainable Catalysis: A Computational Perspective. Front Chem 2019; 7:182. [PMID: 31032245 PMCID: PMC6473102 DOI: 10.3389/fchem.2019.00182] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/07/2019] [Indexed: 11/13/2022] Open
Abstract
The enormous challenge of moving our societies to a more sustainable future offers several exciting opportunities for computational chemists. The first principles approach to "catalysis by design" will enable new and much greener chemical routes to produce vital fuels and fine chemicals. This prospective outlines a wide variety of case studies to underscore how the use of theoretical techniques, from QM/MM to unrestricted DFT and periodic boundary conditions, can be applied to biocatalysis and to both homogeneous and heterogenous catalysts of all sizes and morphologies to provide invaluable insights into the reaction mechanisms they catalyze.
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196
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Yu MJ, Chen SL. From Alkane to Alkene: The Inert Aliphatic C–H Bond Activation Presented by Binuclear Iron Stearoyl-CoA Desaturase with a Long di-Fe Distance of 6 Å. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00456] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ming-Jia Yu
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People’s Republic of China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, People’s Republic of China
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197
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Bikas R, Ajormal F, Emami M, Sanchiz J, Noshiranzadeh N, Kozakiewicz A. Crystal structure and magneto-structural investigation of alkoxido bridged dinuclear Fe(III) complexes with 1,3-oxazolidine ligands. Polyhedron 2019. [DOI: 10.1016/j.poly.2019.01.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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198
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Lyakin OY, Bryliakov KP, Talsi EP. Non-heme oxoiron(V) intermediates in chemo-, regio- and stereoselective oxidation of organic substrates. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2019.01.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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199
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Rajakovich LJ, Pandelia ME, Mitchell AJ, Chang WC, Zhang B, Boal AK, Krebs C, Bollinger JM. A New Microbial Pathway for Organophosphonate Degradation Catalyzed by Two Previously Misannotated Non-Heme-Iron Oxygenases. Biochemistry 2019; 58:1627-1647. [PMID: 30789718 PMCID: PMC6503667 DOI: 10.1021/acs.biochem.9b00044] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The assignment of biochemical functions to hypothetical proteins is challenged by functional diversification within many protein structural superfamilies. This diversification, which is particularly common for metalloenzymes, renders functional annotations that are founded solely on sequence and domain similarities unreliable and often erroneous. Definitive biochemical characterization to delineate functional subgroups within these superfamilies will aid in improving bioinformatic approaches for functional annotation. We describe here the structural and functional characterization of two non-heme-iron oxygenases, TmpA and TmpB, which are encoded by a genomically clustered pair of genes found in more than 350 species of bacteria. TmpA and TmpB are functional homologues of a pair of enzymes (PhnY and PhnZ) that degrade 2-aminoethylphosphonate but instead act on its naturally occurring, quaternary ammonium analogue, 2-(trimethylammonio)ethylphosphonate (TMAEP). TmpA, an iron(II)- and 2-(oxo)glutarate-dependent oxygenase misannotated as a γ-butyrobetaine (γbb) hydroxylase, shows no activity toward γbb but efficiently hydroxylates TMAEP. The product, ( R)-1-hydroxy-2-(trimethylammonio)ethylphosphonate [( R)-OH-TMAEP], then serves as the substrate for the second enzyme, TmpB. By contrast to its purported phosphohydrolytic activity, TmpB is an HD-domain oxygenase that uses a mixed-valent diiron cofactor to enact oxidative cleavage of the C-P bond of its substrate, yielding glycine betaine and phosphate. The high specificities of TmpA and TmpB for their N-trimethylated substrates suggest that they have evolved specifically to degrade TMAEP, which was not previously known to be subject to microbial catabolism. This study thus adds to the growing list of known pathways through which microbes break down organophosphonates to harvest phosphorus, carbon, and nitrogen in nutrient-limited niches.
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Affiliation(s)
- Lauren J. Rajakovich
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Maria-Eirini Pandelia
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02453, United States
| | - Andrew J. Mitchell
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142
| | - Wei-chen Chang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Bo Zhang
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Present address: REG Life Sciences, LLC, South San Francisco, California 94080
| | - Amie K. Boal
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Carsten Krebs
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - J. Martin Bollinger
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
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200
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Mühldorf B, Lennert U, Wolf R. Coupling photoredox and biomimetic catalysis for the visible-light-driven oxygenation of organic compounds. PHYSICAL SCIENCES REVIEWS 2019. [DOI: 10.1515/psr-2018-0030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Abstract
Recent advances in the development of coupled photoredox systems for the oxygenation of organic compounds are reviewed.
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