1
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Gera R, De P, Singh KK, Jannuzzi SAV, Mohanty A, Velasco L, Kulbir, Kumar P, Marco JF, Nagarajan K, Pecharromán C, Rodríguez-Pascual PM, DeBeer S, Moonshiram D, Gupta SS, Dasgupta J. Trapping an Elusive Fe(IV)-Superoxo Intermediate Inside a Self-Assembled Nanocage in Water at Room Temperature. J Am Chem Soc 2024; 146:21729-21741. [PMID: 39078020 DOI: 10.1021/jacs.4c05849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Molecular cavities that mimic natural metalloenzymes have shown the potential to trap elusive reaction intermediates. Here, we demonstrate the formation of a rare yet stable Fe(IV)-superoxo intermediate at room temperature subsequent to dioxygen binding at the Fe(III) site of a (Et4N)2[FeIII(Cl)(bTAML)] complex confined inside the hydrophobic interior of a water-soluble Pd6L412+ nanocage. Using a combination of electron paramagnetic resonance, Mössbauer, Raman/IR vibrational, X-ray absorption, and emission spectroscopies, we demonstrate that the cage-encapsulated complex has a Fe(IV) oxidation state characterized by a stable S = 1/2 spin state and a short Fe-O bond distance of ∼1.70 Å. We find that the O2 reaction in confinement is reversible, while the formed Fe(IV)-superoxo complex readily reacts when presented with substrates having weak C-H bonds, highlighting the lability of the O-O bond. We envision that such optimally trapped high-valent superoxos can show new classes of reactivities catalyzing both oxygen atom transfer and C-H bond activation reactions.
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Affiliation(s)
- Rahul Gera
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
- Department of Education in Science and Mathematics, Regional Institute of Education - Mysuru, NCERT, Mysuru 570006, India
| | - Puja De
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Kundan K Singh
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Pune, Maharashtra 411008, India
- Chemistry Department, Indian Institute of Technology, Dharwad 580007, India
| | - Sergio A V Jannuzzi
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Aisworika Mohanty
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Lucia Velasco
- Instituto de Ciencia de Materiales de Madrid Consejo Superior de Investigaciones Científicas Sor Juana Inés de la Cruz, 3, Madrid 28049, Spain
| | - Kulbir
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India
| | - Pankaj Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India
| | - J F Marco
- Instituto de Quimica Fisica Blas Cabrera, Consejo Superior de Investigaciones Científicas, Serrano 119, Madrid 28006, Spain
| | - Kalaivanan Nagarajan
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Carlos Pecharromán
- Instituto de Ciencia de Materiales de Madrid Consejo Superior de Investigaciones Científicas Sor Juana Inés de la Cruz, 3, Madrid 28049, Spain
| | - P M Rodríguez-Pascual
- Instituto de Ciencia de Materiales de Madrid Consejo Superior de Investigaciones Científicas Sor Juana Inés de la Cruz, 3, Madrid 28049, Spain
| | - Serena DeBeer
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Dooshaye Moonshiram
- Instituto de Ciencia de Materiales de Madrid Consejo Superior de Investigaciones Científicas Sor Juana Inés de la Cruz, 3, Madrid 28049, Spain
| | - Sayam Sen Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Jyotishman Dasgupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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2
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Hardy FJ, Quesne MG, Gérard EF, Zhao J, Ortmayer M, Taylor CJ, Ali HS, Slater JW, Levy CW, Heyes DJ, Bollinger JM, de Visser SP, Green AP. Probing Ferryl Reactivity in a Nonheme Iron Oxygenase Using an Expanded Genetic Code. ACS Catal 2024; 14:11584-11590. [PMID: 39114090 PMCID: PMC11301626 DOI: 10.1021/acscatal.4c02365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 08/10/2024]
Abstract
The ability to introduce noncanonical amino acids as axial ligands in heme enzymes has provided a powerful experimental tool for studying the structure and reactivity of their FeIV=O ("ferryl") intermediates. Here, we show that a similar approach can be used to perturb the conserved Fe coordination environment of 2-oxoglutarate (2OG) dependent oxygenases, a versatile class of enzymes that employ highly-reactive ferryl intermediates to mediate challenging C-H functionalizations. Replacement of one of the cis-disposed histidine ligands in the oxygenase VioC with a less electron donating N δ-methyl-histidine (MeHis) preserves both catalytic function and reaction selectivity. Significantly, the key ferryl intermediate responsible for C-H activation can be accumulated in both the wildtype and the modified protein. In contrast to heme enzymes, where metal-oxo reactivity is extremely sensitive to the nature of the proximal ligand, the rates of C-H activation and the observed large kinetic isotope effects are only minimally affected by axial ligand replacement in VioC. This study showcases a powerful tool for modulating the coordination sphere of nonheme iron enzymes that will enhance our understanding of the factors governing their divergent activities.
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Affiliation(s)
- Florence J. Hardy
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Matthew G. Quesne
- Research
Complex at Harwell, Rutherford Appleton
Laboratory, Harwell Oxford, Didcot, Oxon OX11
0FA, U.K.
- School
of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, U.K.
| | - Emilie F. Gérard
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Jingming Zhao
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Mary Ortmayer
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Christopher J. Taylor
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Hafiz S. Ali
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Jeffrey W. Slater
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Colin W. Levy
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Derren J. Heyes
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - J. Martin Bollinger
- Department
of Chemistry and Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sam P. de Visser
- Department
of Chemical Engineering & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Anthony P. Green
- Department
of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
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3
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Obisesan SV, Parvin M, Tao M, Ramos E, Saunders AC, Farnum BH, Goldsmith CR. Installing Quinol Proton/Electron Mediators onto Non-Heme Iron Complexes Enables Them to Electrocatalytically Reduce O 2 to H 2O at High Rates and Low Overpotentials. Inorg Chem 2024; 63:14126-14141. [PMID: 39008564 DOI: 10.1021/acs.inorgchem.4c01977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
We prepare iron(II) and iron(III) complexes with polydentate ligands that contain quinols, which can act as electron proton transfer mediators. Although the iron(II) complex with N-(2,5-dihydroxybenzyl)-N,N',N'-tris(2-pyridinylmethyl)-1,2-ethanediamine (H2qp1) is inactive as an electrocatalyst, iron complexes with N,N'-bis(2,5-dihydroxybenzyl)-N,N'-bis(2-pyridinylmethyl)-1,2-ethanediamine (H4qp2) and N-(2,5-dihydroxybenzyl)-N,N'-bis(2-pyridinylmethyl)-1,2-ethanediamine (H2qp3) were found to be much more active and more selective for water production than a previously reported cobalt-H2qp1 electrocatalyst while operating at low overpotentials. The catalysts with H2qp3 can enter the catalytic cycle as either Fe(II) or Fe(III) species; entering the cycle through Fe(III) lowers the effective overpotential. On the basis of their TOF0 values, the successful iron-quinol complexes are better electrocatalysts for oxygen reduction than previously reported iron-porphyrin compounds, with the Fe(III)-H2qp3 arguably being the best homogeneous electrocatalyst for this reaction. With iron, the quinol-for-phenol substitution shifts the product selectivity from H2O2 to water with little impact on the overpotential, but unlike cobalt, this substitution also greatly improves the activity, as assessed by TOFmax, by hastening the protonation and oxygen binding steps. The addition of a second quinol further enhances the activity and selectivity for water but modestly increases the effective overpotential.
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Affiliation(s)
- Segun V Obisesan
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Maksuda Parvin
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Matthew Tao
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Eric Ramos
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Alexander C Saunders
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Byron H Farnum
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
| | - Christian R Goldsmith
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849, United States
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4
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Josephy T, Kumar R, Bleher K, Röhs F, Glaser T, Rajaraman G, Comba P. Synthesis, Characterization, and Reactivity of Bispidine-Iron(IV)-Tosylimido Species. Inorg Chem 2024; 63:12109-12119. [PMID: 38875304 DOI: 10.1021/acs.inorgchem.4c01237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2024]
Abstract
Reported are the synthesis and detailed studies of the iron(IV)-tosylimido complexes of two isomeric pentadentate bispidine ligands (bispidines are 3,7-diazabicyclo[3.3.1]nonane derivatives). This completes a series of five tosylimido complexes with comparable pentadentate amine/pyridine ligands, where the corresponding [(L)FeIV═O]2+ oxidants have been studied in detail. The characterization of the two new complexes in solution (UV-vis-NIR, Mössbauer, HR-ESI-MS) shows that these oxidants have an intermediate spin (S = 1) electronic ground state. The reactivities have been studied as oxidants in C-H activation at 1,3-cyclohexadiene and nitrogen atom transfer to thioanisole. For the latter substrate, the entire set of data for the five ligands and for both nitrogen and oxygen atom transfer is now available and the interesting observation is that oxygen atom transfer is, as expected, generally faster than nitrogen atom transfer, with the exception of the two ligands that have four and three pyridine groups oriented parallel to the Fe-O and Fe-N axes. A thorough DFT analysis indicates that this is due to steric effects in the case of the [(L)FeIV═O]2+ species, which are less important in the [(L)FeIV═NTs]2+ compounds due to partial electron transfer from the thioanisole substrate to the iron(IV)-tosylimido oxidant.
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Affiliation(s)
- Thomas Josephy
- Anorganisch-Chemisches Institut, Universität Heidelberg, INF 270,Heidelberg D-69120, Germany
| | - Ravi Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Katharina Bleher
- Anorganisch-Chemisches Institut, Universität Heidelberg, INF 270,Heidelberg D-69120, Germany
- Institute of Functional Interfaces, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen 76344, Germany
| | - Fridolin Röhs
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, Bielefeld D-33615, Germany
| | - Thorsten Glaser
- Lehrstuhl für Anorganische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, Bielefeld D-33615, Germany
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Peter Comba
- Anorganisch-Chemisches Institut, Universität Heidelberg, INF 270,Heidelberg D-69120, Germany
- Interdisziplinäres Zentrum für Wissenschaftliches Rechnen (IWR), Universität Heidelberg, Heidelberg 69120, Germany
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5
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Betts PC, Blakely SJ, Rutkowski BN, Bender B, Klingler C, Froese JT. Engineering of Rieske dioxygenase variants with improved cis-dihydroxylation activity for benzoates. Biotechnol Bioeng 2024. [PMID: 38951963 DOI: 10.1002/bit.28786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/13/2024] [Accepted: 06/16/2024] [Indexed: 07/03/2024]
Abstract
Rieske dioxygenases have a long history of being utilized as green chemical tools in the organic synthesis of high-value compounds, due to their capacity to perform the cis-dihydroxylation of a wide variety of aromatic substrates. The practical utility of these enzymes has been hampered however by steric and electronic constraints on their substrate scopes, resulting in limited reactivity with certain substrate classes. Herein, we report the engineering of a widely used member of the Rieske dioxygenase class of enzymes, toluene dioxygenase (TDO), to produce improved variants with greatly increased activity for the cis-dihydroxylation of benzoates. Through rational mutagenesis and screening, TDO variants with substantially improved activity over the wild-type enzyme were identified. Homology modeling, docking studies, molecular dynamics simulations, and substrate tunnel analysis were applied in an effort to elucidate how the identified mutations resulted in improved activity for this polar substrate class. These analyses revealed modification of the substrate tunnel as the likely cause of the improved activity observed with the best-performing enzyme variants.
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Affiliation(s)
- Phillip C Betts
- Department of Chemistry, Ball State University, Muncie, Indiana, USA
| | - Spencer J Blakely
- Department of Chemistry, Ball State University, Muncie, Indiana, USA
| | | | - Brandon Bender
- Department of Chemistry, Ball State University, Muncie, Indiana, USA
| | - Cole Klingler
- Department of Chemistry, Ball State University, Muncie, Indiana, USA
| | - Jordan T Froese
- Department of Chemistry, Ball State University, Muncie, Indiana, USA
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6
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Fagnano A, Frateloreto F, Paoloni R, Sappino C, Lanzalunga O, Costas M, Di Stefano S, Olivo G. Proximity Effects on the Reactivity of a Nonheme Iron (IV) Oxo Complex in C-H Oxidation. Angew Chem Int Ed Engl 2024; 63:e202401694. [PMID: 38478739 DOI: 10.1002/anie.202401694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Indexed: 04/05/2024]
Abstract
Precise control of substrate positioning and orientation (its proximity to the reactive unit) is often invoked to rationalize the superior enzymatic reaction rates and selectivities when compared to synthetic models. Artificial nonheme iron (IV) oxo (Fe(IV)=O) complexes react with C(sp3)-H bonds via a biomimetic Hydrogen Atom Transfer/Hydroxyl Rebound mechanism, but rates, site-selectivity and even hydroxyl rebound efficiency (ligand rebound versus substrate radical diffusion) are smaller than in oxygenases. Herein, we quantitatively analyze how substrate binding modulates nonheme Fe(IV)=O reactivity by comparing rates and outcomes of C-H oxidation by a pair of Fe(IV)=O complexes that share the same first coordination sphere but only one contains a crown ether receptor that recognizes the substrate. Substrate binding makes the reaction intramolecular, exhibiting Michaelis-Menten kinetics and increased reaction rates. In addition, C-H oxidation occurs with high site selectivity for remote sites. Analysis of Effective Molarity reveals that the system operates at its maximal theoretical capability for the oxidation of these remote sites. Remarkably, substrate positioning also affects Hydroxyl Rebound, whose efficiency only increases on the sites placed in proximity by recognition. Overall, these observations provide evidence that supramolecular control of substrate positioning can effectively modulate the reactivity of oxygenases and its models.
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Affiliation(s)
- Alessandro Fagnano
- Dipartimento di Chimica and Istituto CNR per i Sistemi Biologici (ISB-CNR), Sezione Meccanismi di Reazione, c/o Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro, 5 I-00185, Rome, Italy
| | - Federico Frateloreto
- Dipartimento di Chimica and Istituto CNR per i Sistemi Biologici (ISB-CNR), Sezione Meccanismi di Reazione, c/o Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro, 5 I-00185, Rome, Italy
| | - Roberta Paoloni
- Dipartimento di Chimica and Istituto CNR per i Sistemi Biologici (ISB-CNR), Sezione Meccanismi di Reazione, c/o Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro, 5 I-00185, Rome, Italy
| | - Carla Sappino
- Dipartimento di Chimica and Istituto CNR per i Sistemi Biologici (ISB-CNR), Sezione Meccanismi di Reazione, c/o Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro, 5 I-00185, Rome, Italy
| | - Osvaldo Lanzalunga
- Dipartimento di Chimica and Istituto CNR per i Sistemi Biologici (ISB-CNR), Sezione Meccanismi di Reazione, c/o Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro, 5 I-00185, Rome, Italy
| | - Miquel Costas
- QBIS-Cat, Institut de Química Computacional i Catàlisi (IQCC), Departament de Quimica, Universitat de Girona Campus Montilivi, 17071, Girona, Catalonia, Spain
| | - Stefano Di Stefano
- Dipartimento di Chimica and Istituto CNR per i Sistemi Biologici (ISB-CNR), Sezione Meccanismi di Reazione, c/o Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro, 5 I-00185, Rome, Italy
| | - Giorgio Olivo
- Dipartimento di Chimica and Istituto CNR per i Sistemi Biologici (ISB-CNR), Sezione Meccanismi di Reazione, c/o Dipartimento di Chimica, Università di Roma "La Sapienza", P.le A. Moro, 5 I-00185, Rome, Italy
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7
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Thomas J, Mokkawes T, Senft L, Dey A, Gordon JB, Ivanovic-Burmazovic I, de Visser SP, Goldberg DP. Axial Ligation Impedes Proton-Coupled Electron-Transfer Reactivity of a Synthetic Compound-I Analogue. J Am Chem Soc 2024; 146:12338-12354. [PMID: 38669456 PMCID: PMC11305010 DOI: 10.1021/jacs.3c08950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
The nature of the axial ligand in high-valent iron-oxo heme enzyme intermediates and related synthetic catalysts is a critical structural element for controlling proton-coupled electron-transfer (PCET) reactivity of these species. Herein, we describe the generation and characterization of three new 6-coordinate, iron(IV)-oxo porphyrinoid-π-cation-radical complexes and report their PCET reactivity together with a previously published 5-coordinate analogue, FeIV(O)(TBP8Cz+•) (TBP8Cz = octakis(p-tert-butylphenyl)corrolazinato3-) (2) (Cho, K. A high-valent iron-oxo corrolazine activates C-H bonds via hydrogen-atom transfer. J. Am. Chem. Soc. 2012, 134, 7392-7399). The new complexes FeIV(O)(TBP8Cz+•)(L) (L = 1-methyl imidazole (1-MeIm) (4a), 4-dimethylaminopyridine (DMAP) (4b), cyanide (CN-)(4c)) can be generated from either oxidation of the ferric precursors or by addition of L to the Compound-I (Cpd-I) analogue at low temperatures. These complexes were characterized by UV-vis, electron paramagnetic resonance (EPR), and Mössbauer spectroscopies, and cryospray ionization mass spectrometry (CSI-MS). Kinetic studies using 4-OMe-TEMPOH as a test substrate indicate that coordination of a sixth axial ligand dramatically lowers the PCET reactivity of the Cpd-I analogue (rates up to 7000 times slower). Extensive density functional theory (DFT) calculations together with the experimental data show that the trend in reactivity with the axial ligands does not correlate with the thermodynamic driving force for these reactions or the calculated strengths of the O-H bonds being formed in the FeIV(O-H) products, pointing to non-Bell-Evans-Polanyi behavior. However, the PCET reactivity does follow a trend with the bracketed reduction potential of Cpd-I analogues and calculated electron affinities. The combined data suggest a concerted mechanism (a concerted proton electron transfer (CPET)) and an asynchronous movement of the electron/proton pair in the transition state.
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Affiliation(s)
- Jithin Thomas
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Thirakorn Mokkawes
- The Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Laura Senft
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr., 5-13, Haus D, 81377 München, Germany
| | - Aniruddha Dey
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Jesse B Gordon
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Ivana Ivanovic-Burmazovic
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstr., 5-13, Haus D, 81377 München, Germany
| | - Sam P de Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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8
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Cao Y, Hay S, de Visser SP. An Active Site Tyr Residue Guides the Regioselectivity of Lysine Hydroxylation by Nonheme Iron Lysine-4-hydroxylase Enzymes through Proton-Coupled Electron Transfer. J Am Chem Soc 2024; 146:11726-11739. [PMID: 38636166 PMCID: PMC11066847 DOI: 10.1021/jacs.3c14574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/05/2024] [Accepted: 04/05/2024] [Indexed: 04/20/2024]
Abstract
Lysine dioxygenase (KDO) is an important enzyme in human physiology involved in bioprocesses that trigger collagen cross-linking and blood pressure control. There are several KDOs in nature; however, little is known about the factors that govern the regio- and stereoselectivity of these enzymes. To understand how KDOs can selectively hydroxylate their substrate, we did a comprehensive computational study into the mechanisms and features of 4-lysine dioxygenase. In particular, we selected a snapshot from the MD simulation on KDO5 and created large QM cluster models (A, B, and C) containing 297, 312, and 407 atoms, respectively. The largest model predicts regioselectivity that matches experimental observation with rate-determining hydrogen atom abstraction from the C4-H position, followed by fast OH rebound to form 4-hydroxylysine products. The calculations show that in model C, the dipole moment is positioned along the C4-H bond of the substrate and, therefore, the electrostatic and electric field perturbations of the protein assist the enzyme in creating C4-H hydroxylation selectivity. Furthermore, an active site Tyr233 residue is identified that reacts through proton-coupled electron transfer akin to the axial Trp residue in cytochrome c peroxidase. Thus, upon formation of the iron(IV)-oxo species in the catalytic cycle, the Tyr233 phenol loses a proton to the nearby Asp179 residue, while at the same time, an electron is transferred to the iron to create an iron(III)-oxo active species. This charged tyrosyl residue directs the dipole moment along the C4-H bond of the substrate and guides the selectivity to the C4-hydroxylation of the substrate.
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Affiliation(s)
- Yuanxin Cao
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department
of Chemical Engineering, The University
of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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9
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Ali HS, de Visser SP. QM/MM Study Into the Mechanism of Oxidative C=C Double Bond Cleavage by Lignostilbene-α,β-Dioxygenase. Chemistry 2024; 30:e202304172. [PMID: 38373118 DOI: 10.1002/chem.202304172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/29/2024] [Accepted: 02/19/2024] [Indexed: 02/21/2024]
Abstract
The enzymatic biosynthesis of fragrance molecules from lignin fragments is an important reaction in biotechnology for the sustainable production of fine chemicals. In this work we investigated the biosynthesis of vanillin from lignostilbene by a nonheme iron dioxygenase using QM/MM and tested several suggested proposals via either an epoxide or dioxetane intermediate. Binding of dioxygen to the active site of the protein results in the formation of an iron(II)-superoxo species with lignostilbene cation radical. The dioxygenase mechanism starts with electrophilic attack of the terminal oxygen atom of the superoxo group on the central C=C bond of lignostilbene, and the second-coordination sphere effects in the substrate binding pocket guide the reaction towards dioxetane formation. The computed mechanism is rationalized with thermochemical cycles and valence bond schemes that explain the electron transfer processes during the reaction mechanism. Particularly, the polarity of the protein and the local electric field and dipole moments enable a facile electron transfer and an exergonic dioxetane formation pathway.
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Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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10
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Andrys-Olek J, Kluza A, Tataruch M, Heider J, Korecki J, Borowski T. Bacteria at Work - Experimental and Theoretical Studies Reveal the Catalytic Mechanism of Ectoine Synthase. Chemistry 2024; 30:e202304163. [PMID: 38258332 DOI: 10.1002/chem.202304163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 01/24/2024]
Abstract
Ectoine synthase (EctC) catalyses the ultimate step of ectoine biosynthesis, a kosmotropic compound produced as compatible solute by many bacteria and some archaea or eukaryotes. EctC is an Fe2+-dependent homodimeric cytoplasmic protein. Using Mössbauer spectroscopy, molecular dynamics simulations and QM/MM calculations, we determined the most likely coordination number and geometry of the Fe2+ ion and proposed a mechanism of the EctC-catalysed reaction. Most notably, we show that apart from the three amino acids binding to the iron ion (Glu57, Tyr84 and His92), one water molecule and one hydroxide ion are required as additional ligands for the reaction to occur. They fill the first coordination sphere of the Fe2+-cofactor and act as critical proton donors and acceptors during the cyclization reaction.
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Affiliation(s)
- Justyna Andrys-Olek
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Anna Kluza
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Mateusz Tataruch
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Johann Heider
- Department of Biology, Philipps-Universität Marburg, 35043, Marburg, Germany
| | - Józef Korecki
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, 30-239, Kraków, Poland
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11
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Dolgova N, Uhlemann EME, Boniecki MT, Vizeacoumar FS, Ara A, Nouri P, Ralle M, Tonelli M, Abbas SA, Patry J, Elhasasna H, Freywald A, Vizeacoumar FJ, Dmitriev OY. MEMO1 binds iron and modulates iron homeostasis in cancer cells. eLife 2024; 13:e86354. [PMID: 38640016 PMCID: PMC11081632 DOI: 10.7554/elife.86354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/15/2024] [Indexed: 04/20/2024] Open
Abstract
Mediator of ERBB2-driven cell motility 1 (MEMO1) is an evolutionary conserved protein implicated in many biological processes; however, its primary molecular function remains unknown. Importantly, MEMO1 is overexpressed in many types of cancer and was shown to modulate breast cancer metastasis through altered cell motility. To better understand the function of MEMO1 in cancer cells, we analyzed genetic interactions of MEMO1 using gene essentiality data from 1028 cancer cell lines and found multiple iron-related genes exhibiting genetic relationships with MEMO1. We experimentally confirmed several interactions between MEMO1 and iron-related proteins in living cells, most notably, transferrin receptor 2 (TFR2), mitoferrin-2 (SLC25A28), and the global iron response regulator IRP1 (ACO1). These interactions indicate that cells with high-MEMO1 expression levels are hypersensitive to the disruptions in iron distribution. Our data also indicate that MEMO1 is involved in ferroptosis and is linked to iron supply to mitochondria. We have found that purified MEMO1 binds iron with high affinity under redox conditions mimicking intracellular environment and solved MEMO1 structures in complex with iron and copper. Our work reveals that the iron coordination mode in MEMO1 is very similar to that of iron-containing extradiol dioxygenases, which also display a similar structural fold. We conclude that MEMO1 is an iron-binding protein that modulates iron homeostasis in cancer cells.
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Affiliation(s)
- Natalia Dolgova
- Department of Biochemistry, Microbiology and Immunology, University of SaskatchewanSaskatoonCanada
| | - Eva-Maria E Uhlemann
- Department of Biochemistry, Microbiology and Immunology, University of SaskatchewanSaskatoonCanada
| | - Michal T Boniecki
- Protein Characterization and Crystallization Facility, University of SaskatchewanSaskatoonCanada
| | | | - Anjuman Ara
- Department of Biochemistry, Microbiology and Immunology, University of SaskatchewanSaskatoonCanada
| | - Paria Nouri
- Department of Biochemistry, Microbiology and Immunology, University of SaskatchewanSaskatoonCanada
| | - Martina Ralle
- Department of Molecular and Medical Genetics, Oregon Health and Sciences UniversityPortlandUnited States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison (NMRFAM), University of WisconsinMadisonUnited States
| | - Syed A Abbas
- Department of Biochemistry, Microbiology and Immunology, University of SaskatchewanSaskatoonCanada
| | - Jaala Patry
- Department of Biochemistry, Microbiology and Immunology, University of SaskatchewanSaskatoonCanada
| | - Hussain Elhasasna
- Department of Pathology and Laboratory Medicine, University of SaskatchewanSaskatoonCanada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, University of SaskatchewanSaskatoonCanada
| | - Franco J Vizeacoumar
- Cancer Research Department, Saskatchewan Cancer AgencySaskatoonCanada
- Division of Oncology, University of SaskatchewanSaskatoonCanada
| | - Oleg Y Dmitriev
- Department of Biochemistry, Microbiology and Immunology, University of SaskatchewanSaskatoonCanada
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12
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Hardy FG, Wong HPH, de Visser SP. Computational Study Into the Oxidative Ring-Closure Mechanism During the Biosynthesis of Deoxypodophyllotoxin. Chemistry 2024; 30:e202400019. [PMID: 38323740 DOI: 10.1002/chem.202400019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/01/2024] [Accepted: 02/07/2024] [Indexed: 02/08/2024]
Abstract
The nonheme iron dioxygenase deoxypodophyllotoxin synthase performs an oxidative ring-closure reaction as part of natural product synthesis in plants. How the enzyme enables the oxidative ring-closure reaction of (-)-yatein and avoids substrate hydroxylation remains unknown. To gain insight into the reaction mechanism and understand the details of the pathways leading to products and by-products we performed a comprehensive computational study. The work shows that substrate is bound tightly into the substrate binding pocket with the C7'-H bond closest to the iron(IV)-oxo species. The reaction proceeds through a radical mechanism starting with hydrogen atom abstraction from the C7'-H position followed by ring-closure and a final hydrogen transfer to form iron(II)-water and deoxypodophyllotoxin. Alternative mechanisms including substrate hydroxylation and an electron transfer pathway were explored but found to be higher in energy. The mechanism is guided by electrostatic perturbations of charged residues in the second-coordination sphere that prevent alternative pathways.
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Affiliation(s)
- Fintan G Hardy
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Henrik P H Wong
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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13
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Semenya J, Yang Y, Picazo E. Cross-Electrophile Coupling of Benzyl Halides and Disulfides Catalyzed by Iron. J Am Chem Soc 2024; 146:4903-4912. [PMID: 38346333 PMCID: PMC10910570 DOI: 10.1021/jacs.3c13984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/22/2024] [Accepted: 01/24/2024] [Indexed: 02/22/2024]
Abstract
Cross-electrophile couplings are influential reactions that typically require a terminal reductant or photoredox conditions. We discovered an iron-catalyzed reaction that couples benzyl halides with disulfides to yield thioether products in the absence of a terminal reductant and under photoredox conditions. The disclosed platform proceeds without sulfur-induced catalyst poisoning or the use of an exogenous base, supporting a broad scope and circumventing undesired elimination pathways. We applied the developed chemistry in a new mode of disulfide bioconjugation, drug synthesis, gram-scale synthesis, and product derivatization. Lastly, we performed mechanistic experiments to better understand the stereoablative reaction between two electrophiles. Disulfides and benzylic thioethers are imperative for biological and pharmaceutical applications but remain severely understudied in comparison to their ethereal and amino counterparts. Hence, we expect this platform of iron catalysis and the downstream applications to be of interest to the greater scientific community.
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Affiliation(s)
- Julius Semenya
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of
Southern California, 837 Bloom Walk, Los Angeles, California 90089-1661, United States
| | - Yuanjie Yang
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of
Southern California, 837 Bloom Walk, Los Angeles, California 90089-1661, United States
| | - Elias Picazo
- Department of Chemistry, Loker Hydrocarbon Research Institute, University of
Southern California, 837 Bloom Walk, Los Angeles, California 90089-1661, United States
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14
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Kumar M, Gupta MK, Ansari M, Ansari A. C-H bond activation by high-valent iron/cobalt-oxo complexes: a quantum chemical modeling approach. Phys Chem Chem Phys 2024; 26:4349-4362. [PMID: 38235511 DOI: 10.1039/d3cp05866b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
High-valent metal-oxo species serve as key intermediates in the activation of inert C-H bonds. Here, we present a comprehensive DFT analysis of the parameters that have been proposed as influencing factors in modeled high-valent metal-oxo mediated C-H activation reactions. Our approach involves utilizing DFT calculations to explore the electronic structures of modeled FeIVO (species 1) and CoIVO ↔ CoIII-O˙ (species 2), scrutinizing their capacity to predict improved catalytic activity. DFT and DLPNO-CCSD(T) calculations predict that the iron-oxo species possesses a triplet as the ground state, while the cobalt-oxo has a doublet as the ground state. Furthermore, we have investigated the mechanistic pathways for the first C-H bond activation, as well as the desaturation of the alkanes. The mechanism was determined to be a two-step process, wherein the first hydrogen atom abstraction (HAA) represents the rate-limiting step, involving the proton-coupled electron transfer (PCET) process. However, we found that the second HAA step is highly exothermic for both species. Our calculations suggest that the iron-oxo species (Fe-O = 1.672 Å) exhibit relatively sluggish behavior compared to the cobalt-oxo species (Co-O = 1.854 Å) in C-H bond activation, attributed to a weak metal-oxygen bond. MO, NBO, and deformation energy analysis reveal the importance of weakening the M-O bond in the cobalt species, thereby reducing the overall barrier to the reaction. This catalyst was found to have a C-H activation barrier relatively smaller than that previously reported in the literature.
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Affiliation(s)
- Manjeet Kumar
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India.
| | - Manoj Kumar Gupta
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India.
| | - Mursaleem Ansari
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, Mahendergarh-123031, Haryana, India.
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15
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Katoch A, Mandal D. High-valent nonheme Fe(IV)O/Ru(IV)O complexes catalyze C-H activation reactivity and hydrogen tunneling: a comparative DFT investigation. Dalton Trans 2024; 53:2386-2394. [PMID: 38214597 DOI: 10.1039/d3dt03155a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
A comprehensive density functional theory investigation has been presented towards the comparison of the C-H activation reactivity between high-valent iron-oxo and ruthenium-oxo complexes. A total of four compounds, e.g., [Ru(IV)O(tpy-dcbpy)] (1), [Fe(IV)O(tpy-dcbpy)] (1'), [Ru(IV)O(TMCS)] (2), and [Fe(IV)O(TMCS)] (2'), have been considered for this investigation. The macrocyclic ligand framework tpy(dcbpy) implies tpy = 2,2':6',2''-terpyridine, dcbpy = 5,5'-dicarboxy-2,2'-bipyridine, and TMCS is TMC with an axially tethered -SCH2CH2 group. Compounds 1 and 2' are experimentally synthesized standard complexes with Ru and Fe, whereas compounds 1' and 2 were considered to keep the macrocycle intact when switching the central metal atom. Three reactants including benzyl alcohol, ethyl benzene, and dihydroanthracene were selected as substrates for C-H activation. It is noteworthy to mention that Fe(IV)O complexes exhibit higher reactivity than those of their Ru(IV)O counterparts. Furthermore, regardless of the central metal, the complex featuring a tpy-dcbpy macrocycle demonstrates higher reactivity than that of TMCS. Here, a thorough analysis of the reactivity-controlling characteristics-such as spin state, steric factor, distortion energy, energy of the electron acceptor orbital, and quantum mechanical tunneling-was conducted. Fe(IV)O exhibits the exchanged enhanced two-state-reactivity with the quintet reactive state, whereas Ru(IV)O has only a triplet reactive state. Both the distortion energy and acceptor orbital energy are low in the case of Fe(IV)O supporting its higher reactivity. All the investigated C-H activation processes involve a significant contribution from hydrogen tunneling, which is more pronounced in the case of Ru, although it cannot alter the reactivity pattern. Furthermore, it has also been found that, independent of the central metal, aliphatic hydroxylation is always preferable to aromatic hydroxylation. Overall, this work is successful in establishing and investigating the cause of enzymes' natural preference for Fe over Ru as a cofactor for C-H activation enzymes.
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Affiliation(s)
- Akanksha Katoch
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala-147001, Punjab, India.
| | - Debasish Mandal
- Department of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala-147001, Punjab, India.
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16
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Lakk-Bogáth D, Pintarics D, Török P, Kaizer J. Influence of Equatorial Co-Ligands on the Reactivity of LFe IIIOIPh. Molecules 2023; 29:58. [PMID: 38202641 PMCID: PMC10779584 DOI: 10.3390/molecules29010058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Previous biomimetic studies clearly proved that equatorial ligands significantly influence the redox potential and thus the stability/reactivity of biologically important oxoiron intermediates; however, no such studies were performed on FeIIIOIPh species. In this study, the influence of substituted pyridine co-ligands on the reactivity of iron(III)-iodosylbenzene adduct has been investigated in sulfoxidation and epoxidation reactions. Selective oxidation of thioanisole, cis-cyclooctene, and cis- and trans-stilbene in the presence of a catalytic amount of [FeII(PBI)3](OTf)2 with PhI(OAc)2 provide products in good to excellent yields through an FeIIIOIPh intermediate depending on the co-ligand (4R-Py) used. Several mechanistic studies were performed to gain more insight into the mechanism of oxygen atom transfer (OAT) reactions to support the reactive intermediate and investigate the effect of the equatorial co-ligands. Based on competitive experiments, including a linear free-energy relationship between the relative reaction rates (logkrel) and the σp (4R-Py) parameters, strong evidence has been observed for the electrophilic character of the reactive species. The presence of the [(PBI)2(4R-Py)FeIIIOIPh]3+ intermediates and the effect of the co-ligands was also supported by UV-visible measurements, including the color change from red to green and the hypsochromic shifts in the presence of co-ligands. This is another indication that the title iron(III)-iodosylbenzene adduct is able to oxygenate sulfides and alkenes before it is transformed into the oxoiron form by cleavage of the O-I bond.
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Affiliation(s)
| | | | | | - József Kaizer
- Research Group of Bioorganic and Biocoordination Chemistry, University of Pannonia, H-8201 Veszprém, Hungary; (D.L.-B.); (D.P.); (P.T.)
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17
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Hädeler J, Velmurugan G, Lauer R, Radhamani R, Keppler F, Comba P. Natural Abiotic Iron-Oxido-Mediated Formation of C 1 and C 2 Compounds from Environmentally Important Methyl-Substituted Substrates. J Am Chem Soc 2023. [PMID: 37930326 DOI: 10.1021/jacs.3c06709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Organic and inorganic volatile compounds containing one carbon atom (C1), such as carbon dioxide, methane, methanol, formaldehyde, carbon monoxide, and chloromethane, are ubiquitous in the environment, are key components in global carbon cycling, play an important role in atmospheric physics and chemistry, e.g., as greenhouse gases, destroy stratospheric and tropospheric ozone, and control the atmospheric oxidation capacity. Up to now, most C1 compounds in the environment were associated with complex metabolic and enzymatic pathways in organisms or to combustion processes of organic matter. We now present compelling evidence that many C1 and C2 compounds have a common origin in methyl groups of methyl-substituted substrates that are cleaved by the iron oxide-mediated formation of methyl radicals. This scenario is derived from experiments with a mechanistically well-studied bispidine-iron-oxido complex as oxidant and dimethyl sulfoxide as the environmentally relevant model substrate and is supported by computational modeling based on density functional theory and ab initio quantum-chemical studies. The exhaustive experimental model studies, also involving extensive isotope labeling, are complemented with the substitution of the bispidine model system by environmentally relevant iron oxides and, finally, a collection of soils with varying iron and organic matter contents. The combination of all data suggests that the iron oxide-mediated formation of methyl radicals from methyl-substituted substrates is a common abiotic source for widespread C1 and C2 compounds in the environment.
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Affiliation(s)
- Jonas Hädeler
- Institut für Geowissenschaften, INF 234-236, Universität Heidelberg, D-69120 Heidelberg, Germany
| | - Gunasekaran Velmurugan
- Anorganisch-Chemisches Institut INF 270, Universität Heidelberg, D-69120 Heidelberg, Germany
| | - Rebekka Lauer
- Institut für Geowissenschaften, INF 234-236, Universität Heidelberg, D-69120 Heidelberg, Germany
| | - Rejith Radhamani
- Anorganisch-Chemisches Institut INF 270, Universität Heidelberg, D-69120 Heidelberg, Germany
| | - Frank Keppler
- Institut für Geowissenschaften, INF 234-236, Universität Heidelberg, D-69120 Heidelberg, Germany
- Heidelberg Center for the Environment (HCE), Universität Heidelberg, D-69120 Heidelberg, Germany
| | - Peter Comba
- Anorganisch-Chemisches Institut INF 270, Universität Heidelberg, D-69120 Heidelberg, Germany
- Interdisciplinary Center for Scientific Computing, INF 205, Universität Heidelberg, D-69120 Heidelberg, Germany
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18
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Yamaguchi K, Isobe H, Shoji M, Kawakami T, Miyagawa K. The Nature of the Chemical Bonds of High-Valent Transition-Metal Oxo (M=O) and Peroxo (MOO) Compounds: A Historical Perspective of the Metal Oxyl-Radical Character by the Classical to Quantum Computations. Molecules 2023; 28:7119. [PMID: 37894598 PMCID: PMC10609222 DOI: 10.3390/molecules28207119] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
This review article describes a historical perspective of elucidation of the nature of the chemical bonds of the high-valent transition metal oxo (M=O) and peroxo (M-O-O) compounds in chemistry and biology. The basic concepts and theoretical backgrounds of the broken-symmetry (BS) method are revisited to explain orbital symmetry conservation and orbital symmetry breaking for the theoretical characterization of four different mechanisms of chemical reactions. Beyond BS methods using the natural orbitals (UNO) of the BS solutions, such as UNO CI (CC), are also revisited for the elucidation of the scope and applicability of the BS methods. Several chemical indices have been derived as the conceptual bridges between the BS and beyond BS methods. The BS molecular orbital models have been employed to explain the metal oxyl-radical character of the M=O and M-O-O bonds, which respond to their radical reactivity. The isolobal and isospin analogy between carbonyl oxide R2C-O-O and metal peroxide LFe-O-O has been applied to understand and explain the chameleonic chemical reactivity of these compounds. The isolobal and isospin analogy among Fe=O, O=O, and O have also provided the triplet atomic oxygen (3O) model for non-heme Fe(IV)=O species with strong radical reactivity. The chameleonic reactivity of the compounds I (Cpd I) and II (Cpd II) is also explained by this analogy. The early proposals obtained by these theoretical models have been examined based on recent computational results by hybrid DFT (UHDFT), DLPNO CCSD(T0), CASPT2, and UNO CI (CC) methods and quantum computing (QC).
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Affiliation(s)
- Kizashi Yamaguchi
- SANKEN, Osaka University, Ibaraki 567-0047, Osaka, Japan
- Center for Quantum Information and Quantum Biology (QIQB), Osaka University, Toyonaka 560-0043, Osaka, Japan
| | - Hiroshi Isobe
- Research Institute for Interdisciplinary Science, Okayama University, Okayama 700-8530, Okayama, Japan;
| | - Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan; (M.S.); (K.M.)
| | - Takashi Kawakami
- Department of Chemistry, Graduate School of Science, Osaka University, Toyonaka 560-0043, Osaka, Japan;
| | - Koichi Miyagawa
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Ibaraki, Japan; (M.S.); (K.M.)
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19
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Mokkawes T, De Visser T, Cao Y, De Visser SP. Melatonin Activation by Human Cytochrome P450 Enzymes: A Comparison between Different Isozymes. Molecules 2023; 28:6961. [PMID: 37836804 PMCID: PMC10574541 DOI: 10.3390/molecules28196961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/30/2023] [Accepted: 10/02/2023] [Indexed: 10/15/2023] Open
Abstract
Cytochrome P450 enzymes in the human body play a pivotal role in both the biosynthesis and the degradation of the hormone melatonin. Melatonin plays a key role in circadian rhythms in the body, but its concentration is also linked to mood fluctuations as well as emotional well-being. In the present study, we present a computational analysis of the binding and activation of melatonin by various P450 isozymes that are known to yield different products and product distributions. In particular, the P450 isozymes 1A1, 1A2, and 1B1 generally react with melatonin to provide dominant aromatic hydroxylation at the C6-position, whereas the P450 2C19 isozyme mostly provides O-demethylation products. To gain insight into the origin of these product distributions of the P450 isozymes, we performed a comprehensive computational study of P450 2C19 isozymes and compared our work with previous studies on alternative isozymes. The work covers molecular mechanics, molecular dynamics and quantum mechanics approaches. Our work highlights major differences in the size and shape of the substrate binding pocket amongst the different P450 isozymes. Consequently, substrate binding and positioning in the active site varies substantially within the P450 isozymes. Thus, in P450 2C19, the substrate is oriented with its methoxy group pointing towards the heme, and therefore reacts favorably through hydrogen atom abstraction, leading to the production of O-demethylation products. On the other hand, the substrate-binding pockets in P450 1A1, 1A2, and 1B1 are tighter, direct the methoxy group away from the heme, and consequently activate an alternative site and lead to aromatic hydroxylation instead.
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Affiliation(s)
| | | | | | - Sam P. De Visser
- Department of Chemical Engineering, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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20
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Wu Z, Zhang X, Gao L, Sun D, Zhao Y, Nam W, Wang Y. Elusive Active Intermediates and Reaction Mechanisms of ortho-/ ipso-Hydroxylation of Benzoic Acid by Hydrogen Peroxide Mediated by Bioinspired Iron(II) Catalysts. Inorg Chem 2023; 62:14261-14278. [PMID: 37604675 DOI: 10.1021/acs.inorgchem.3c01576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
Abstract
Aromatic hydroxylation of benzoic acids (BzOH) to salicylates and phenolates is fundamentally interesting in industrial chemistry. However, key mechanistic uncertainties and dichotomies remain after decades of effort. Herein, the elusive mechanism of the competitive ortho-/ipso-hydroxylation of BzOH by H2O2 mediated by a nonheme iron(II) catalyst was comprehensively investigated using density functional theory calculations. Results revealed that the long-postulated FeV(O)(anti-BzO) oxidant is an FeIV(O)(anti-BzO•) species 2 (anti- and syn- are defined by the orientation of the carboxyl oxygen of BzO to the oxo), which rules out the noted two-oxidant mechanism proposed previously. We propose a new mechanism in which, following the formation of an FeV(O)(syn-BzO) species (3) and its electromer FeIV(O)(syn-BzO•) (3'), 3/3' either converts to salicylate and phenolate via intramolecular self-hydroxylation (route A) or acts as an oxidant to oxygenate another BzOH to generate the same products (route B). In route A, the rotation of the BzO group along the C-O bond forms 2, in which the BzO group is orientated by π-π stacking interactions. An electrophilic ipso-addition forms a phenolate by concomitant decarboxylation or an ortho-attack forms a cationic complex, which readily undergoes an NIH shift and a BzOH-assisted proton shift to form a salicylate. In route B, 3 oxidizes an additional BzOH molecule directed by hydrogen bonding and π-π stacking interactions. In both routes, selectivity is determined by the chemical property of the BzO ring. These mechanistic findings provide a clear mechanistic scenario and enrich the knowledge of hydroxylation of aromatic acids.
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Affiliation(s)
- Zhimin Wu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Xuan Zhang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Lanping Gao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Dongru Sun
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Yong Wang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, Zhejiang, China
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, Zhejiang, China
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21
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Li L, Shen S, Bickler P, Jacobson MP, Wu LF, Altschuler SJ. Searching for molecular hypoxia sensors among oxygen-dependent enzymes. eLife 2023; 12:e87705. [PMID: 37494095 PMCID: PMC10371230 DOI: 10.7554/elife.87705] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/09/2023] [Indexed: 07/27/2023] Open
Abstract
The ability to sense and respond to changes in cellular oxygen levels is critical for aerobic organisms and requires a molecular oxygen sensor. The prototypical sensor is the oxygen-dependent enzyme PHD: hypoxia inhibits its ability to hydroxylate the transcription factor HIF, causing HIF to accumulate and trigger the classic HIF-dependent hypoxia response. A small handful of other oxygen sensors are known, all of which are oxygen-dependent enzymes. However, hundreds of oxygen-dependent enzymes exist among aerobic organisms, raising the possibility that additional sensors remain to be discovered. This review summarizes known and potential hypoxia sensors among human O2-dependent enzymes and highlights their possible roles in hypoxia-related adaptation and diseases.
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Affiliation(s)
- Li Li
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Susan Shen
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
- Department of Psychiatry, University of California, San FranciscoSan FranciscoUnited States
| | - Philip Bickler
- Hypoxia Research Laboratory, University of California San Francisco, San FranciscoSan FranciscoUnited States
- Center for Health Equity in Surgery and Anesthesia, University of California San Francisco, San FranciscoSan FranciscoUnited States
- Anesthesia and Perioperative Care, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Lani F Wu
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
| | - Steven J Altschuler
- Department of Pharmaceutical Chemistry, University of California San Francisco, San FranciscoSan FranciscoUnited States
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22
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Bleher K, Comba P, Kass D, Ray K, Wadepohl H. Reactivities of iron(IV)-oxido compounds with pentadentate bispidine ligands. J Inorg Biochem 2023; 241:112123. [PMID: 36701984 DOI: 10.1016/j.jinorgbio.2023.112123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 01/05/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023]
Abstract
The FeIVO complexes of bispidines (3,7-diazabicyclo[3.3.1]nonane derivatives) are known to be highly reactive oxidants - with the tetradentate bispidine, the so far most reactive ferryl complex has been reported and two isomeric pentadentate ligands also lead to very reactive high-valent oxidants. With a series of 4 new bispidine derivatives we now try to address the question why the bispidine scaffold in general leads to very reactive oxidants and how this can be tuned by ligand modifications. The study is based on a full structural, spectroscopic and electrochemical analysis of the iron(II) precursors, spectroscopic data of the iron(IV)-oxido complexes, a kinetic analysis of the stoichiometric oxidation of thioanisole by five different bispidine‑iron(IV)-oxido complexes and on product analyses of reactions by the five ferryl oxidants with thioanisole, β-methylstyrene and cis-stilbene as substrates.
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Affiliation(s)
- Katharina Bleher
- Universität Heidelberg, Anorganisch-Chemisches Institut, INF 270, D-69120 Heidelberg, Germany
| | - Peter Comba
- Universität Heidelberg, Anorganisch-Chemisches Institut, INF 270, D-69120 Heidelberg, Germany; Universität Heidelberg, Interdisziplinäres Zentrum für Wissenschaftliches Rechnen (IWR), Germany.
| | - Dustin Kass
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor Strasse 2, D-12489 Berlin, Germany
| | - Kallol Ray
- Humboldt-Universität zu Berlin, Department of Chemistry, Brook-Taylor Strasse 2, D-12489 Berlin, Germany
| | - Hubert Wadepohl
- Universität Heidelberg, Anorganisch-Chemisches Institut, INF 270, D-69120 Heidelberg, Germany
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23
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Zhu W, Sharma N, Lee YM, El-Khouly ME, Fukuzumi S, Nam W. Use of Singlet Oxygen in the Generation of a Mononuclear Nonheme Iron(IV)-Oxo Complex. Inorg Chem 2023; 62:4116-4123. [PMID: 36862977 DOI: 10.1021/acs.inorgchem.2c04020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Nonheme iron(III)-superoxo intermediates are generated in the activation of dioxygen (O2) by nonheme iron(II) complexes and then converted to iron(IV)-oxo species by reacting with hydrogen donor substrates with relatively weak C-H bonds. If singlet oxygen (1O2) with ca. 1 eV higher energy than the ground state triplet oxygen (3O2) is employed, iron(IV)-oxo complexes can be synthesized using hydrogen donor substrates with much stronger C-H bonds. However, 1O2 has never been used in generating iron(IV)-oxo complexes. Herein, we report that a nonheme iron(IV)-oxo species, [FeIV(O)(TMC)]2+ (TMC = tetramethylcyclam), is generated using 1O2, which is produced with boron subphthalocyanine chloride (SubPc) as a photosensitizer, and hydrogen donor substrates with relatively strong C-H bonds, such as toluene (BDE = 89.5 kcal mol-1), via electron transfer from [FeII(TMC)]2+ to 1O2, which is energetically more favorable by 0.98 eV, as compared with electron transfer from [FeII(TMC)]2+ to 3O2. Electron transfer from [FeII(TMC)]2+ to 1O2 produces an iron(III)-superoxo complex, [FeIII(O2)(TMC)]2+, followed by abstracting a hydrogen atom from toluene by [FeIII(O2)(TMC)]2+ to form an iron(III)-hydroperoxo complex, [FeIII(OOH)(TMC)]2+, that is further converted to the [FeIV(O)(TMC)]2+ species. Thus, the present study reports the first example of generating a mononuclear nonheme iron(IV)-oxo complex with the use of singlet oxygen, instead of triplet oxygen, and a hydrogen atom donor with relatively strong C-H bonds. Detailed mechanistic aspects, such as the detection of 1O2 emission, the quenching by [FeII(TMC)]2+, and the quantum yields, have also been discussed to provide valuable mechanistic insights into understanding nonheme iron-oxo chemistry.
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Affiliation(s)
- Wenjuan Zhu
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Namita Sharma
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Mohamed E El-Khouly
- Institute of Basic and Applied Sciences, Egypt-Japan University of Science and Technology, New Borg El-Arab 21934, Alexandria, Egypt
| | - Shunichi Fukuzumi
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
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24
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Heim P, Gericke R, Spedalotto G, Lovisari M, Farquhar ER, McDonald AR. Aromatic and aliphatic hydrocarbon hydroxylation via a formally Ni IVO oxidant. Dalton Trans 2023; 52:2663-2671. [PMID: 36745393 PMCID: PMC9972353 DOI: 10.1039/d2dt03949d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The reaction of (NMe4)2[NiII(LPh)(OAc)] (1[OAc], LPh = 2,2',2''-nitrilo-tris-(N-phenylacetamide); OAc = acetate) with 3-chloroperoxybenzoic acid (m-CPBA) resulted in the formation of a self-hydroxylated NiIII-phenolate complex, 2, where one of the phenyl groups of LPh underwent hydroxylation. 2 was characterised by UV-Vis, EPR, and XAS spectroscopies and ESI-MS. 2 decayed to yield a previously characterised NiII-phenolate complex, 3. We postulate that self-hydroxylation was mediated by a formally NiIVO oxidant, formed from the reaction of 1[OAc] with m-CPBA, which undergoes electrophilic aromatic substitution to yield 2. This is supported by an analysis of the kinetic and thermodynamic properties of the reaction of 1[OAc] with m-CPBA. Addition of exogenous hydrocarbon substrates intercepted the self-hydroxylation process, producing hydroxylated products, providing further support for the formally NiIVO entity. This study demonstrates that the reaction between NiII salts and m-CPBA can lead to potent metal-based oxidants, in contrast to recent studies demonstrating carboxyl radical is a radical free-chain reaction initiator in NiII/m-CPBA hydrocarbon oxidation catalysis.
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Affiliation(s)
- Philipp Heim
- School of Chemistry and CRANN/AMBER Nanoscience Institute, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland.
| | - Robert Gericke
- School of Chemistry and CRANN/AMBER Nanoscience Institute, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland.
| | - Giuseppe Spedalotto
- School of Chemistry and CRANN/AMBER Nanoscience Institute, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland.
| | - Marta Lovisari
- School of Chemistry and CRANN/AMBER Nanoscience Institute, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland.
| | - Erik R Farquhar
- Center for Synchrotron Biosciences, National Synchrotron Light Source II, Brookhaven, National Laboratory Case Western Reserve University, Upton, NY 11973, USA
| | - Aidan R McDonald
- School of Chemistry and CRANN/AMBER Nanoscience Institute, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland.
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25
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Guo M, Zhou S, Sun X. Room-Temperature Conversion of Methane to Methanediol by [FeO 2] . J Phys Chem Lett 2023; 14:1633-1640. [PMID: 36752636 DOI: 10.1021/acs.jpclett.2c03786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Inspired by the activities of P-450 enzyme and Rieske oxygenases in nature, in which the high-valent Fe-oxo complexes play a key role for oxidation of alkanes, the oxidation process of methane by the high-valent iron oxide cation [FeO2]+ has been explored by using Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometry complemented by high-level quantum chemical calculations. In contrast to the previously reported [FeO]+/CH4 and [Fe(O)OH]+/CH4 systems, which afford [FeOH]+ as the main product, the generation of Fe+ dominates the reaction of [FeO2]+ with CH4. Theoretical calculations suggest a novel "oxygen rebound" pathway for the liberation of methanediol. In particular, the inevitable valence increase of Fe prior to C-H activation is similar to the cytochrome P-450 mediated processes. To our best knowledge, this study provides the first example of methane activation by the high-valent Fe(V)-oxo species in the gas phase, which may thus bridge the gas-phase model and the condensed-phase biosystems.
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Affiliation(s)
- Mengdi Guo
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
| | - Shaodong Zhou
- College of Chemical and Biological Engineering, Zhejiang Provincial Key Laboratory of Advanced Chemical Engineering Manufacture Technology, Zhejiang University, Hangzhou 310027, China
- Institute of Zhejiang University─Quzhou, Zheda Road No. 99, Quzhou 324000, China
| | - Xiaoyan Sun
- Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao 266101, China
- Shandong Energy Institute, Qingdao 266101, China
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26
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Samani M, Ardakani MH, Sabet M. Dioxo-molybdenum(VI) unsymmetrical Schiff base complex supported on CoFe2O4@SiO2 nanoparticles as a new magnetically recoverable nanocatalyst for selective epoxidation of alkenes. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2022. [DOI: 10.1007/s13738-022-02546-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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27
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Van Stappen C, Deng Y, Liu Y, Heidari H, Wang JX, Zhou Y, Ledray AP, Lu Y. Designing Artificial Metalloenzymes by Tuning of the Environment beyond the Primary Coordination Sphere. Chem Rev 2022; 122:11974-12045. [PMID: 35816578 DOI: 10.1021/acs.chemrev.2c00106] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes catalyze a variety of reactions using a limited number of natural amino acids and metallocofactors. Therefore, the environment beyond the primary coordination sphere must play an important role in both conferring and tuning their phenomenal catalytic properties, enabling active sites with otherwise similar primary coordination environments to perform a diverse array of biological functions. However, since the interactions beyond the primary coordination sphere are numerous and weak, it has been difficult to pinpoint structural features responsible for the tuning of activities of native enzymes. Designing artificial metalloenzymes (ArMs) offers an excellent basis to elucidate the roles of these interactions and to further develop practical biological catalysts. In this review, we highlight how the secondary coordination spheres of ArMs influence metal binding and catalysis, with particular focus on the use of native protein scaffolds as templates for the design of ArMs by either rational design aided by computational modeling, directed evolution, or a combination of both approaches. In describing successes in designing heme, nonheme Fe, and Cu metalloenzymes, heteronuclear metalloenzymes containing heme, and those ArMs containing other metal centers (including those with non-native metal ions and metallocofactors), we have summarized insights gained on how careful controls of the interactions in the secondary coordination sphere, including hydrophobic and hydrogen bonding interactions, allow the generation and tuning of these respective systems to approach, rival, and, in a few cases, exceed those of native enzymes. We have also provided an outlook on the remaining challenges in the field and future directions that will allow for a deeper understanding of the secondary coordination sphere a deeper understanding of the secondary coordintion sphere to be gained, and in turn to guide the design of a broader and more efficient variety of ArMs.
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Affiliation(s)
- Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yunling Deng
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yiwei Liu
- Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Hirbod Heidari
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Jing-Xiang Wang
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yu Zhou
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, 105 East 24th Street, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois, Urbana-Champaign, 505 South Mathews Avenue, Urbana, Illinois 61801, United States
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28
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Cook EN, Hooe SL, Dickie DA, Machan CW. Homogeneous Catalytic Reduction of O 2 to H 2O by a Terpyridine-Based FeN 3O Complex. Inorg Chem 2022; 61:8387-8392. [PMID: 35594192 DOI: 10.1021/acs.inorgchem.2c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a new terpyridine-based FeN3O catalyst, Fe(tpytbupho)Cl2, which reduces O2 to H2O. Variable concentration and variable temperature spectrochemical studies with decamethylferrocene as a chemical reductant in acetonitrile solution enabled the elucidation of key reaction parameters for the catalytic reduction of O2 to H2O by Fe(tpytbupho)Cl2. These mechanistic studies suggest that a 2 + 2 mechanism is operative, where hydrogen peroxide is produced as a discrete intermediate, prior to further reduction to H2O. Consistent with this proposal, the spectrochemically measured first-order rate constant k (s-1) value for H2O2 reduction is larger than that for O2 reduction. Further, significant H2O2 production is observed under hydrodynamic conditions in rotating ring-disk electrode measurements, where the product can be swept away from the cathode surface before further reduction occurs.
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Affiliation(s)
- Emma N Cook
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, Virginia 22904-4319, United States
| | - Shelby L Hooe
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, Virginia 22904-4319, United States
| | - Diane A Dickie
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, Virginia 22904-4319, United States
| | - Charles W Machan
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, Virginia 22904-4319, United States
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29
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Yeh CCG, Mokkawes T, Bradley J, Le Brun NE, de Visser S. Second coordination sphere effects on the mechanistic pathways for dioxygen activation by a ferritin: involvement of a Tyr radical and the identification of a cation binding site. Chembiochem 2022; 23:e202200257. [PMID: 35510795 PMCID: PMC9401865 DOI: 10.1002/cbic.202200257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/05/2022] [Indexed: 11/09/2022]
Abstract
Ferritins are ubiquitous diiron enzymes involved in iron(II) detoxification and oxidative stress responses and can act as metabolic iron stores. The overall reaction mechanisms of ferritin enzymes are still unclear, particularly concerning the role of the conserved, near catalytic center Tyr residue. Thus, we carried out a computational study of a ferritin using a large cluster model of well over 300 atoms including its first- and second-coordination sphere. The calculations reveal important insight into the structure and reactivity of ferritins. Specifically, the active site Tyr residue delivers a proton and electron in the catalytic cycle prior to iron(II) oxidation. In addition, the calculations highlight a likely cation binding site at Asp65, which through long-range electrostatic interactions, influences the electronic configuration and charge distributions of the metal center. The results are consistent with experimental observations but reveal novel detail of early mechanistic steps that lead to an unusual mixed-valent iron(III)-iron(II) center.
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Affiliation(s)
- Chieh-Chih George Yeh
- The University of Manchester, Department of Chemical Engineering, Oxford Road, Manchester, UNITED KINGDOM
| | - Thirakorn Mokkawes
- The University of Manchester, Department of Chemical Engineering, Manchester, UNITED KINGDOM
| | - Justin Bradley
- University of East Anglia, School of Chemistry, UNITED KINGDOM
| | - Nick E Le Brun
- University of East Anglia, School of Chemistry, UNITED KINGDOM
| | - Samuel de Visser
- The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN, Manchester, UNITED KINGDOM
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30
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Conde-Giménez M, Galano-Frutos JJ, Galiana-Cameo M, Mahía A, Victor BL, Salillas S, Velázquez-Campoy A, Brito RMM, Gálvez JA, Díaz-de-Villegas MD, Sancho J. Alchemical Design of Pharmacological Chaperones with Higher Affinity for Phenylalanine Hydroxylase. Int J Mol Sci 2022; 23:ijms23094502. [PMID: 35562892 PMCID: PMC9100405 DOI: 10.3390/ijms23094502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/14/2022] [Accepted: 04/16/2022] [Indexed: 11/17/2022] Open
Abstract
Phenylketonuria (PKU) is a rare metabolic disease caused by variations in a human gene, PAH, encoding phenylalanine hydroxylase (PAH), and the enzyme converting the essential amino acid phenylalanine into tyrosine. Many PKU-causing variations compromise the conformational stability of the encoded enzyme, decreasing or abolishing its catalytic activity, and leading to an elevated concentration of phenylalanine in the blood, which is neurotoxic. Several therapeutic approaches have been developed to treat the more severe manifestations of the disorder, but they are either not entirely effective or difficult to adhere to throughout life. In a search for novel pharmacological chaperones to treat PKU, a lead compound was discovered (compound IV) that exhibited promising in vitro and in vivo chaperoning activity on PAH. The structure of the PAH-IV complex has been reported. Here, using alchemical free energy calculations (AFEC) on the structure of the PAH-IV complex, we design a new generation of compound IV-analogues with a higher affinity for the enzyme. Seventeen novel analogues were synthesized, and thermal shift and isothermal titration calorimetry (ITC) assays were performed to experimentally evaluate their stabilizing effect and their affinity for the enzyme. Most of the new derivatives bind to PAH tighter than lead compound IV and induce a greater thermostabilization of the enzyme upon binding. Importantly, the correspondence between the calculated alchemical binding free energies and the experimentally determined ΔΔGb values is excellent, which supports the use of AFEC to design pharmacological chaperones to treat PKU using the X-ray structure of their complexes with the target PAH enzyme.
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Affiliation(s)
- María Conde-Giménez
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; (M.C.-G.); (J.J.G.-F.); (M.G.-C.); (A.M.); (S.S.); (A.V.-C.)
- Biocomputation and Complex Systems Physics Institute (BIFI)-GBsC-CSIC Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Juan José Galano-Frutos
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; (M.C.-G.); (J.J.G.-F.); (M.G.-C.); (A.M.); (S.S.); (A.V.-C.)
- Biocomputation and Complex Systems Physics Institute (BIFI)-GBsC-CSIC Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - María Galiana-Cameo
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; (M.C.-G.); (J.J.G.-F.); (M.G.-C.); (A.M.); (S.S.); (A.V.-C.)
- Biocomputation and Complex Systems Physics Institute (BIFI)-GBsC-CSIC Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Alejandro Mahía
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; (M.C.-G.); (J.J.G.-F.); (M.G.-C.); (A.M.); (S.S.); (A.V.-C.)
- Biocomputation and Complex Systems Physics Institute (BIFI)-GBsC-CSIC Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Bruno L. Victor
- Coimbra Chemistry Center-Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal; (B.L.V.); (R.M.M.B.)
| | - Sandra Salillas
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; (M.C.-G.); (J.J.G.-F.); (M.G.-C.); (A.M.); (S.S.); (A.V.-C.)
- Biocomputation and Complex Systems Physics Institute (BIFI)-GBsC-CSIC Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
| | - Adrián Velázquez-Campoy
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; (M.C.-G.); (J.J.G.-F.); (M.G.-C.); (A.M.); (S.S.); (A.V.-C.)
- Biocomputation and Complex Systems Physics Institute (BIFI)-GBsC-CSIC Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
- CIBER de Enfermedades Hepáticas y Digestivas CIBERehd, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Rui M. M. Brito
- Coimbra Chemistry Center-Institute of Molecular Sciences (CQC-IMS), Department of Chemistry, University of Coimbra, 3004-535 Coimbra, Portugal; (B.L.V.); (R.M.M.B.)
| | - José Antonio Gálvez
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain;
| | - María D. Díaz-de-Villegas
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Departamento de Química Orgánica, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain;
- Correspondence: (M.D.D.-d.-V.); (J.S.)
| | - Javier Sancho
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Universidad de Zaragoza, 50009 Zaragoza, Spain; (M.C.-G.); (J.J.G.-F.); (M.G.-C.); (A.M.); (S.S.); (A.V.-C.)
- Biocomputation and Complex Systems Physics Institute (BIFI)-GBsC-CSIC Joint Unit, Universidad de Zaragoza, 50018 Zaragoza, Spain
- Aragon Health Research Institute (IIS Aragón), 50009 Zaragoza, Spain
- Correspondence: (M.D.D.-d.-V.); (J.S.)
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31
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Osifalujo EA, Preston‐Herrera C, Betts PC, Satterwhite LR, Froese JT. Improving Toluene Dioxygenase Activity for Ester‐Functionalized Substrates through Enzyme Engineering. ChemistrySelect 2022. [DOI: 10.1002/slct.202200753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Cristina Preston‐Herrera
- Department of Chemistry Ball State University 1600 W Ashland Avenue Muncie IN USA 47306
- Cristina Preston-Herrera Department of Chemistry and Chemical Biology Cornell University 122 Baker Laboratory Ithaca NY USA 14853
| | - Phillip C. Betts
- Department of Chemistry Ball State University 1600 W Ashland Avenue Muncie IN USA 47306
| | - Louis R. Satterwhite
- Department of Chemistry Ball State University 1600 W Ashland Avenue Muncie IN USA 47306
| | - Jordan T. Froese
- Department of Chemistry Ball State University 1600 W Ashland Avenue Muncie IN USA 47306
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32
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Csizi KS, Eckert L, Brunken C, Hofstetter TB, Reiher M. The Apparently Unreactive Substrate Facilitates the Electron Transfer for Dioxygen Activation in Rieske Dioxygenases. Chemistry 2022; 28:e202103937. [PMID: 35072969 PMCID: PMC9306888 DOI: 10.1002/chem.202103937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 12/29/2022]
Abstract
Rieske dioxygenases belong to the non‐heme iron family of oxygenases and catalyze important cis‐dihydroxylation as well as O‐/N‐dealkylation and oxidative cyclization reactions for a wide range of substrates. The lack of substrate coordination at the non‐heme ferrous iron center, however, makes it particularly challenging to delineate the role of the substrate for productive O2
activation. Here, we studied the role of the substrate in the key elementary reaction leading to O2
activation from a theoretical perspective by systematically considering (i) the 6‐coordinate to 5‐coordinate conversion of the non‐heme FeII upon abstraction of a water ligand, (ii) binding of O2
, and (iii) transfer of an electron from the Rieske cluster. We systematically evaluated the spin‐state‐dependent reaction energies and structural effects at the active site for all combinations of the three elementary processes in the presence and absence of substrate using naphthalene dioxygenase as a prototypical Rieske dioxygenase. We find that reaction energies for the generation of a coordination vacancy at the non‐heme FeII
center through thermoneutral H2O reorientation and exothermic O2
binding prior to Rieske cluster oxidation are largely insensitive to the presence of naphthalene and do not lead to formation of any of the known reactive Fe‐oxygen species. By contrast, the role of the substrate becomes evident after Rieske cluster oxidation and exclusively for the 6‐coordinate non‐heme FeII
sites in that the additional electron is found at the substrate instead of at the iron and oxygen atoms. Our results imply an allosteric control of the substrate on Rieske dioxygenase reactivity to happen prior to changes at the non‐heme FeII
in agreement with a strategy that avoids unproductive O2
activation.
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Affiliation(s)
- Katja-Sophia Csizi
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Lina Eckert
- ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Christoph Brunken
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Thomas B Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Markus Reiher
- ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
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33
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Yeh CCG, Ghafoor S, Satpathy JK, Mokkawes T, Sastri CV, de Visser SP. Cluster Model Study into the Catalytic Mechanism of α-Ketoglutarate Biodegradation by the Ethylene-Forming Enzyme Reveals Structural Differences with Nonheme Iron Hydroxylases. ACS Catal 2022. [DOI: 10.1021/acscatal.1c04029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- C.-C. George Yeh
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Sidra Ghafoor
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | | | - Thirakorn Mokkawes
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Chivukula V. Sastri
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
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34
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Bagha UK, Satpathy JK, Mukherjee G, Barman P, Kumar D, de Visser SP, Sastri CV. Oxidative dehalogenation of halophenols by high-valent nonheme iron(IV)-oxo intermediates. Faraday Discuss 2022; 234:58-69. [PMID: 35170590 DOI: 10.1039/d1fd00064k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mononuclear high-valent iron(IV)-oxo intermediates are excellent oxidants towards oxygenation reactions by heme and nonheme metalloenzymes and their model systems. One of the most important functions of these intermediates in nature is to detoxify various environmental pollutants. Organic substrates, such as halogenated phenols, are known to be water pollutants which can be degraded to their less hazardous forms through an oxidation reaction by iron(IV)-oxo complexes. Metalloproteins in nature utilize various types of second-coordination sphere interactions to anchor the substrate in the vicinity of the active site. This concept of substrate-binding is well-known for natural enzymes, but is elusive for the relevant biomimetic model systems. Herein, we report the oxidative reactivity patterns of an iron(IV)-oxo intermediate, [FeIV(O)(2PyN2Q)]2+, (2PyN2Q = 1,1-di(pyridin-2yl)-N,N-bis(quinolin-2-ylmethyl)methanamine) with a series of mono-, di- and tri-halophenols. A detailed experimental study shows that the dehalogenation reactions of the halophenols by such iron(IV)-oxo intermediates proceed via an initial hydrogen atom abstraction from the phenolic O-H group. Furthermore, based on the size and nucleophilicity of the halophenol, an intermediate substrate-bound species forms that is a phenolate adduct to the ferric species, which thereafter leads to the formation of the corresponding products.
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Affiliation(s)
- Umesh Kumar Bagha
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, India.
| | | | - Gourab Mukherjee
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, India. .,Department of Chemical Science, Tata Institute of Fundamental Research, Dr. Homi Bhabha Road, Colaba, Mumbai, 400005, India
| | - Prasenjit Barman
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, India. .,Department of Chemistry, Kaliyaganj College, West Bengal, 733129, India
| | - Devesh Kumar
- Department of Applied Physics, School for Physical Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India.
| | - Sam P de Visser
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, India. .,The Manchester Institute of Biotechnology, Department of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam, 781039, India.
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35
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Comba P, Nunn G, Scherz F, Walton PH. Intermediate-spin iron(IV)-oxido species with record reactivity. Faraday Discuss 2022; 234:232-244. [PMID: 35156976 DOI: 10.1039/d1fd00073j] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The nonheme iron(IV)-oxido complex trans-N3-[(L1)FeIVO(Cl)]+, where L1 is a derivative of the tetradentate bispidine 2,4-di(pyridine-2-yl)-3,7-diazabicyclo[3.3.1]nonane-1-one, has an S = 1 electronic ground state and is the most reactive nonheme iron model system known so far, of a similar order of reactivity as nonheme iron enzymes (C-H abstraction of cyclohexane, -90 °C (propionitrile), t1/2 = 3.5 s). The reaction with cyclohexane selectively leads to chlorocyclohexane, but "cage escape" at the [(L1)FeIII(OH)(Cl)]+/cyclohexyl radical intermediate lowers the productivity. Ligand field theory is used herein to analyze the d-d transitions of [(L1)FeIVO(X)]n+ (X = Cl-, Br-, MeCN) in comparison with the thoroughly characterized ferryl complex of tetramethylcyclam (TMC = L2; [(L2)FeIVO(MeCN)]2+). The ligand field parameters and d-d transition energies are shown to provide important information on the triplet-quintet gap and its correlation with oxidation reactivity.
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Affiliation(s)
- Peter Comba
- Universität Heidelberg, Anorganisch-Chemisches Institut, INF 270, D-69120 Heidelberg, Germany. .,Universität Heidelberg, Interdisziplinäres Zentrum für Wissenschaftliches Rechnen (IWR), Germany
| | - George Nunn
- Department of Chemistry, University of York, Heslington, YORK, YO10 5DD, UK
| | - Frederik Scherz
- Universität Heidelberg, Anorganisch-Chemisches Institut, INF 270, D-69120 Heidelberg, Germany.
| | - Paul H Walton
- Department of Chemistry, University of York, Heslington, YORK, YO10 5DD, UK
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36
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de Visser SP, Mukherjee G, Ali HS, Sastri CV. Local Charge Distributions, Electric Dipole Moments, and Local Electric Fields Influence Reactivity Patterns and Guide Regioselectivities in α-Ketoglutarate-Dependent Non-heme Iron Dioxygenases. Acc Chem Res 2022; 55:65-74. [PMID: 34915695 DOI: 10.1021/acs.accounts.1c00538] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Non-heme iron dioxygenases catalyze vital processes for human health related to the biosynthesis of essential products and the biodegradation of toxic metabolites. Often the natural product biosyntheses by these non-heme iron dioxygenases is highly regio- and chemoselective, which are commonly assigned to tight substrate-binding and positioning. However, recent high-level computational modeling has shown that substrate-binding and positioning is only part of the story and long-range electrostatic interactions can play a major additional role.In this Account, we review and summarize computational viewpoints on the high regio- and chemoselectivity of α-ketoglutarate-dependent non-heme iron dioxygenases and how external perturbations affect the catalysis. In particular, studies from our groups have shown that often a regioselectivity in enzymes can be accomplished by stabilization of the rate-determining transition state for the reaction through external charges, electric dipole moments, or local electric field effects. Furthermore, bond dissociation energies in molecules are shown to be influenced by an electric field effect, and through targeting a specific bond in an electric field, this can lead to an unusually specific reaction. For instance, in the carbon-induced starvation protein, we studied two substrate-bound conformations and showed that regardless of what C-H bond of the substrate is closest to the iron(IV)-oxo oxidant, the lowest hydrogen atom abstraction barrier is always for the pro-S C2-H abstraction due to an induced dipole moment of the protein that weakens this bond. In another example of the hygromycin biosynthesis enzyme, an oxidative ring-closure reaction in the substrate forms an ortho-δ-ester ring. Calculations on this enzyme show that the selectivity is guided by a protonated lysine residue in the active site that, through its positive charge, triggers a low energy hydrogen atom abstraction barrier. A final set of examples in this Account discuss the viomycin biosynthesis enzyme and the 2-(trimethylammonio)ethylphosphonate dioxygenase (TmpA) enzyme. Both of these enzymes are shown to possess a significant local dipole moment and local electric field effect due to charged residues surrounding the substrate and oxidant binding pockets. The protein dipole moment and local electric field strength changes the C-H bond strengths of the substrate as compared to the gas-phase triggers the regioselectivity of substrate activation. In particular, we show that in the gas phase and in a protein environment C-H bond strengths are different due to local electric dipole moments and electric field strengths. These examples show that enzymes have an intricately designed structure that enables a chemical reaction under ambient conditions through the positioning of positively and negatively charged residues that influence and enhance reaction mechanisms. These computational insights create huge possibilities in bioengineering to apply local electric field and dipole moments in proteins to achieve an unusual selectivity and specificity and trigger a fit-for-purpose biocatalyst for unique biotransformations.
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Affiliation(s)
- 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
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039 Assam, India
| | - Gourab Mukherjee
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039 Assam, India
| | - Hafiz Saqib Ali
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Chivukula V. Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039 Assam, India
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37
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Singha A, Mittra K, Dey A. Synthetic heme dioxygen adducts: electronic structure and reactivity. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2021.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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38
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Wong HPH, Mokkawes T, de Visser SP. Can the isonitrile biosynthesis enzyme ScoE assist with the biosynthesis of isonitrile groups in drug molecules? A computational study. Phys Chem Chem Phys 2022; 24:27250-27262. [DOI: 10.1039/d2cp03409c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Computational studies show that the isonitrile synthesizing enzyme ScoE can catalyse the conversion of γ-Gly substituents in substrates to isonitrile. This enables efficient isonitrile substitution into target molecules such as axisonitrile-1.
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Affiliation(s)
- Henrik P. H. Wong
- Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
- Department of Chemical Engineering, Oxford Road, Manchester M13 9PL, UK
| | - Thirakorn Mokkawes
- Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
- Department of Chemical Engineering, Oxford Road, Manchester M13 9PL, UK
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, 131 Princess Street, Manchester M1 7DN, UK
- Department of Chemical Engineering, Oxford Road, Manchester M13 9PL, UK
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39
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Ali HS, de Visser S, de Visser SP. Electrostatic perturbations in the substrate-binding pocket of taurine/α-ketoglutarate dioxygenase determine its selectivity. Chemistry 2021; 28:e202104167. [PMID: 34967481 PMCID: PMC9304159 DOI: 10.1002/chem.202104167] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Indexed: 11/17/2022]
Abstract
Taurine/α‐ketoglutarate dioxygenase is an important enzyme that takes part in the cysteine catabolism process in the human body and selectively hydroxylates taurine at the C1‐position. Recent computational studies showed that in the gas‐phase the C2−H bond of taurine is substantially weaker than the C1−H bond, yet no evidence exists of 2‐hydroxytaurine products. To this end, a detailed computational study on the selectivity patterns in TauD was performed. The calculations show that the second‐coordination sphere and the protonation states of residues play a major role in guiding the enzyme to the right selectivity. Specifically, a single proton on an active site histidine residue can change the regioselectivity of the reaction through its electrostatic perturbations in the active site and effectively changes the C1−H and C2−H bond strengths of taurine. This is further emphasized by many polar and hydrogen bonding interactions of the protein cage in TauD with the substrate and the oxidant that weaken the pro‐R C1−H bond and triggers a chemoselective reaction process. The large cluster models reproduce the experimental free energy of activation excellently.
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Affiliation(s)
- Hafiz Saqib Ali
- The University of Manchester, School of Chemistry, UNITED KINGDOM
| | - Samuel de Visser
- The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN, Manchester, UNITED KINGDOM
| | - Sam P de Visser
- The University of Manchester, Department of Chemical Engineering, UNITED KINGDOM
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40
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Lin YT, Ali HS, de Visser S. Biodegradation of herbicides by a plant nonheme iron dioxygenase: mechanism and selectivity of substrate analogues. Chemistry 2021; 28:e202103982. [PMID: 34911156 DOI: 10.1002/chem.202103982] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Indexed: 11/11/2022]
Abstract
Aryloxyalkanoate dioxygenases are unique herbicide biodegrading nonheme iron enzymes found in plants and hence, from environmental and agricultural point of view they are important and valuable. However, they often are substrate specific and little is known on the details of the mechanism and the substrate scope. To this end, we created enzyme models and calculate the mechanism for 2,4-dichlorophenoxyacetic acid biodegradation and 2-methyl substituted analogs by density functional theory. The work shows that the substrate binding is tight and positions the aliphatic group close to the metal center to enable a chemoselective reaction mechanism to form the C 2 -hydroxy products, whereas the aromatic hydroxylation barriers are well higher in energy. Subsequently, we investigated the metabolism of R - and S -methyl substituted inhibitors and show that these do not react as efficiently as 2,4-dichlorophenoxyacetic acid substrate due to stereochemical clashes in the active site and particularly for the R -isomer give high rebound barriers.
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Affiliation(s)
- Yen-Ting Lin
- UoM: The University of Manchester, Chemical Engineering and Analytical Science, UNITED KINGDOM
| | - Hafiz S Ali
- UoM: The University of Manchester, Chemistry, UNITED KINGDOM
| | - Samuel de Visser
- The University of Manchester, Manchester Institute of Biotechnology, 131 Princess Street, M1 7DN, Manchester, UNITED KINGDOM
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41
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PCET to bound-superoxide by NADH and NADHX in aqueous-acid media: a kinetic inspection. J CHEM SCI 2021. [DOI: 10.1007/s12039-021-01994-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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42
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Valdez-Moreira JA, Beagan DM, Yang H, Telser J, Hoffman BM, Pink M, Carta V, Smith JM. Hydrocarbon Oxidation by an Exposed, Multiply Bonded Iron(III) Oxo Complex. ACS CENTRAL SCIENCE 2021; 7:1751-1755. [PMID: 34729418 PMCID: PMC8554833 DOI: 10.1021/acscentsci.1c00890] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Indexed: 06/10/2023]
Abstract
The iron oxo unit, [Fe=O] n+ is a critical intermediate in biological oxidation reactions. While its higher oxidation states are well studied, relatively little is known about the least-oxidized form [FeIII=O]+. Here, the thermally stable complex PhB(AdIm)3Fe=O has been structurally, spectroscopically, and computationally characterized as a bona fide iron(III) oxo. An unusually short Fe-O bond length is consistent with iron-oxygen multiple bond character and is supported by electronic structure calculations. The complex is thermally stable yet is able to perform hydrocarbon oxidations, facilitating both C-O bond formation and dehydrogenation reactions.
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Affiliation(s)
- Juan A. Valdez-Moreira
- Department
of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington Indiana 47405, United States
| | - Daniel M. Beagan
- Department
of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington Indiana 47405, United States
| | - Hao Yang
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Joshua Telser
- Department
of Biological, Physical and Health Sciences, Roosevelt University, Chicago, Illinois 60605, United States
| | - Brian M. Hoffman
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Maren Pink
- Department
of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington Indiana 47405, United States
| | - Veronica Carta
- Department
of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington Indiana 47405, United States
| | - Jeremy M. Smith
- Department
of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington Indiana 47405, United States
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43
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Cook EN, Dickie DA, Machan CW. Catalytic Reduction of Dioxygen to Water by a Bioinspired Non-Heme Iron Complex via a 2+2 Mechanism. J Am Chem Soc 2021; 143:16411-16418. [PMID: 34606274 DOI: 10.1021/jacs.1c04572] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report a bioinspired non-heme Fe complex with a tripodal [N3O]- ligand framework (Fe(PMG)(Cl)2) that is electrocatalytically active toward dioxygen reduction with acetic acid as a proton source in acetonitrile solution. Under electrochemical and chemical conditions, Fe(PMG)(Cl)2 selectively produces water via a 2+2 mechanism, where H2O2 is generated as a discrete intermediate species before further reduction to two equivalents of H2O. Mechanistic studies support a catalytic cycle for dioxygen reduction where an off-cycle peroxo dimer species is the resting state of the catalyst. Spectroscopic analysis of the reduced complex FeII(PMG)Cl shows the stoichiometric formation of an Fe(III)-hydroxide species following exposure to H2O2; no catalytic activity for H2O2 disproportionation is observed, although the complex is electrochemically active for H2O2 reduction to H2O. Electrochemical studies, spectrochemical experiments, and DFT calculations suggest that the carboxylate moiety of the ligand is sensitive to hydrogen-bonding interactions with the acetic acid proton donor upon reduction from Fe(III)/(II), favoring chloride loss trans to the tris-alkyl amine moiety of the ligand framework. These results offer insight into how mononuclear non-heme Fe active sites in metalloproteins distribute added charge and poise proton donors during reactions with dioxygen.
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Affiliation(s)
- Emma N Cook
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, Virginia 22904-4319, United States
| | - Diane A Dickie
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, Virginia 22904-4319, United States
| | - Charles W Machan
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, Virginia 22904-4319, United States
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44
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Li XX, Lu X, Park JW, Cho KB, Nam W. Nonheme Iron Imido Complexes Bearing a Non-Innocent Ligand: A Synthetic Chameleon Species in Oxidation Reactions. Chemistry 2021; 27:17495-17503. [PMID: 34590742 DOI: 10.1002/chem.202103295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Indexed: 11/07/2022]
Abstract
High-valent iron-imido complexes can perform C-H activation and sulfimidation reactions, but are far less studied than the more ubiquitous iron-oxo species. As case studies, we have looked at a recently published iron(V)-imido ligand π-cation radical complex, which is formally an iron(VI)-imido complex [FeV (NTs)(TAML+. )] (1; NTs=tosylimido), and an iron(V)-imido complex [FeV (NTs)(TAML)]- (2). Using a theoretical approach, we found that they have multiple energetically close-lying electromers, sometimes even without changing spin states, reminiscent of the so-called Compound I in Cytochrome P450. When studying their reactivity theoretically, it is indeed found that their electronic structures may change to perform efficient oxidations, emulating the multi-spin state reactivity in FeIV O systems. This is actually in contrast to the known [FeV (O)(TAML)]- species (3), where the reactions occur only on the ground spin state. We also looked into the whole reaction pathway for the C-H bond activation of 1,4-cyclohexadiene by these intermediates to reproduce the experimentally observed products, including steps that usually attract no interest (neither theoretically nor experimentally) due to their non-rate-limiting status and fast reactivity. A new "clustering non-rebound mechanism" is presented for this C-H activation reaction.
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Affiliation(s)
- Xiao-Xi Li
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 03760, Korea
| | - Xiaoyan Lu
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 03760, Korea
| | - Jae Woo Park
- Department of Chemistry, Chungbuk National University, Cheongju, 28644, Korea
| | - Kyung-Bin Cho
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul, 03760, Korea
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45
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Barman SK, Yang MY, Parsell TH, Green MT, Borovik AS. Semiempirical method for examining asynchronicity in metal-oxido-mediated C-H bond activation. Proc Natl Acad Sci U S A 2021; 118:e2108648118. [PMID: 34465626 PMCID: PMC8433561 DOI: 10.1073/pnas.2108648118] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The oxidation of substrates via the cleavage of thermodynamically strong C-H bonds is an essential part of mammalian metabolism. These reactions are predominantly carried out by enzymes that produce high-valent metal-oxido species, which are directly responsible for cleaving the C-H bonds. While much is known about the identity of these transient intermediates, the mechanistic factors that enable metal-oxido species to accomplish such difficult reactions are still incomplete. For synthetic metal-oxido species, C-H bond cleavage is often mechanistically described as synchronous, proton-coupled electron transfer (PCET). However, data have emerged that suggest that the basicity of the M-oxido unit is the key determinant in achieving enzymatic function, thus requiring alternative mechanisms whereby proton transfer (PT) has a more dominant role than electron transfer (ET). To bridge this knowledge gap, the reactivity of a monomeric MnIV-oxido complex with a series of external substrates was studied, resulting in a spread of over 104 in their second-order rate constants that tracked with the acidity of the C-H bonds. Mechanisms that included either synchronous PCET or rate-limiting PT, followed by ET, did not explain our results, which led to a proposed PCET mechanism with asynchronous transition states that are dominated by PT. To support this premise, we report a semiempirical free energy analysis that can predict the relative contributions of PT and ET for a given set of substrates. These findings underscore why the basicity of M-oxido units needs to be considered in C-H functionalization.
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Affiliation(s)
- Suman K Barman
- Department of Chemistry, University of California Irvine, CA 92697;
| | - Meng-Yin Yang
- Department of Chemistry, University of California Irvine, CA 92697
| | | | - Michael T Green
- Department of Chemistry, University of California Irvine, CA 92697;
- Department of Molecular Biosciences and Biochemistry, University of California Irvine, CA 92697
| | - A S Borovik
- Department of Chemistry, University of California Irvine, CA 92697;
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46
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Abu‐Odeh M, Bleher K, Johnee Britto N, Comba P, Gast M, Jaccob M, Kerscher M, Krieg S, Kurth M. Pathways of the Extremely Reactive Iron(IV)-oxido complexes with Tetradentate Bispidine Ligands. Chemistry 2021; 27:11377-11390. [PMID: 34121233 PMCID: PMC8456976 DOI: 10.1002/chem.202101045] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Indexed: 11/07/2022]
Abstract
The nonheme iron(IV)-oxido complex trans-N3-[(L1 )FeIV =O(Cl)]+ , where L1 is a derivative of the tetradentate bispidine 2,4-di(pyridine-2-yl)-3,7-diazabicyclo[3.3.1]nonane-1-one, is known to have an S=1 electronic ground state and to be an extremely reactive oxidant for oxygen atom transfer (OAT) and hydrogen atom abstraction (HAA) processes. Here we show that, in spite of this ferryl oxidant having the "wrong" spin ground state, it is the most reactive nonheme iron model system known so far and of a similar order of reactivity as nonheme iron enzymes (C-H abstraction of cyclohexane, -90 °C (propionitrile), t1/2 =3.5 sec). Discussed are spectroscopic and kinetic data, supported by a DFT-based theoretical analysis, which indicate that substrate oxidation is significantly faster than self-decay processes due to an intramolecular demethylation pathway and formation of an oxido-bridged diiron(III) intermediate. It is also shown that the iron(III)-chlorido-hydroxido/cyclohexyl radical intermediate, resulting from C-H abstraction, selectively produces chlorocyclohexane in a rebound process. However, the life-time of the intermediate is so long that other reaction channels (known as cage escape) become important, and much of the C-H abstraction therefore is unproductive. In bulk reactions at ambient temperature and at longer time scales, there is formation of significant amounts of oxidation product - selectively of chlorocyclohexane - and it is shown that this originates from oxidation of the oxido-bridged diiron(III) resting state.
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Affiliation(s)
- Mahmud Abu‐Odeh
- Anorganisch-Chemisches InstitutUniversität HeidelbergINF 27069120HeidelbergGermany
| | - Katharina Bleher
- Anorganisch-Chemisches InstitutUniversität HeidelbergINF 27069120HeidelbergGermany
| | | | - Peter Comba
- Anorganisch-Chemisches InstitutUniversität HeidelbergINF 27069120HeidelbergGermany
- Interdisziplinäres Zentrum für Wissenschaftliches Rechnen (IWR) MathematikonIm Neuenheimer Feld 20569120HeidelbergGermany
| | - Michael Gast
- Anorganisch-Chemisches InstitutUniversität HeidelbergINF 27069120HeidelbergGermany
| | | | - Marion Kerscher
- Anorganisch-Chemisches InstitutUniversität HeidelbergINF 27069120HeidelbergGermany
| | - Saskia Krieg
- Anorganisch-Chemisches InstitutUniversität HeidelbergINF 27069120HeidelbergGermany
| | - Marius Kurth
- Anorganisch-Chemisches InstitutUniversität HeidelbergINF 27069120HeidelbergGermany
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Yeh CCG, Pierides C, Jameson GNL, de Visser SP. Structure and Functional Differences of Cysteine and 3-Mercaptopropionate Dioxygenases: A Computational Study. Chemistry 2021; 27:13793-13806. [PMID: 34310770 DOI: 10.1002/chem.202101878] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Indexed: 11/09/2022]
Abstract
Thiol dioxygenases are important enzymes for human health; they are involved in the detoxification and catabolism of toxic thiol-containing natural products such as cysteine. As such, these enzymes have relevance to the development of Alzheimer's and Parkinson's diseases in the brain. Recent crystal structure coordinates of cysteine and 3-mercaptopropionate dioxygenase (CDO and MDO) showed major differences in the second-coordination spheres of the two enzymes. To understand the difference in activity between these two analogous enzymes, we created large, active-site cluster models. We show that CDO and MDO have different iron(III)-superoxo-bound structures due to differences in ligand coordination. Furthermore, our studies show that the differences in the second-coordination sphere and particularly the position of a positively charged Arg residue results in changes in substrate positioning, mobility and enzymatic turnover. Furthermore, the substrate scope of MDO is explored with cysteinate and 2-mercaptosuccinic acid and their reactivity is predicted.
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Affiliation(s)
- C-C George Yeh
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Christos Pierides
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Guy N L Jameson
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Vic, 3010, Australia
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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Mukherjee G, Satpathy JK, Bagha UK, Mubarak MQE, Sastri CV, de Visser SP. Inspiration from Nature: Influence of Engineered Ligand Scaffolds and Auxiliary Factors on the Reactivity of Biomimetic Oxidants. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01993] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Gourab Mukherjee
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Jagnyesh K. Satpathy
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Umesh K. Bagha
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - M. Qadri E. Mubarak
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Fakulti Sains dan Teknologi, Universiti Sains Islam Malaysia, Bandar Baru Nilai, 71800 Nilai, Negeri Sembilan Malaysia
| | - Chivukula V. Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
| | - Sam P. de Visser
- Department of Chemistry, Indian Institute of Technology Guwahati, 781039, Assam, India
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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49
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Tomboc GM, Park Y, Lee K, Jin K. Directing transition metal-based oxygen-functionalization catalysis. Chem Sci 2021; 12:8967-8995. [PMID: 34276926 PMCID: PMC8261717 DOI: 10.1039/d1sc01272j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/07/2021] [Indexed: 11/21/2022] Open
Abstract
This review presents the recent progress of oxygen functionalization reactions based on non-electrochemical (conventional organic synthesis) and electrochemical methods. Although both methods have their advantages and limitations, the former approach has been used to synthesize a broader range of organic substances as the latter is limited by several factors, such as poor selectivity and high energy cost. However, because electrochemical methods can replace harmful terminal oxidizers with external voltage, organic electrosynthesis has emerged as greener and more eco-friendly compared to conventional organic synthesis. The progress of electrochemical methods toward oxygen functionalization is presented by an in-depth discussion of different types of electrically driven-chemical organic synthesis, with particular attention to recently developed electrochemical systems and catalyst designs. We hope to direct the attention of readers to the latest breakthroughs of traditional oxygen functionalization reactions and to the potential of electrochemistry for the transformation of organic substrates to useful end products.
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Affiliation(s)
- Gracita M Tomboc
- Department of Chemistry and Research Institute for Natural Sciences, Korea University Seoul 02841 Republic of Korea
| | - Yeji Park
- Department of Chemistry and Research Institute for Natural Sciences, Korea University Seoul 02841 Republic of Korea
| | - Kwangyeol Lee
- Department of Chemistry and Research Institute for Natural Sciences, Korea University Seoul 02841 Republic of Korea
| | - Kyoungsuk Jin
- Department of Chemistry and Research Institute for Natural Sciences, Korea University Seoul 02841 Republic of Korea
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50
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Lin YT, de Visser SP. Product Distributions of Cytochrome P450 OleT JE with Phenyl-Substituted Fatty Acids: A Computational Study. Int J Mol Sci 2021; 22:7172. [PMID: 34281222 PMCID: PMC8269385 DOI: 10.3390/ijms22137172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022] Open
Abstract
There are two types of cytochrome P450 enzymes in nature, namely, the monooxygenases and the peroxygenases. Both enzyme classes participate in substrate biodegradation or biosynthesis reactions in nature, but the P450 monooxygenases use dioxygen, while the peroxygenases take H2O2 in their catalytic cycle instead. By contrast to the P450 monooxygenases, the P450 peroxygenases do not require an external redox partner to deliver electrons during the catalytic cycle, and also no external proton source is needed. Therefore, they are fully self-sufficient, which affords them opportunities in biotechnological applications. One specific P450 peroxygenase, namely, P450 OleTJE, reacts with long-chain linear fatty acids through oxidative decarboxylation to form hydrocarbons and, as such, has been implicated as a suitable source for the biosynthesis of biofuels. Unfortunately, the reactions were shown to produce a considerable amount of side products originating from Cα and Cβ hydroxylation and desaturation. These product distributions were found to be strongly dependent on whether the substrate had substituents on the Cα and/or Cβ atoms. To understand the bifurcation pathways of substrate activation by P450 OleTJE leading to decarboxylation, Cα hydroxylation, Cβ hydroxylation and Cα-Cβ desaturation, we performed a computational study using 3-phenylpropionate and 2-phenylbutyrate as substrates. We set up large cluster models containing the heme, the substrate and the key features of the substrate binding pocket and calculated (using density functional theory) the pathways leading to the four possible products. This work predicts that the two substrates will react with different reaction rates due to accessibility differences of the substrates to the active oxidant, and, as a consequence, these two substrates will also generate different products. This work explains how the substrate binding pocket of P450 OleTJE guides a reaction to a chemoselectivity.
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Affiliation(s)
- Yen-Ting Lin
- Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK;
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Manchester M13 9PL, UK
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK;
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Manchester M13 9PL, UK
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