1
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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 DOI: 10.1021/jacs.3c08950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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2
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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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3
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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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4
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Satpathy JK, Yadav R, Bagha UK, Kumar D, Sastri CV, de Visser SP. Enhanced Reactivity through Equatorial Sulfur Coordination in Nonheme Iron(IV)-Oxo Complexes: Insights from Experiment and Theory. Inorg Chem 2024; 63:6752-6766. [PMID: 38551622 DOI: 10.1021/acs.inorgchem.4c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Sulfur ligation in metalloenzymes often gives the active site unique properties, whether it is the axial cysteinate ligand in the cytochrome P450s or the equatorial sulfur/thiol ligation in nonheme iron enzymes. To understand sulfur ligation to iron complexes and how it affects the structural, spectroscopic, and intrinsic properties of the active species and the catalysis of substrates, we pursued a systematic study and compared sulfur with amine-ligated iron(IV)-oxo complexes. We synthesized and characterized a biomimetic N4S-ligated iron(IV)-oxo complex and compared the obtained results with an analogous N5-ligated iron(IV)-oxo complex. Our work shows that the amine for sulfur replacement in the equatorial ligand framework leads to a rate enhancement for oxygen atom and hydrogen atom transfer reactions. Moreover, the sulfur-ligated iron(IV)-oxo complex reacts through a different reaction mechanism as compared to the N5-ligated iron(IV)-oxo complex, where the former reacts through hydride transfer with the latter reacting via radical pathways. We show that the reactivity differences are caused by a dramatic change in redox potential between the two complexes. Our studies highlight the importance of implementing a sulfur ligand into the equatorial ligand framework of nonheme iron(IV)-oxo complexes and how it affects the physicochemical properties of the oxidant and its reactivity.
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Affiliation(s)
- Jagnyesh K Satpathy
- Department of Chemistry, Indian Institute of Technology, Guwahati 781039, Assam, India
| | - Rolly Yadav
- 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
| | - Devesh Kumar
- Department of Applied Physics, Babasaheb Bhimrao Ambedkar University, School for Physical Sciences, Vidya Vihar, Rae Bareilly Road, Lucknow 226025, UP, India
| | - 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
- The Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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5
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Ali HS, de Visser SP. Catalytic divergencies in the mechanism of L-arginine hydroxylating nonheme iron enzymes. Front Chem 2024; 12:1365494. [PMID: 38406558 PMCID: PMC10884159 DOI: 10.3389/fchem.2024.1365494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 01/22/2024] [Indexed: 02/27/2024] Open
Abstract
Many enzymes in nature utilize a free arginine (L-Arg) amino acid to initiate the biosynthesis of natural products. Examples include nitric oxide synthases, which generate NO from L-Arg for blood pressure control, and various arginine hydroxylases involved in antibiotic biosynthesis. Among the groups of arginine hydroxylases, several enzymes utilize a nonheme iron(II) active site and let L-Arg react with dioxygen and α-ketoglutarate to perform either C3-hydroxylation, C4-hydroxylation, C5-hydroxylation, or C4-C5-desaturation. How these seemingly similar enzymes can react with high specificity and selectivity to form different products remains unknown. Over the past few years, our groups have investigated the mechanisms of L-Arg-activating nonheme iron dioxygenases, including the viomycin biosynthesis enzyme VioC, the naphthyridinomycin biosynthesis enzyme NapI, and the streptothricin biosynthesis enzyme OrfP, using computational approaches and applied molecular dynamics, quantum mechanics on cluster models, and quantum mechanics/molecular mechanics (QM/MM) approaches. These studies not only highlight the differences in substrate and oxidant binding and positioning but also emphasize on electronic and electrostatic differences in the substrate-binding pockets of the enzymes. In particular, due to charge differences in the active site structures, there are changes in the local electric field and electric dipole moment orientations that either strengthen or weaken specific substrate C-H bonds. The local field effects, therefore, influence and guide reaction selectivity and specificity and give the enzymes their unique reactivity patterns. Computational work using either QM/MM or density functional theory (DFT) on cluster models can provide valuable insights into catalytic reaction mechanisms and produce accurate and reliable data that can be used to engineer proteins and synthetic catalysts to perform novel reaction pathways.
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Affiliation(s)
- Hafiz Saqib Ali
- Chemistry Research Laboratory, Department of Chemistry and the INEOS Oxford Institute for Antimicrobial Research, University of Oxford, Oxford, United Kingdom
| | - Sam P. de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering, The University of Manchester, Manchester, United Kingdom
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6
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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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7
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Mukherjee G, Velmurugan G, Kerscher M, Kumar Satpathy J, Sastri CV, Comba P. Mechanistic Insights into Amphoteric Reactivity of an Iron-Bispidine Complex. Chemistry 2024; 30:e202303127. [PMID: 37942658 DOI: 10.1002/chem.202303127] [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: 09/26/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/10/2023]
Abstract
The reactivity of FeIII -alkylperoxido complexes has remained a riddle to inorganic chemists owing to their thermal instability and impotency towards organic substrates. These iron-oxygen adducts have been known as sluggish oxidants towards oxidative electrophilic and nucleophilic reactions. Herein, we report the synthesis and spectroscopic characterization of a relatively stable mononuclear high-spin FeIII -alkylperoxido complex supported by an engineered bispidine framework. Against the notion, this FeIII -alkylperoxido complex serves as a rare example of versatile reactivity in both electrophilic and nucleophilic reactions. Detailed mechanistic studies and computational calculations reveal a novel reaction mechanism, where a putative superoxido intermediate orchestrates the amphoteric property of the oxidant. The design of the backbone is pivotal to convey stability and reactivity to alkylperoxido and superoxido intermediates. Contrary to the well-known O-O bond cleavage that generates an FeIV -oxido species, the FeIII -alkylperoxido complex reported here undergoes O-C bond scission to generate a superoxido moiety that is responsible for the amphiphilic reactivity.
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Affiliation(s)
- Gourab Mukherjee
- Department of Catalysis & Fine Chemicals, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad, 500007, India
| | - Gunasekaran Velmurugan
- Anorganisch-Chemisches Institut and, Interdisciplinary Center for Scientific Computing (IWR), Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany)
| | - Marion Kerscher
- Anorganisch-Chemisches Institut and, Interdisciplinary Center for Scientific Computing (IWR), Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany)
| | - Jagnyesh Kumar Satpathy
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Peter Comba
- Anorganisch-Chemisches Institut and, Interdisciplinary Center for Scientific Computing (IWR), Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany)
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8
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Zhu C, D'Agostino C, de Visser SP. Mechanism of CO 2 Reduction to Methanol with H 2 on an Iron(II)-scorpionate Catalyst. Chemistry 2023; 29:e202302832. [PMID: 37694535 DOI: 10.1002/chem.202302832] [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: 09/07/2023] [Revised: 09/09/2023] [Accepted: 09/11/2023] [Indexed: 09/12/2023]
Abstract
CO2 utilization is an important process in the chemical industry with great environmental power. In this work we show how CO2 and H2 can be reacted to form methanol on an iron(II) center and highlight the bottlenecks for the reaction and what structural features of the catalyst are essential for efficient turnover. The calculations predict the reactions to proceed through three successive reaction cycles that start with heterolytic cleavage of H2 followed by sequential hydride and proton transfer processes. The H2 splitting process is an endergonic process and hence high pressures will be needed to overcome this step and trigger the hydrogenation reaction. Moreover, H2 cleavage into a hydride and proton requires a metal to bind hydride and a nearby source to bind the proton, such as an amide or pyrazolyl group, which the scorpionate ligand used here facilitates. As such the computations highlight the non-innocence of the ligand scaffold through proton shuttle from H2 to substrate as an important step in the reaction mechanism.
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Affiliation(s)
- Chengxu Zhu
- 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
| | - Carmine D'Agostino
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Dipartimento di Ingegneria Civile, Chimica, Ambientale e dei Materiali (DICAM), Alma Mater Studiorum, Università di Bologna, Via Terracini, 28, 40131, Bologna, Italy
| | - 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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Zhang Y, Mokkawes T, de Visser SP. Insights into Cytochrome P450 Enzyme Catalyzed Defluorination of Aromatic Fluorides. Angew Chem Int Ed Engl 2023; 62:e202310785. [PMID: 37641517 DOI: 10.1002/anie.202310785] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 08/31/2023]
Abstract
Density functional calculations establish a novel mechanism of aromatic defluorination by P450 Compound I. This is achieved via either an initial epoxide intermediate or through a 1,2-fluorine shift in an electrophilic intermediate, which highlights that the P450s can defluorinate fluoroarenes. However, in the absence of a proton donor a strong Fe-F bond can be obtained as shown from the calculations.
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Affiliation(s)
- Yi Zhang
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M17DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Thirakorn Mokkawes
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M17DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M17DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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Lv H, Zhang XP, Guo K, Han J, Guo H, Lei H, Li X, Zhang W, Apfel UP, Cao R. Coordination Tuning of Metal Porphyrins for Improved Oxygen Evolution Reaction. Angew Chem Int Ed Engl 2023; 62:e202305938. [PMID: 37550259 DOI: 10.1002/anie.202305938] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/06/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
The nucleophilic attack of water or hydroxide on metal-oxo units forms an O-O bond in the oxygen evolution reaction (OER). Coordination tuning to improve this attack is intriguing but has been rarely realized. We herein report on improved OER catalysis by metal porphyrin 1-M (M=Co, Fe) with a coordinatively unsaturated metal ion. We designed and synthesized 1-M by sterically blocking one porphyrin side with a tethered tetraazacyclododecane unit. With this protection, the metal-oxo species generated in OER can maintain an unoccupied trans axial site. Importantly, 1-M displays a higher OER activity in alkaline solutions than analogues lacking such an axial protection by decreasing up to 150-mV overpotential to achieve 10 mA/cm2 current density. Theoretical studies suggest that with an unoccupied trans axial site, the metal-oxo unit becomes more positively charged and thus is more favoured for the hydroxide nucleophilic attack as compared to metal-oxo units bearing trans axial ligands.
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Affiliation(s)
- Haoyuan Lv
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 710119, Xi'an, China
| | - Xue-Peng Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 710119, Xi'an, China
| | - Kai Guo
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 710119, Xi'an, China
| | - Jinxiu Han
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 710119, Xi'an, China
| | - Hongbo Guo
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 710119, Xi'an, China
| | - Haitao Lei
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 710119, Xi'an, China
| | - Xialiang Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 710119, Xi'an, China
| | - Wei Zhang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 710119, Xi'an, China
| | - Ulf-Peter Apfel
- Ruhr-Universität Bochum, Fakultät für Chemie und Biochemie, Anorganische Chemie I, Universitätsstrasse 150, 44801, Bochum, Germany
- Fraunhofer UMSICHT, Osterfelder Strasse 3, 46047, Oberhausen, Germany
| | - Rui Cao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 710119, Xi'an, China
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11
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Barchenko M, O’Malley PJ, de Visser SP. Mechanism of Nitrogen Reduction to Ammonia in a Diiron Model of Nitrogenase. Inorg Chem 2023; 62:14715-14726. [PMID: 37650683 PMCID: PMC10498488 DOI: 10.1021/acs.inorgchem.3c02089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Indexed: 09/01/2023]
Abstract
Nitrogenase is a fascinating enzyme in biology that reduces dinitrogen from air to ammonia through stepwise reduction and protonation. Despite it being studied in detail by experimental and computational groups, there are still many unknown factors in the catalytic cycle of nitrogenase, especially related to the addition of protons and electrons and their order. A recent biomimetic study characterized a potential dinitrogen-bridged diiron cluster as a synthetic model of nitrogenase. Using strong acid and reductants, the dinitrogen was converted into ammonia molecules, but details of the mechanism remains unknown. In particular, it was unclear from the experimental studies whether the proton and electron transfer steps are sequential or alternating. Moreover, the work failed to establish what the function of the diiron core is and whether it split into mononuclear iron fragments during the reaction. To understand the structure and reactivity of the biomimetic dinitrogen-bridged diiron complex [(P2P'PhFeH)2(μ-N2)] with triphenylphosphine ligands, we performed a density functional theory study. Our computational methods were validated against experimental crystal structure coordinates, Mössbauer parameters, and vibrational frequencies and show excellent agreement. Subsequently, we investigated the alternating and consecutive addition of electrons and protons to the system. The calculations identify a number of possible reaction channels, namely, same-site protonation, alternating protonation, and complex dissociation into mononuclear iron centers. The calculations show that the overall mechanism is not a pure sequential set of electron and proton transfers but a mixture of alternating and consecutive steps. In particular, the first reaction steps will start with double proton transfer followed by an electron transfer, while thereafter, there is another proton transfer and a second electron transfer to give a complex whereby ammonia can split off with a low energetic barrier. The second channel starts with alternating protonation of the two nitrogen atoms, whereafter the initial double proton transfer, electrons and protons are added sequentially to form a hydrazine-bound complex. The latter split off ammonia spontaneously after further protonation. The various reaction channels are analyzed with valence bond and orbital diagrams. We anticipate the nitrogenase enzyme to operate with mixed alternating and consecutive protonation and electron transfer steps.
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Affiliation(s)
- Maxim Barchenko
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Patrick J. O’Malley
- Department
of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K.
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
- Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.
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12
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Wu H, Xu S, Du P, Liu Y, Li H, Yang H, Wang T, Wang ZG. A nucleotide-copper(II) complex possessing a monooxygenase-like catalytic function. J Mater Chem B 2023. [PMID: 37409588 DOI: 10.1039/d3tb00780d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/07/2023]
Abstract
The de novo design of artificial biocatalysts with enzyme-like active sites and catalytic functions has long been an attractive yet challenging goal. In this study, we present a nucleotide-Cu2+ complex, synthesized through a one-pot approach, capable of catalyzing ortho-hydroxylation reactions resembling those of minimalist monooxygenases. Both experimental and theoretical findings demonstrate that the catalyst, in which Cu2+ coordinates with both the nucleobase and phosphate moieties, forms a ternary-complex intermediate with H2O2 and tyramine substrates through multiple weak interactions. The subsequent electron transfer and hydrogen (or proton) transfer steps lead to the ortho-hydroxylation of tyramine, where the single copper center exhibits a similar function to natural dicopper sites. Moreover, Cu2+ bound to nucleotides or oligonucleotides exhibits thermophilic catalytic properties within the temperature range of 25 °C to 75 °C, while native enzymes are fully deactivated above 35 °C. This study may provide insights for the future design of oxidase-mimetic catalysts and serve as a guide for the design of primitive metallocentre-dependent enzymes.
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Affiliation(s)
- Haifeng Wu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Shichao Xu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Peidong Du
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Yuanxi Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Hui Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
| | - Haijun Yang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ting Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, P. R. China.
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13
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Serafim LF, Jayasinghe-Arachchige VM, Wang L, Rathee P, Yang J, Moorkkannur N S, Prabhakar R. Distinct chemical factors in hydrolytic reactions catalyzed by metalloenzymes and metal complexes. Chem Commun (Camb) 2023. [PMID: 37366367 DOI: 10.1039/d3cc01380d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The selective hydrolysis of the extremely stable phosphoester, peptide and ester bonds of molecules by bio-inspired metal-based catalysts (metallohydrolases) is required in a wide range of biological, biotechnological and industrial applications. Despite the impressive advances made in the field, the ultimate goal of designing efficient enzyme mimics for these reactions is still elusive. Its realization will require a deeper understanding of the diverse chemical factors that influence the activities of both natural and synthetic catalysts. They include catalyst-substrate complexation, non-covalent interactions and the electronic nature of the metal ion, ligand environment and nucleophile. Based on our computational studies, their roles are discussed for several mono- and binuclear metallohydrolases and their synthetic analogues. Hydrolysis by natural metallohydrolases is found to be promoted by a ligand environment with low basicity, a metal bound water and a heterobinuclear metal center (in binuclear enzymes). Additionally, peptide and phosphoester hydrolysis is dominated by two competing effects, i.e. nucleophilicity and Lewis acid activation, respectively. In synthetic analogues, hydrolysis is facilitated by the inclusion of a second metal center, hydrophobic effects, a biological metal (Zn, Cu and Co) and a terminal hydroxyl nucleophile. Due to the absence of the protein environment, hydrolysis by these small molecules is exclusively influenced by nucleophile activation. The results gleaned from these studies will enhance the understanding of fundamental principles of multiple hydrolytic reactions. They will also advance the development of computational methods as a predictive tool to design more efficient catalysts for hydrolysis, Diels-Alder reaction, Michael addition, epoxide opening and aldol condensation.
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Affiliation(s)
- Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | | | - Lukun Wang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | - Parth Rathee
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | - Jiawen Yang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
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14
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Sun C, Jaimes JL, Follmer AH, Ziller JW, Borovik AS. Selective C-H Bond Cleavage with a High-Spin Fe IV-Oxido Complex. Molecules 2023; 28:4755. [PMID: 37375309 DOI: 10.3390/molecules28124755] [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: 03/10/2023] [Revised: 05/23/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
Non-heme Fe monooxygenases activate C-H bonds using intermediates with high-spin FeIV-oxido centers. To mimic these sites, a new tripodal ligand [pop]3- was prepared that contains three phosphoryl amido groups that are capable of stabilizing metal centers in high oxidation states. The ligand was used to generate [FeIVpop(O)]-, a new FeIV-oxido complex with an S = 2 spin ground state. Spectroscopic measurements, which included low-temperature absorption and electron paramagnetic resonance spectroscopy, supported the assignment of a high-spin FeIV center. The complex showed reactivity with benzyl alcohol as the external substrate but not with related compounds (e.g., ethyl benzene and benzyl methyl ether), suggesting the possibility that hydrogen bonding interaction(s) between the substrate and [FeIVpop(O)]- was necessary for reactivity. These results exemplify the potential role of the secondary coordination sphere in metal-mediated processes.
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Affiliation(s)
- Chen Sun
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - Jennifer L Jaimes
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - Alec H Follmer
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - Joseph W Ziller
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697, USA
| | - Andrew S Borovik
- Department of Chemistry, University of California-Irvine, Irvine, CA 92697, USA
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15
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Skipworth T, Klaine S, Zhang R. Photochemical generation and reactivity of a new phthalocyanine-manganese-oxo intermediate. Chem Commun (Camb) 2023; 59:6540-6543. [PMID: 37161771 DOI: 10.1039/d3cc01275a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The first phthalocyanine-manganese-oxo intermediate was successfully generated by visible-light photolysis of chlorate or nitrite manganese(III) precursors, and its reactivity towards organic substrates was kinetically probed and compared with other related porphyrin-metal-oxo intermediates.
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Affiliation(s)
- Tristan Skipworth
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd., Bowling Green, Kentucky, USA.
| | - Seth Klaine
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd., Bowling Green, Kentucky, USA.
| | - Rui Zhang
- Department of Chemistry, Western Kentucky University, 1906 College Heights Blvd., Bowling Green, Kentucky, USA.
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16
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Diao D, Simaan AJ, Martinez A, Colomban C. Bioinspired complexes confined in well-defined capsules: getting closer to metalloenzyme functionalities. Chem Commun (Camb) 2023; 59:4288-4299. [PMID: 36946593 DOI: 10.1039/d2cc06990c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Reproducing the key features offered by metalloprotein binding cavities is an attractive approach to overcome the main bottlenecks of current open artificial models (in terms of stability, efficiency and selectivity). In this context, this featured article brings together selected examples of recent developments in the field of confined bioinspired complexes with an emphasis on the emerging hemicryptophane caged ligands. In particular, we focused on (1) the strategies allowing the insulation and protection of complexes sharing similarities with metalloprotein active sites, (2) the confinement-induced improvement of catalytic efficiencies and selectivities and (3) very recent efforts that have been made toward the development of bioinspired complexes equipped with weakly binding artificial cavities.
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Affiliation(s)
- Donglin Diao
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France.
| | - A Jalila Simaan
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France.
| | | | - Cédric Colomban
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France.
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17
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Chen J, Song W, Yao J, Wu Z, Lee YM, Wang Y, Nam W, Wang B. Hydrogen Bonding-Assisted and Nonheme Manganese-Catalyzed Remote Hydroxylation of C-H Bonds in Nitrogen-Containing Molecules. J Am Chem Soc 2023; 145:5456-5466. [PMID: 36811463 DOI: 10.1021/jacs.2c13832] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
The development of catalytic systems capable of oxygenating unactivated C-H bonds with excellent site-selectivity and functional group tolerance under mild conditions remains a challenge. Inspired by the secondary coordination sphere (SCS) hydrogen bonding in metallooxygenases, reported herein is an SCS solvent hydrogen bonding strategy that employs 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) as a strong hydrogen bond donor solvent to enable remote C-H hydroxylation in the presence of basic aza-heteroaromatic rings with a low loading of a readily available and inexpensive manganese complex as a catalyst and hydrogen peroxide as a terminal oxidant. We demonstrate that this strategy represents a promising compliment to the current state-of-the-art protection approaches that rely on precomplexation with strong Lewis and/or Brønsted acids. Mechanistic studies with experimental and theoretical approaches reveal the existence of a strong hydrogen bonding between the nitrogen-containing substrate and HFIP, which prevents the catalyst deactivation by nitrogen binding and deactivates the basic nitrogen atom toward oxygen atom transfer and the α-C-H bonds adjacent to the nitrogen center toward H-atom abstraction. Moreover, the hydrogen bonding exerted by HFIP has also been demonstrated not only to facilitate the O-O bond heterolytic cleavage of a putative MnIII-OOH precursor to generate MnV(O)(OC(O)CH2Br) as an active oxidant but also to affect the stability and the activity of MnV(O)(OC(O)CH2Br).
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Affiliation(s)
- Jie Chen
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Wenxun Song
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Jinping Yao
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Zhimin Wu
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Yong Wang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Bin Wang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
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18
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Metallocavitins as Advanced Enzyme Mimics and Promising Chemical Catalysts. Catalysts 2023. [DOI: 10.3390/catal13020415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
The supramolecular approach is becoming increasingly dominant in biomimetics and chemical catalysis due to the expansion of the enzyme active center idea, which now includes binding cavities (hydrophobic pockets), channels and canals for transporting substrates and products. For a long time, the mimetic strategy was mainly focused on the first coordination sphere of the metal ion. Understanding that a highly organized cavity-like enzymatic pocket plays a key role in the sophisticated functionality of enzymes and that the activity and selectivity of natural metalloenzymes are due to the effects of the second coordination sphere, created by the protein framework, opens up new perspectives in biomimetic chemistry and catalysis. There are two main goals of mimicking enzymatic catalysis: (1) scientific curiosity to gain insight into the mysterious nature of enzymes, and (2) practical tasks of mankind: to learn from nature and adopt from its many years of evolutionary experience. Understanding the chemistry within the enzyme nanocavity (confinement effect) requires the use of relatively simple model systems. The performance of the transition metal catalyst increases due to its retention in molecular nanocontainers (cavitins). Given the greater potential of chemical synthesis, it is hoped that these promising bioinspired catalysts will achieve catalytic efficiency and selectivity comparable to and even superior to the creations of nature. Now it is obvious that the cavity structure of molecular nanocontainers and the real possibility of modifying their cavities provide unlimited possibilities for simulating the active centers of metalloenzymes. This review will focus on how chemical reactivity is controlled in a well-defined cavitin nanospace. The author also intends to discuss advanced metal–cavitin catalysts related to the study of the main stages of artificial photosynthesis, including energy transfer and storage, water oxidation and proton reduction, as well as highlight the current challenges of activating small molecules, such as H2O, CO2, N2, O2, H2, and CH4.
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19
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Mokkawes T, de Visser SP. Melatonin Activation by Cytochrome P450 Isozymes: How Does CYP1A2 Compare to CYP1A1? Int J Mol Sci 2023; 24:ijms24043651. [PMID: 36835057 PMCID: PMC9959256 DOI: 10.3390/ijms24043651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Cytochrome P450 enzymes are versatile enzymes found in most biosystems that catalyze mono-oxygenation reactions as a means of biosynthesis and biodegradation steps. In the liver, they metabolize xenobiotics, but there are a range of isozymes with differences in three-dimensional structure and protein chain. Consequently, the various P450 isozymes react with substrates differently and give varying product distributions. To understand how melatonin is activated by the P450s in the liver, we did a thorough molecular dynamics and quantum mechanics study on cytochrome P450 1A2 activation of melatonin forming 6-hydroxymelatonin and N-acetylserotonin products through aromatic hydroxylation and O-demethylation pathways, respectively. We started from crystal structure coordinates and docked substrate into the model, and obtained ten strong binding conformations with the substrate in the active site. Subsequently, for each of the ten substrate orientations, long (up to 1 μs) molecular dynamics simulations were run. We then analyzed the orientations of the substrate with respect to the heme for all snapshots. Interestingly, the shortest distance does not correspond to the group that is expected to be activated. However, the substrate positioning gives insight into the protein residues it interacts with. Thereafter, quantum chemical cluster models were created and the substrate hydroxylation pathways calculated with density functional theory. These relative barrier heights confirm the experimental product distributions and highlight why certain products are obtained. We make a detailed comparison with previous results on CYP1A1 and identify their reactivity differences with melatonin.
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Affiliation(s)
- Thirakorn Mokkawes
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
- Department of Chemical Engineering, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
- Correspondence:
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20
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Jeong D, Kim H, Cho J. Oxidation of Aldehydes into Carboxylic Acids by a Mononuclear Manganese(III) Iodosylbenzene Complex through Electrophilic C-H Bond Activation. J Am Chem Soc 2023; 145:888-897. [PMID: 36598425 DOI: 10.1021/jacs.2c09274] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The oxidation of aldehyde is one of the fundamental reactions in the biological system. Various synthetic procedures and catalysts have been developed to convert aldehydes into corresponding carboxylic acids efficiently under ambient conditions. In this work, we report the oxidation of aldehydes by a mononuclear manganese(III) iodosylbenzene complex, [MnIII(TBDAP)(OIPh)(OH)]2+ (1), with kinetic and mechanistic studies in detail. The reaction of 1 with aldehydes resulted in the formation of corresponding carboxylic acids via a pre-equilibrium state. Hammett plot and reaction rates of 1 with 1°-, 2°-, and 3°-aldehydes revealed the electrophilicity of 1 in the aldehyde oxidation. A kinetic isotope effect experiment and reactivity of 1 toward cyclohexanecarboxaldehyde (CCA) analogues indicate that the reaction of 1 with aldehyde occurs through the rate-determining C-H bond activation at the formyl group. The reaction rate of 1 with CCA is correlated to the bond dissociation energy of the formyl group plotting a linear correlation with other aliphatic C-H bonds. Density functional theory calculations found that 1 electrostatically interacts with CCA at the pre-equilibrium state in which the C-H bond activation of the formyl group is performed as the most feasible pathway. Surprisingly, the rate-determining step is characterized as hydride transfer from CCA to 1, affording an (oxo)methylium intermediate. At the fundamental level, it is revealed that the hydride transfer is composed of H atom abstraction followed by a fast electron transfer. Catalytic reactions of aldehydes by 1 are also presented with a broad substrate scope. This novel mechanistic study gives better insights into the metal oxygen chemistry and would be prominently valuable for development of transition metal catalysts.
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Affiliation(s)
- Donghyun Jeong
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan44919, Republic of Korea
| | - Hyokyung Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan44919, Republic of Korea
| | - Jaeheung Cho
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan44919, Republic of Korea.,Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), Ulsan44919, Republic of Korea
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21
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Mokkawes T, Lim ZQ, de Visser SP. Mechanism of Melatonin Metabolism by CYP1A1: What Determines the Bifurcation Pathways of Hydroxylation versus Deformylation? J Phys Chem B 2022; 126:9591-9606. [PMID: 36380557 PMCID: PMC9706573 DOI: 10.1021/acs.jpcb.2c07200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Melatonin, a widely applied cosmetic active ingredient, has a variety of uses as a skin protector through antioxidant and anti-inflammatory functions as well as giving the body UV-induced defenses and immune system support. In the body, melatonin is synthesized from a tryptophan amino acid in a cascade of reactions, but as melatonin is toxic at high concentrations, it is metabolized in the human skin by the cytochrome P450 enzymes. The P450s are diverse heme-based mono-oxygenases that catalyze oxygen atom-transfer processes that trigger metabolism and detoxification reactions in the body. In the catalytic cycle of the P450s, a short-lived high-valent iron(IV)-oxo heme cation radical is formed that has been proposed to be the active oxidant. How and why it activates melatonin in the human body and what the origin of the product distributions is, are unknown. This encouraged us to do a detailed computational study on a typical human P450 isozyme, namely CYP1A1. We initially did a series of molecular dynamics simulations with substrate docked into several orientations. These simulations reveal a number of stable substrate-bound positions in the active site, which may lead to differences in substrate activation channels. Using tunneling analysis on the full protein structures, we show that two of the four binding conformations lead to open substrate-binding pockets. As a result, in these open pockets, the substrate is not tightly bound and can escape back into the solution. In the closed conformations, in contrast, the substrate is mainly oriented with the methoxy group pointing toward the heme, although under a different angle. We then created large quantum cluster models of the enzyme and focused on the chemical reaction mechanisms for melatonin activation, leading to competitive O-demethylation and C6-aromatic hydroxylation pathways. The calculations show that active site positioning determines the product distributions, but the bond that is activated is not necessarily closest to the heme in the enzyme-substrate complex. As such, the docking and molecular dynamics positioning of the substrate versus oxidant can give misleading predictions on product distributions. In particular, in quantum mechanics cluster model I, we observe that through a tight hydrogen bonding network, a preferential 6-hydroxylation of melatonin is obtained. However, O-demethylation becomes possible in alternative substrate-binding orientations that have the C6-aromatic ring position shielded. Finally, we investigated enzymatic and non-enzymatic O-demethylation processes and show that the hydrogen bonding network in the substrate-binding pocket can assist and perform this step prior to product release from the enzyme.
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Affiliation(s)
- Thirakorn Mokkawes
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.,Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.
| | - Ze Qing Lim
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.,Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.
| | - Sam P. de Visser
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess
Street, Manchester M1 7DN, U.K.,Department
of Chemical Engineering, The University
of Manchester, Oxford
Road, Manchester M13 9PL, U.K.,
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22
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Wei Q, Lee Y, Liang W, Chen X, Mu BS, Cui XY, Wu W, Bai S, Liu Z. Photocatalytic direct borylation of carboxylic acids. Nat Commun 2022; 13:7112. [PMID: 36402764 PMCID: PMC9675845 DOI: 10.1038/s41467-022-34833-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 11/09/2022] [Indexed: 11/21/2022] Open
Abstract
The preparation of high value-added boronic acids from cheap and plentiful carboxylic acids is desirable. To date, the decarboxylative borylation of carboxylic acids is generally realized through the extra step synthesized redox-active ester intermediate or in situ generated carboxylic acid covalent derivatives above 150 °C reaction temperature. Here, we report a direct decarboxylative borylation method of carboxylic acids enabled by visible-light catalysis and that does not require any extra stoichiometric additives or synthesis steps. This operationally simple process produces CO2 and proceeds under mild reaction conditions, in terms of high step economy and good functional group compatibility. A guanidine-based biomimetic active decarboxylative mechanism is proposed and rationalized by mechanistic studies. The methodology reported herein should see broad application extending beyond borylation.
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Affiliation(s)
- Qiang Wei
- grid.11135.370000 0001 2256 9319Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China
| | - Yuhsuan Lee
- grid.9227.e0000000119573309Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190 China
| | - Weiqiu Liang
- grid.11135.370000 0001 2256 9319Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China
| | - Xiaolei Chen
- grid.32566.340000 0000 8571 0482Radiochemistry Laboratory, School of Nuclear Science and Technology, Lanzhou University, Lanzhou, 730000 China
| | - Bo-shuai Mu
- grid.11135.370000 0001 2256 9319Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China
| | - Xi-Yang Cui
- grid.11135.370000 0001 2256 9319Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China
| | - Wangsuo Wu
- grid.32566.340000 0000 8571 0482Radiochemistry Laboratory, School of Nuclear Science and Technology, Lanzhou University, Lanzhou, 730000 China
| | - Shuming Bai
- grid.9227.e0000000119573309Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190 China
| | - Zhibo Liu
- grid.11135.370000 0001 2256 9319Beijing National Laboratory for Molecular Sciences, Radiochemistry and Radiation Chemistry Key Laboratory of Fundamental Science, NMPA Key Laboratory for Research and Evaluation of Radiopharmaceuticals, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871 China ,grid.11135.370000 0001 2256 9319Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871 China
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23
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Awasthi A, Leach IF, Engbers S, Kumar R, Eerlapally R, Gupta S, Klein JEMN, Draksharapu A. Formation and Reactivity of a Fleeting Ni III Bisphenoxyl Diradical Species. Angew Chem Int Ed Engl 2022; 61:e202211345. [PMID: 35978531 PMCID: PMC9826141 DOI: 10.1002/anie.202211345] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 01/11/2023]
Abstract
Cytochrome P450s and Galactose Oxidases exploit redox active ligands to form reactive high valent intermediates for oxidation reactions. This strategy works well for the late 3d metals where accessing high valent states is rather challenging. Herein, we report the oxidation of NiII (salen) (salen=N,N'-bis(3,5-di-tert-butyl-salicylidene)-1,2-cyclohexane-(1R,2R)-diamine) with mCPBA (meta-chloroperoxybenzoic acid) to form a fleeting NiIII bisphenoxyl diradical species, in CH3 CN and CH2 Cl2 at -40 °C. Electrochemical and spectroscopic analyses using UV/Vis, EPR, and resonance Raman spectroscopies revealed oxidation events both on the ligand and the metal centre to yield a NiIII bisphenoxyl diradical species. DFT calculations found the electronic structure of the ligand and the d-configuration of the metal center to be consistent with a NiIII bisphenoxyl diradical species. This three electron oxidized species can perform hydrogen atom abstraction and oxygen atom transfer reactions.
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Affiliation(s)
- Ayushi Awasthi
- Southern Laboratories-208 ADepartment of ChemistryIndian Institute of Technology KanpurKanpur208016India
| | - Isaac F. Leach
- Molecular Inorganic ChemistryStratingh Institute for ChemistryUniversity of Groningen9747 AGGroningenThe Netherlands
| | - Silène Engbers
- Molecular Inorganic ChemistryStratingh Institute for ChemistryUniversity of Groningen9747 AGGroningenThe Netherlands
| | - Rakesh Kumar
- Southern Laboratories-208 ADepartment of ChemistryIndian Institute of Technology KanpurKanpur208016India
| | - Raju Eerlapally
- Southern Laboratories-208 ADepartment of ChemistryIndian Institute of Technology KanpurKanpur208016India
| | - Sikha Gupta
- Southern Laboratories-208 ADepartment of ChemistryIndian Institute of Technology KanpurKanpur208016India
| | - Johannes E. M. N. Klein
- Molecular Inorganic ChemistryStratingh Institute for ChemistryUniversity of Groningen9747 AGGroningenThe Netherlands
| | - Apparao Draksharapu
- Southern Laboratories-208 ADepartment of ChemistryIndian Institute of Technology KanpurKanpur208016India
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Awasthi A, Leach IF, Engbers S, Kumar R, Eerlapally R, Gupta S, Klein JEMN, Draksharapu A. Formation and Reactivity of a Fleeting Ni(III) Bisphenoxyl Diradical Species. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202211345] [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)
| | - Isaac F. Leach
- University of Groningen Zernike Institute for Advanced Materials: Rijksuniversiteit Groningen Zernike Institute for Advanced Materials Stratingh Institute for Chemistry NETHERLANDS
| | - Silène Engbers
- University of Groningen Zernike Institute for Advanced Materials: Rijksuniversiteit Groningen Zernike Institute for Advanced Materials Stratingh Institute for Chemistry NETHERLANDS
| | - Rakesh Kumar
- Indian Institute of Technology Kanpur Chemistry INDIA
| | | | - Sikha Gupta
- Indian Institute of Technology Kanpur Chemistry INDIA
| | - Johannes E. M. N. Klein
- University of Groningen Zernike Institute for Advanced Materials: Rijksuniversiteit Groningen Zernike Institute for Advanced Materials Stratingh Institute for Chemistry NETHERLANDS
| | - Apparao Draksharapu
- IITK: Indian Institute of Technology Kanpur Chemistry SL-208A 208016 Kanpur INDIA
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25
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Rajeev A, Balamurugan M, Sankaralingam M. Rational Design of First-Row Transition Metal Complexes as the Catalysts for Oxidation of Arenes: A Homogeneous Approach. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01928] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anjana Rajeev
- Bioinspired & Biomimetic Inorganic Chemistry Lab, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
| | - Mani Balamurugan
- Department of Materials Science and Engineering, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Muniyandi Sankaralingam
- Bioinspired & Biomimetic Inorganic Chemistry Lab, Department of Chemistry, National Institute of Technology Calicut, Kozhikode, Kerala 673601, India
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26
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Co-Crystal Structure-Guided Optimization of Dual-Functional Small Molecules for Improving the Peroxygenase Activity of Cytochrome P450BM3. Int J Mol Sci 2022; 23:ijms23147901. [PMID: 35887253 PMCID: PMC9317928 DOI: 10.3390/ijms23147901] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 12/24/2022] Open
Abstract
We recently developed an artificial P450–H2O2 system assisted by dual-functional small molecules (DFSMs) to modify the P450BM3 monooxygenase into its peroxygenase mode, which could be widely used for the oxidation of non-native substrates. Aiming to further improve the DFSM-facilitated P450–H2O2 system, a series of novel DFSMs having various unnatural amino acid groups was designed and synthesized, based on the co-crystal structure of P450BM3 and a typical DFSM, N-(ω-imidazolyl)-hexanoyl-L-phenylalanine, in this study. The size and hydrophobicity of the amino acid residue in the DFSM drastically affected the catalytic activity (up to 5-fold), stereoselectivity, and regioselectivity of the epoxidation and hydroxylation reactions. Docking simulations illustrated that the differential catalytic ability among the DFSMs is closely related to the binding affinity and the distance between the catalytic group and heme iron. This study not only enriches the DFSM toolbox to provide more options for utilizing the peroxide-shunt pathway of cytochrome P450BM3, but also sheds light on the great potential of the DFSM-driven P450 peroxygenase system in catalytic applications based on DFSM tunability.
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Matsumura H, Faponle AS, Hagedoorn PL, Tosha T, de Visser SP, Moënne-Loccoz P. Mechanism of substrate inhibition in cytochrome-c dependent NO reductases from denitrifying bacteria (cNORs). J Inorg Biochem 2022; 231:111781. [DOI: 10.1016/j.jinorgbio.2022.111781] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/21/2022] [Accepted: 02/24/2022] [Indexed: 12/24/2022]
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Gérard EF, Yadav V, Goldberg DP, de Visser SP. What Drives Radical Halogenation versus Hydroxylation in Mononuclear Nonheme Iron Complexes? A Combined Experimental and Computational Study. J Am Chem Soc 2022; 144:10752-10767. [PMID: 35537044 PMCID: PMC9228086 DOI: 10.1021/jacs.2c01375] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
Nonheme iron halogenases
are unique enzymes in nature that selectively
activate an aliphatic C–H bond of a substrate to convert it
into C–X (X = Cl/Br, but not F/I). It is proposed that they
generate an FeIII(OH)(X) intermediate in their catalytic
cycle. The analogous FeIII(OH) intermediate in nonheme
iron hydroxylases transfers OH• to give alcohol
product, whereas the halogenases transfer X• to
the carbon radical substrate. There remains significant debate regarding
what factors control their remarkable selectivity of the halogenases.
The reactivity of the complexes FeIII(BNPAPh2O)(OH)(X) (X = Cl, Br) with a secondary carbon radical (R•) is described. It is found that X• transfer occurs
with a secondary carbon radical, as opposed to OH• transfer with tertiary radicals. Comprehensive computational studies
involving density functional theory were carried out to examine the
possible origins of this selectivity. The calculations reproduce the
experimental findings, which indicate that halogen transfer is not
observed for the tertiary radicals because of a nonproductive equilibrium
that results from the endergonic nature of these reactions, despite
a potentially lower reaction barrier for the halogenation pathway.
In contrast, halogen transfer is favored for secondary carbon radicals,
for which the halogenated product complex is thermodynamically more
stable than the reactant complex. These results are rationalized by
considering the relative strengths of the C–X bonds that are
formed for tertiary versus secondary carbon centers. The computational
analysis also shows that the reaction barrier for halogen transfer
is significantly dependent on secondary coordination sphere effects,
including steric and H-bonding interactions.
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Affiliation(s)
- Emilie F Gérard
- 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
| | - Vishal Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - 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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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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Zhou A, Cao X, Chen H, Sun D, Zhao Y, Nam W, Wang Y. The chameleon-like nature of elusive cobalt-oxygen intermediates in C-H bond activation reactions. Dalton Trans 2022; 51:4317-4323. [PMID: 35212349 DOI: 10.1039/d2dt00224h] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High-valence metal-oxo (M-O, M = Fe, Mn, etc.) species are well-known reaction intermediates that are responsible for a wide range of pivotal oxygenation reactions and water oxidation reactions in metalloenzymes. Although extensive efforts have been devoted to synthesizing and identifying such complexes in biomimetic studies, the structure-function relationship and related reaction mechanisms of these reaction intermediates remain elusive, especially for the cobalt-oxygen species. In the present manuscript, the calculated results demonstrate that the tetraamido macrocycle ligated cobalt complex, Co(O)(TAML) (1), behaves like a chameleon: the electronic structure varies from a cobalt(III)-oxyl species to a cobalt(IV)-oxo species when a Lewis acid Sc3+ salt coordinates or an acidic hydrocarbon attacks 1. The dichotomous correlation between the reaction rates of C-H bond activation by 1 and the bond dissociation energy (BDE) vs. the acidity (pKa) was rationalized for the first time by different reaction mechanisms: for normal C-H bond activation, the Co(III)-oxyl species directly activates the C-H bond via a hydrogen atom transfer (HAT) mechanism, whereas for acidic C-H bond activation, the Co(III)-oxyl species evolves to a Co(IV)-oxo species to increase the basicity of the oxygen to activate the acidic C-H bond, via a novel PCET(PT) mechanism (proton-coupled electron transfer with a PT(proton-transfer)-like transition state). These theoretical findings will enrich the knowledge of biomimetic metal-oxygen chemistry.
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Affiliation(s)
- Anran Zhou
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Xuanyu Cao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Huanhuan Chen
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Dongru Sun
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Yufen Zhao
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea.
| | - Yong Wang
- Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China. .,Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Ningbo University, Ningbo 315211, China
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31
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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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32
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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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33
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Vicens L, Olivo G, Costas M. Remote Amino Acid Recognition Enables Effective Hydrogen Peroxide Activation at a Manganese Oxidation Catalyst. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114932] [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)
- Laia Vicens
- Institut de Química Computacional i Catàlisi (IQCC) Departament de Química Universitat de Girona Campus Montilivi 17071 Girona, Catalonia Spain
| | - Giorgio Olivo
- Institut de Química Computacional i Catàlisi (IQCC) Departament de Química Universitat de Girona Campus Montilivi 17071 Girona, Catalonia Spain
- Dipartamento di Chimica Università “La Sapienza” di Roma Piazzale Aldo Moro 5 00185 Rome Italy
| | - Miquel Costas
- Institut de Química Computacional i Catàlisi (IQCC) Departament de Química Universitat de Girona Campus Montilivi 17071 Girona, Catalonia Spain
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34
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Mondal P, Rajapakse S, Wijeratne GB. Following Nature's Footprint: Mimicking the High-Valent Heme-Oxo Mediated Indole Monooxygenation Reaction Landscape of Heme Enzymes. J Am Chem Soc 2022; 144:3843-3854. [PMID: 35112858 DOI: 10.1021/jacs.1c11068] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Pathways for direct conversion of indoles to oxindoles have accumulated considerable interest in recent years due to their significance in the clear comprehension of various pathogenic processes in humans and the multipotent therapeutic value of oxindole pharmacophores. Heme enzymes are predominantly responsible for this conversion in biology and are thought to proceed with a compound-I active oxidant. These heme-enzyme-mediated indole monooxygenation pathways are rapidly emerging therapeutic targets; however, a clear mechanistic understanding is still lacking. Additionally, such knowledge holds promise in the rational design of highly specific indole monooxygenation synthetic protocols that are also cost-effective and environmentally benign. We herein report the first examples of synthetic compound-I and activated compound-II species that can effectively monooxygenate a diverse array of indoles with varied electronic and steric properties to exclusively produce the corresponding 2-oxindole products in good to excellent yields. Rigorous kinetic, thermodynamic, and mechanistic interrogations clearly illustrate an initial rate-limiting epoxidation step that takes place between the heme oxidant and indole substrate, and the resulting indole epoxide intermediate undergoes rearrangement driven by a 2,3-hydride shift on indole ring to ultimately produce 2-oxindole. The complete elucidation of the indole monooxygenation mechanism of these synthetic heme models will help reveal crucial insights into analogous biological systems, directly reinforcing drug design attempts targeting those heme enzymes. Moreover, these bioinspired model compounds are promising candidates for the future development of better synthetic protocols for the selective, efficient, and sustainable generation of 2-oxindole motifs, which are already known for a plethora of pharmacological benefits.
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Affiliation(s)
- Pritam Mondal
- Department of Chemistry and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35205, United States
| | - Shanuk Rajapakse
- Department of Chemistry and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35205, United States
| | - Gayan B Wijeratne
- Department of Chemistry and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama 35205, United States
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35
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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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36
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Cao X, Song H, Li XX, Zhao Y, Qiao Q, Wang Y. Which is the real oxidant in the competitive ligand self-hydroxylation and substrate oxidation, a biomimetic iron(II)-hydroperoxo species or an oxo-iron(IV)-hydroxy one? Dalton Trans 2022; 51:7571-7580. [DOI: 10.1039/d2dt00797e] [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
Nonheme iron(II)-hydroperoxo species (FeII-(η2-OOH)) 1 and the concomitant oxo-iron(IV)-hydroxyl one 2 are proposed as the key intermediates of a large class of 2-oxoglutarate dependent dioxygenases (e.g., isopenicillin N synthase). Extensive...
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37
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Mandal D, Katoch A. Effect of Substituent on C-H Activation Catalysed by a nonheme Fe(IV)O Complex: A Computational Investigation of Reactivity and Hydrogen Tunneling. Dalton Trans 2022; 51:11641-11649. [DOI: 10.1039/d2dt01529c] [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
A density functional theory investigation has been presented here to address the C-H activation reactivity and the influence of quantum mechanical tunneling catalyzed by a non-heme iron(IV)-Oxo complex viz. [FeIVOdpaq-X]+...
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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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Pantalon Juraj N, Tandarić T, Tadić V, Perić B, Moreth D, Schatzschneider U, Brozovic A, Vianello R, Kirin SI. Tuning the coordination properties of chiral pseudopeptide bis(2-picolyl)amine and iminodiacetamide ligands in Zn( ii) and Cu( ii) complexes. Dalton Trans 2022; 51:17008-17021. [DOI: 10.1039/d2dt02895f] [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
Modifications of the chiral side chains of bpa and imda ligands lead to different metal ion coordination and hydrogen bonding ability.
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Affiliation(s)
| | | | | | | | - Dominik Moreth
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Ulrich Schatzschneider
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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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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Vicens L, Olivo G, Costas M. Remote Amino Acid Recognition Enables Effective Hydrogen Peroxide Activation at a Manganese Oxidation Catalyst. Angew Chem Int Ed Engl 2021; 61:e202114932. [PMID: 34854188 PMCID: PMC9304166 DOI: 10.1002/anie.202114932] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Indexed: 12/14/2022]
Abstract
Precise delivery of a proton plays a key role in O2 activation at iron oxygenases, enabling the crucial O−O cleavage step that generates the oxidizing high‐valent metal–oxo species. Such a proton is delivered by acidic residues that may either directly bind the iron center or lie in its second coordination sphere. Herein, a supramolecular strategy for enzyme‐like H2O2 activation at a biologically inspired manganese catalyst, with a nearly stoichiometric amount (1–1.5 equiv) of a carboxylic acid is disclosed. Key for this strategy is the incorporation of an α,ω‐amino acid in the second coordination sphere of a chiral catalyst via remote ammonium‐crown ether recognition. The properly positioned carboxylic acid function enables effective activation of hydrogen peroxide, leading to catalytic asymmetric epoxidation. Modulation of both amino acid and catalyst structure can tune the efficiency and the enantioselectivity of the reaction, and a study on the oxidative degradation pathway of the system is presented.
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Affiliation(s)
- Laia Vicens
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17071, Girona, Catalonia, Spain
| | - Giorgio Olivo
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17071, Girona, Catalonia, Spain.,Dipartamento di Chimica, Università "La Sapienza" di Roma, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Miquel Costas
- Institut de Química Computacional i Catàlisi (IQCC), Departament de Química, Universitat de Girona, Campus Montilivi, 17071, Girona, Catalonia, Spain
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