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Huang Z, Qin D, Abuduwupuer X, Cao L, Piao Y, Shao Z, Jiang L, Guo Z, Gao R. Regulate catalytic performance by engineering non-regular structure of extradiol dioxygenase: An entrance to bottom strategy. Int J Biol Macromol 2024; 281:136246. [PMID: 39366601 DOI: 10.1016/j.ijbiomac.2024.136246] [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: 06/24/2024] [Revised: 09/28/2024] [Accepted: 09/30/2024] [Indexed: 10/06/2024]
Abstract
Extradiol dioxygenase Tcu3516 is a home-sourced enzyme demonstrating potent aromatic phenol degradation capacity. To add to the advantageous modifications inside active cavity, this work reported a novel strategy to engineer rarely concerned non-regular structures around the entrance towards the active site at the bottom of cavity. Three structures, Loop region 1 (Loop1: Met173-Arg185), Loop region 2 (Loop2: Ala201-Val212) and C-terminal (C-tail: His290-Lys306) were therefore identified through structural flexibility analysis. Highly rigid prolines within the structures were mutated into smaller alanine, glycine, or serine to improve structural flexibilities; while only P183S on Loop1 showed 3-fold activity enhancement vs the WT when subjected to cleavage of mono-cyclic catechol analogues. The analysis of Root Mean Square Fluctuation showed that P183S presents certain enhancement on Loop1 flexibility without dramatic changes of other domains. Furthermore, the synergetic effects from mutation P183S and cavity-based mutations V186L, V212N and D285A were evaluated by characterizing combinatorial mutants. Temperature dependence and thermostability of the combined mutants showed a more flexible catalytic domain without sacrificing structural integrity and stability. kcat value of P183S/V186L (SL) towards monocyclic catechols significantly surpasses any other combinatorial mutants around Tcu3516 active sites. Moreover, the synergetic effects on conformational plasticity were analyzed by molecular dynamic simulations to shed light into the interplay between structural changes and catalytic performance.
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Affiliation(s)
- Zihao Huang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Deyuan Qin
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xiemuxinuer Abuduwupuer
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Luxin Cao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yingdan Piao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Zhengkang Shao
- GeneScience Pharmaceuticals Co., Ltd., Changchun 130012, China
| | - Liyan Jiang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Zheng Guo
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark.
| | - Renjun Gao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China.
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2
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Zhang P, Lee WZ, Ye S. Insights into dioxygen binding on metal centers: an ab initio multireference electronic structure analysis. Phys Chem Chem Phys 2024; 26:25057-25068. [PMID: 39301704 DOI: 10.1039/d4cp02915a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Why does binding of dioxygen (O2) to metal centers, the initial step of O2 storage, transportation, and activation, almost inevitably induce metal-to-O2 single-electron transfer and generate superoxo (O2-˙) species, instead of genuine O02 adducts? To address this question, this study describes highly correlated wavefunction-based ab initio calculations using CASSCF/NEVPT2 (CASSCF = complete active space self-consistent field, and NEVPT2 = N-electron valence state second-order perturbation theory) approaches to explore the electronic-structure evolution of O2 association on Fe(II)(BDPP) (H2BDPP = 2,6-bis((2-(S)-diphenylhydroxylmethyl-1-pyrrolidinyl)methyl)pyridine) and Co(II)(BDPP) to produce S = 3 Fe(III)(BDPP)(O2-˙) (1) and Co(III)(BDPP)(O2-˙) (2). CASSCF/NEVPT2 calculations suggest that the processes furnishing 1 and 2 feature an avoided crossing resulting from interactions of two diabatic curves, of which one is characterized as Co(II) and Fe(II) centers interacting with a triplet O2 ligand and the other as Co(III) and Fe(III) centers bound to a superoxo ligand. In both cases, the avoided crossing induces a one-electron transfer from the divalent metal center to the incoming O2 ligand and leads to formation of trivalent metal-O2-˙ complexes. To facilitate the interpretation of complicated multireference wavefunctions, we formulated two-fragment spin eigenfunctions utilizing Clebsch-Gordan coefficients (CGCs) to rationalize computed spin populations on the metal centers and the O2 ligand and compared these results with usual valence bonding (VB) analyses. It turns out that both methods give the same results and are complementary to each other. Finally, the limitation of DFT approaches in describing complex electronic structures involving metal-ligand magnetic couplings is delineated.
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Affiliation(s)
- Peng Zhang
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Way-Zen Lee
- Department of Chemistry, National Taiwan Normal University, Taipei 11677, Taiwan
- Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Shengfa Ye
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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3
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Devkota L, Xiong J, Fischer AA, Murphy K, Kumar P, Balensiefen EL, Lindeman SV, Popescu CV, Fiedler AT. Observation of oxygenated intermediates in functional mimics of aminophenol dioxygenase. J Inorg Biochem 2024; 259:112632. [PMID: 38950482 DOI: 10.1016/j.jinorgbio.2024.112632] [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: 03/15/2024] [Revised: 05/31/2024] [Accepted: 06/01/2024] [Indexed: 07/03/2024]
Abstract
Aminophenol dioxygenases (APDO) are mononuclear nonheme iron enzymes that utilize dioxygen (O2) to catalyze the conversion of o-aminophenols to 2-picolinic acid derivatives in metabolic pathways. This study describes the synthesis and O2 reactivity of two synthetic models of substrate-bound APDO: [FeII(TpMe2)(tBu2APH)] (1) and [FeII(TpMe2)(tBuAPH)] (2), where TpMe2 = hydrotris(3,5-dimethylpyrazole-1-yl)borate, tBu2APH = 4,6-di-tert-butyl-2-aminophenolate, and tBuAPH2 = 4-tert-butyl-2-aminophenolate. Both Fe(II) complexes behave as functional APDO mimics, as exposure to O2 results in oxidative CC bond cleavage of the o-aminophenolate ligand. The ring-cleaved products undergo spontaneous cyclization to give substituted 2-picolinic acids, as verified by 1H NMR spectroscopy, mass spectrometry, and X-ray crystallography. Reaction of the APDO models with O2 at low temperature reveals multiple intermediates, which were probed with UV-vis absorption, electron paramagnetic resonance (EPR), Mössbauer (MB), and resonance Raman (rRaman) spectroscopies. The most stable intermediate at -70 °C in THF exhibits multiple isotopically-sensitive features in rRaman samples prepared with 16O2 and 18O2, confirming incorporation of O2-derived atom(s) into its molecular structure. Insights into the geometric structures, electronic properties, and spectroscopic features of the observed intermediates were obtained from density functional theory (DFT) calculations. Although functional APDO models have been previously reported, this is the first time that an oxygenated ligand-based radical has been detected and spectroscopically characterized in the ring-cleaving mechanism of a relevant synthetic system.
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Affiliation(s)
- Laxmi Devkota
- Department of Chemistry, Marquette University, 1414 W. Clybourn St., Milwaukee, WI 53233, United States
| | - Jin Xiong
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA
| | - Anne A Fischer
- Department of Chemistry, Marquette University, 1414 W. Clybourn St., Milwaukee, WI 53233, United States
| | - Kate Murphy
- Department of Chemistry, The College of Arts and Sciences, University of St. Thomas, St. Paul, MN 55105, United States
| | - Praveen Kumar
- Department of Chemistry, Marquette University, 1414 W. Clybourn St., Milwaukee, WI 53233, United States
| | - Ellie L Balensiefen
- Department of Chemistry, Marquette University, 1414 W. Clybourn St., Milwaukee, WI 53233, United States
| | - Sergey V Lindeman
- Department of Chemistry, Marquette University, 1414 W. Clybourn St., Milwaukee, WI 53233, United States
| | - Codrina V Popescu
- Department of Chemistry, The College of Arts and Sciences, University of St. Thomas, St. Paul, MN 55105, United States.
| | - Adam T Fiedler
- Department of Chemistry, Marquette University, 1414 W. Clybourn St., Milwaukee, WI 53233, United States.
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4
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Gera R, De P, Singh KK, Jannuzzi SAV, Mohanty A, Velasco L, Kulbir, Kumar P, Marco JF, Nagarajan K, Pecharromán C, Rodríguez-Pascual PM, DeBeer S, Moonshiram D, Gupta SS, Dasgupta J. Trapping an Elusive Fe(IV)-Superoxo Intermediate Inside a Self-Assembled Nanocage in Water at Room Temperature. J Am Chem Soc 2024; 146:21729-21741. [PMID: 39078020 DOI: 10.1021/jacs.4c05849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Molecular cavities that mimic natural metalloenzymes have shown the potential to trap elusive reaction intermediates. Here, we demonstrate the formation of a rare yet stable Fe(IV)-superoxo intermediate at room temperature subsequent to dioxygen binding at the Fe(III) site of a (Et4N)2[FeIII(Cl)(bTAML)] complex confined inside the hydrophobic interior of a water-soluble Pd6L412+ nanocage. Using a combination of electron paramagnetic resonance, Mössbauer, Raman/IR vibrational, X-ray absorption, and emission spectroscopies, we demonstrate that the cage-encapsulated complex has a Fe(IV) oxidation state characterized by a stable S = 1/2 spin state and a short Fe-O bond distance of ∼1.70 Å. We find that the O2 reaction in confinement is reversible, while the formed Fe(IV)-superoxo complex readily reacts when presented with substrates having weak C-H bonds, highlighting the lability of the O-O bond. We envision that such optimally trapped high-valent superoxos can show new classes of reactivities catalyzing both oxygen atom transfer and C-H bond activation reactions.
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Affiliation(s)
- Rahul Gera
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
- Department of Education in Science and Mathematics, Regional Institute of Education - Mysuru, NCERT, Mysuru 570006, India
| | - Puja De
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Kundan K Singh
- Chemical Engineering Division, CSIR-National Chemical Laboratory, Pune, Maharashtra 411008, India
- Chemistry Department, Indian Institute of Technology, Dharwad 580007, India
| | - Sergio A V Jannuzzi
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Aisworika Mohanty
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Lucia Velasco
- Instituto de Ciencia de Materiales de Madrid Consejo Superior de Investigaciones Científicas Sor Juana Inés de la Cruz, 3, Madrid 28049, Spain
| | - Kulbir
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India
| | - Pankaj Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Tirupati 517507, India
| | - J F Marco
- Instituto de Quimica Fisica Blas Cabrera, Consejo Superior de Investigaciones Científicas, Serrano 119, Madrid 28006, Spain
| | - Kalaivanan Nagarajan
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
| | - Carlos Pecharromán
- Instituto de Ciencia de Materiales de Madrid Consejo Superior de Investigaciones Científicas Sor Juana Inés de la Cruz, 3, Madrid 28049, Spain
| | - P M Rodríguez-Pascual
- Instituto de Ciencia de Materiales de Madrid Consejo Superior de Investigaciones Científicas Sor Juana Inés de la Cruz, 3, Madrid 28049, Spain
| | - Serena DeBeer
- Department of Inorganic Spectroscopy, Max Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, Mülheim an der Ruhr 45470, Germany
| | - Dooshaye Moonshiram
- Instituto de Ciencia de Materiales de Madrid Consejo Superior de Investigaciones Científicas Sor Juana Inés de la Cruz, 3, Madrid 28049, Spain
| | - Sayam Sen Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West Bengal 741246, India
| | - Jyotishman Dasgupta
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai 400005, India
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5
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Zhao Q, Rui J, Huang X. Radical-relay C(sp 3)-H azidation catalyzed by an engineered nonheme iron enzyme. Methods Enzymol 2024; 703:195-213. [PMID: 39260996 DOI: 10.1016/bs.mie.2024.07.003] [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] [Indexed: 09/13/2024]
Abstract
Nonheme iron enzymes are versatile biocatalysts for a broad range of unique and powerful transformations, such as hydroxylation, chlorination, and epimerization as well as cyclization/ring-opening of organic molecules. Beyond their native biological functions, these enzymes are robust for engineering due to their structural diversity and high evolvability. Based on enzyme promiscuity and directed evolution as well as inspired by synthetic organic chemistry, nonheme iron enzymes can be repurposed to catalyze reactions previously only accessible with synthetic catalysts. To this end, our group has engineered a series of nonheme iron enzymes to employ non-natural radical-relay mechanisms for new-to-nature radical transformations. In particular, we have demonstrated that a nonheme iron enzyme, (4-hydroxyphenyl)pyruvate dioxygenase from streptomyces avermitilis (SavHppD), can be repurposed to enable abiological radical-relay process to access C(sp3)-H azidation products. This represents the first known instance of enzymatic radical relay azidation reactions. In this chapter, we describe the detailed experimental protocol to convert promiscuous nonheme iron enzymes into efficient and selective biocatalyst for radical relay azidation reactions. One round of directed evolution is described in detail, which includes the generation and handling of site-saturation mutagenesis, protein expression and whole-cell reactions screening in a 96-well plate. These protocol details might be useful to engineer various nonheme iron enzymes for other applications.
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Affiliation(s)
- Qun Zhao
- School of Biotechnology and Key Laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi, P.R. China.
| | - Jinyan Rui
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, United States
| | - Xiongyi Huang
- Department of Chemistry, Johns Hopkins University, Baltimore, MD, United States.
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6
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Huang Z, Gu Z, Abuduwupuer X, Qin D, Liu Y, Guo Z, Gao R. Engineering non-conservative substrate recognition sites of extradiol dioxygenase: Computation guided design to diversify and accelerate degradation of aromatic compounds. Int J Biol Macromol 2024; 264:130739. [PMID: 38460639 DOI: 10.1016/j.ijbiomac.2024.130739] [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: 12/26/2023] [Revised: 02/16/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
Extradiol dioxygenases (EDOs) catalyzing meta-cleavage of catecholic compounds promise an effective way to detoxify aromatic pollutants. This work reported a novel scenario to engineer our recently identified Type I EDO from Tcu3516 for a broader substrate scope and enhanced activity, which was based on 2,3-dihydroxybiphenyl (2,3-DHB)-liganded molecular docking of Tcu3516 and multiple sequence alignment with other 22 Type I EDOs. 11 non-conservative residues of Tcu3516 within 6 Å distance to the 2,3-DHB ligand center were selected as potential hotspots and subjected to semi-rational design using 6 catecholic analogues as substrates; the mutants V186L and V212N returned with progressive evolution in substrate scope and catalytic activity. Both mutants were combined with D285A for construction of double mutants and final triple mutant V186L/V212N/D285A. Except for 2,3-DHB (the mutant V186L/D285A gave the best catalytic performance), the triple mutant prevailed all other 5 catecholic compounds for their degradation; affording the catalytic efficiency kcat/Km value increase by 10-30 folds, protein Tm (structural rigidity) increase by 15 °C and the half-life time enhancement by 10 times compared to the wild type Tcu3516. The molecular dynamic simulation suggested that a stabler core and a more flexible entrance are likely accounting for enhanced catalytic activity and stability of enzymes.
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Affiliation(s)
- Zihao Huang
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Zhenyu Gu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Xiemuxinuer Abuduwupuer
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Deyuan Qin
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yuchen Liu
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China
| | - Zheng Guo
- Department of Biological and Chemical Engineering, Faculty of Technical Sciences, Aarhus University, Gustav Wieds Vej 10, Aarhus 8000, Denmark.
| | - Renjun Gao
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun 130012, China.
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7
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Zhu W, Wu P, Larson VA, Kumar A, Li XX, Seo MS, Lee YM, Wang B, Lehnert N, Nam W. Electronic Structure and Reactivity of Mononuclear Nonheme Iron-Peroxo Complexes as a Biomimetic Model of Rieske Oxygenases: Ring Size Effects of Macrocyclic Ligands. J Am Chem Soc 2024; 146:250-262. [PMID: 38147793 DOI: 10.1021/jacs.3c08559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
We report the macrocyclic ring size-electronic structure-electrophilic reactivity correlation of mononuclear nonheme iron(III)-peroxo complexes bearing N-tetramethylated cyclam analogues (n-TMC), [FeIII(O2)(12-TMC)]+ (1), [FeIII(O2)(13-TMC)]+ (2), and [FeIII(O2)(14-TMC)]+ (3), as a model study of Rieske oxygenases. The Fe(III)-peroxo complexes show the same δ and pseudo-σ bonds between iron and the peroxo ligand. However, the strength of these interactions varies depending on the ring size of the n-TMC ligands; the overall Fe-O bond strength and the strength of the Fe-O2 δ bond increase gradually as the ring size of the n-TMC ligands becomes smaller, such as from 14-TMC to 13-TMC to 12-TMC. MCD spectroscopy plays a key role in assigning the characteristic low-energy δ → δ* LMCT band, which provides direct insight into the strength of the Fe-O2 δ bond and which, in turn, is correlated with the superoxo character of the iron-peroxo group. In oxidation reactions, reactivities of 1-3 toward hydrocarbon C-H bond activation are compared, revealing the reactivity order of 1 > 2 > 3; the [FeIII(O2)(n-TMC)]+ complex with a smaller n-TMC ring size, 12-TMC, is much more reactive than that with a larger n-TMC ring size, 14-TMC. DFT analysis shows that the Fe(III)-peroxo complex is not reactive toward C-H bonds, but it is the end-on Fe(II)-superoxo valence tautomer that is responsible for the observed reactivity. The hydrogen atom abstraction (HAA) reactivity of these intermediates is correlated with the overall donicity of the n-TMC ligand, which modulates the energy of the singly occupied π* superoxo frontier orbital that serves as the electron acceptor in the HAA reaction. The implications of these results for the mechanism of Rieske oxygenases are further discussed.
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Affiliation(s)
- Wenjuan Zhu
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Peng Wu
- State Key Laboratory of High-Efficiency Utilization of Coal and Green Chemical Engineering, School of Chemistry and Chemical Engineering, Ningxia University, Yinchuan 750021, P. R. China
| | - Virginia A Larson
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Akhilesh Kumar
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Xiao-Xi Li
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
- Institute of Molecular Sciences and Engineering, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao 266237, P. R. China
| | - Mi Sook Seo
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
| | - Binju Wang
- Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Nicolai Lehnert
- Department of Chemistry and Department of Biophysics, University of Michigan, Ann Arbor, Michigan 48109-1055, United States
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, Seoul 03760, Korea
- College of Chemistry and Chemical Engineering, Yan'an University, Yan'an, Shaanxi Province 716000, P. R. China
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8
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Devi T, Dutta K, Deutscher J, Mebs S, Kuhlmann U, Haumann M, Cula B, Dau H, Hildebrandt P, Ray K. A high-spin alkylperoxo-iron(iii) complex with cis-anionic ligands: implications for the superoxide reductase mechanism. Chem Sci 2024; 15:528-533. [PMID: 38179538 PMCID: PMC10762717 DOI: 10.1039/d3sc05603a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024] Open
Abstract
The N3O macrocycle of the 12-TMCO ligand stabilizes a high spin (S = 5/2) [FeIII(12-TMCO)(OOtBu)Cl]+ (3-Cl) species in the reaction of [FeII(12-TMCO)(OTf)2] (1-(OTf)2) with tert-butylhydroperoxide (tBuOOH) in the presence of tetraethylammonium chloride (NEt4Cl) in acetonitrile at -20 °C. In the absence of NEt4Cl the oxo-iron(iv) complex 2 [FeIV(12-TMCO)(O)(CH3CN)]2+ is formed, which can be further converted to 3-Cl by adding NEt4Cl and tBuOOH. The role of the cis-chloride ligand in the stabilization of the FeIII-OOtBu moiety can be extended to other anions including the thiolate ligand relevant to the enzyme superoxide reductase (SOR). The present study underlines the importance of subtle electronic changes and secondary interactions in the stability of the biologically relevant metal-dioxygen intermediates. It also provides some rationale for the dramatically different outcomes of the chemistry of iron(iii)peroxy intermediates formed in the catalytic cycles of SOR (Fe-O cleavage) and cytochrome P450 (O-O bond lysis) in similar N4S coordination environments.
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Affiliation(s)
- Tarali Devi
- Institut für Chemie, Humboldt-Universitat zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
- Department of Inorganic and Physical Chemistry, Indian Institute of Science Bangalore Karnataka-560012 India
| | - Kuheli Dutta
- Institut für Chemie, Humboldt-Universitat zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Jennifer Deutscher
- Institut für Chemie, Humboldt-Universitat zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Stefan Mebs
- Department of Physics, Freie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | - Uwe Kuhlmann
- Institut für Chemie, Technische Universität Berlin Fakultät II, Straße des 17. Juni 135 10623 Berlin Germany
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | - Beatrice Cula
- Institut für Chemie, Humboldt-Universitat zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
| | - Holger Dau
- Department of Physics, Freie Universität Berlin Arnimallee 14 14195 Berlin Germany
| | - Peter Hildebrandt
- Institut für Chemie, Technische Universität Berlin Fakultät II, Straße des 17. Juni 135 10623 Berlin Germany
| | - Kallol Ray
- Institut für Chemie, Humboldt-Universitat zu Berlin Brook-Taylor-Straße 2 12489 Berlin Germany
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9
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Chatterjee S, Paine TK. Dioxygen Reduction and Bioinspired Oxidations by Non-heme Iron(II)-α-Hydroxy Acid Complexes. Acc Chem Res 2023; 56:3175-3187. [PMID: 37938969 DOI: 10.1021/acs.accounts.3c00449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
Aerobic organisms involve dioxygen-activating iron enzymes to perform various metabolically relevant chemical transformations. Among these enzymes, mononuclear non-heme iron enzymes reductively activate dioxygen to catalyze diverse biological oxidations, including oxygenation of C-H and C═C bonds and C-C bond cleavage with amazing selectivity. Several non-heme enzymes utilize organic cofactors as electron sources for dioxygen reduction, leading to the generation of iron-oxygen intermediates that act as active oxidants in the catalytic cycle. These unique enzymatic reactions influence the design of small molecule synthetic compounds to emulate enzyme functions and to develop bioinspired catalysts for performing selective oxidation of organic substrates with dioxygen. Selective electron transfer during dioxygen reduction on iron centers of synthetic models by a sacrificial reductant requires appropriate design strategies. Taking lessons from the role of enzyme-cofactor complexes in the selective electron transfer process, our group utilized ternary iron(II)-α-hydroxy acid complexes supported by polydentate ligands for dioxygen reduction and bioinspired oxidations. This Account focuses on the role of coordinated sacrificial reductants in the selective electron transfer for dioxygen reduction by iron complexes and highlights the versatility of iron(II)-α-hydroxy acid complexes in affecting dioxygen-dependent oxidation/oxygenation reactions. The iron(II)-coordinated α-hydroxy acid anions undergo two-electron oxidative decarboxylation concomitant with the generation of reactive iron-oxygen oxidants. A nucleophilic iron(II)-hydroperoxo species was intercepted in the decarboxylation pathway. In the presence of a Lewis acid, the O-O bond of the nucleophilic oxidant is heterolytically cleaved to generate an electrophilic iron(IV)-oxo-hydroxo oxidant. Most importantly, the oxidants generated with or without Lewis acid can carry out cis-dihydroxylation of alkenes. Furthermore, the electrophilic iron-oxygen oxidant selectively hydroxylates strong C-H bonds. Another electrophilic iron(IV)-oxo oxidant, generated from the iron(II)-α-hydroxy acid complexes in the presence of a protic acid, carries out C-H bond halogenation by using a halide anion.Thus, different metal-oxygen intermediates could be generated from dioxygen using a single reductant, and the reactivity of the ternary complexes can be tuned using external additives (Lewis/protic acid). The catalytic potential of the iron(II)-α-hydroxy complexes in performing O2-dependent oxygenations has been demonstrated. Different factors that govern the reactivity of iron-oxygen oxidants from ternary iron(II) complexes are presented. The versatile reactivity of the oxidants provides useful insights into developing catalytic methods for the selective incorporation of oxidized functionalities under environmentally benign conditions using aerial oxygen as the terminal oxidant.
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Affiliation(s)
- Sayanti Chatterjee
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A&2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Tapan Kanti Paine
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A&2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
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10
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Zhou B, Gabbaï FP. Four-Electron Reduction of O 2 Using Distibines in the Presence of ortho-Quinones. J Am Chem Soc 2023; 145:13758-13767. [PMID: 37306561 PMCID: PMC10863049 DOI: 10.1021/jacs.3c02223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Indexed: 06/13/2023]
Abstract
This study, which aims to identify atypical platforms for the reduction of dioxygen, describes the reaction of O2 with two distibines, namely, 4,5-bis(diphenylstibino)-2,7-di-tert-butyl-9,9-dimethylxanthene and 4,5-bis(diphenylstibino)-2,7-di-tert-butyl-9,9-dimethyldihydroacridine, in the presence of an ortho-quinone such as phenanthraquinone. The reaction proceeds by oxidation of the two antimony atoms to the + V state in concert with reductive cleavage of the O2 molecule. As confirmed by 18O labeling experiments, the two resulting oxo units combine with the ortho-quinone to form an α,α,β,β-tetraolate ligand that bridges the two antimony(V) centers. This process, which has been studied both experimentally and computationally, involves the formation of asymmetric, mixed-valent derivatives featuring a stibine as well as a catecholatostiborane formed by oxidative addition of the quinone to only one of the antimony centers. Under aerobic conditions, the catecholatostiborane moiety reacts with O2 to form a semiquinone/peroxoantimony intermediate, as supported by NMR spectroscopy in the case of the dimethyldihydroacridine derivative. These intermediates swiftly evolve into the symmetrical bis(antimony(V)) α,α,β,β-tetraolate complexes via low barrier processes. Finally, the controlled protonolysis and reduction of the bis(antimony(V)) α,α,β,β-tetraolate complex based on the 9,9-dimethylxanthene platform have been investigated and shown to regenerate the starting distibine and the ortho-quinone. More importantly, these last reactions also produce two equivalents of water as the product of O2 reduction.
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Affiliation(s)
- Benyu Zhou
- Texas A&M University, Department of Chemistry, College
Station, Texas 77843, United States
| | - François P. Gabbaï
- Texas A&M University, Department of Chemistry, College
Station, Texas 77843, United States
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11
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Roby O, Moutaouakil M, Tighadouini S, Loukhmi Z, Aboulmouhajir A, Saddik R. Highly Active Catecholase-Like Catalyst Based on the In-Situ Combination of Benzodiazepine Derivatives and Copper (II) Salts. CHEMISTRY AFRICA 2023. [DOI: 10.1007/s42250-023-00638-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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12
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Kass D, Yao S, Krause KB, Corona T, Richter L, Braun T, Mebs S, Haumann M, Dau H, Lohmiller T, Limberg C, Drieß M, Ray K. Spectroscopic Properties of a Biologically Relevant [Fe 2 (μ-O) 2 ] Diamond Core Motif with a Short Iron-Iron Distance. Angew Chem Int Ed Engl 2023; 62:e202209437. [PMID: 36541062 DOI: 10.1002/anie.202209437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 12/05/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Diiron cofactors in enzymes perform diverse challenging transformations. The structures of high valent intermediates (Q in methane monooxygenase and X in ribonucleotide reductase) are debated since Fe-Fe distances of 2.5-3.4 Å were attributed to "open" or "closed" cores with bridging or terminal oxido groups. We report the crystallographic and spectroscopic characterization of a FeIII 2 (μ-O)2 complex (2) with tetrahedral (4C) centres and short Fe-Fe distance (2.52 Å), persisting in organic solutions. 2 shows a large Fe K-pre-edge intensity, which is caused by the pronounced asymmetry at the TD FeIII centres due to the short Fe-μ-O bonds. A ≈2.5 Å Fe-Fe distance is unlikely for six-coordinate sites in Q or X, but for a Fe2 (μ-O)2 core containing four-coordinate (or by possible extension five-coordinate) iron centres there may be enough flexibility to accommodate a particularly short Fe-Fe separation with intense pre-edge transition. This finding may broaden the scope of models considered for the structure of high-valent diiron intermediates formed upon O2 activation in biology.
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Affiliation(s)
- Dustin Kass
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Shenglai Yao
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, 10623, Berlin, Germany
| | - Konstantin B Krause
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Teresa Corona
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Liza Richter
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Thomas Braun
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Stefan Mebs
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Michael Haumann
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Holger Dau
- Fachbereich Physik, Freie Universität Berlin, Arnimallee 14, 14195, Berlin, Germany
| | - Thomas Lohmiller
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany.,EPR4Energy Joint Lab, Department Spins in Energy Conversion and Quantum Information Science, Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Straße 16, 12489, Berlin, Germany
| | - Christian Limberg
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
| | - Matthias Drieß
- Institut für Chemie, Technische Universität Berlin, Straße des 17. Juni 115, 10623, Berlin, Germany
| | - Kallol Ray
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Straße 2, 12489, Berlin, Germany
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13
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Reduction of a Heme Cofactor Initiates N-Nitroglycine Degradation by NnlA. Appl Environ Microbiol 2022; 88:e0102322. [PMID: 35916514 PMCID: PMC9397103 DOI: 10.1128/aem.01023-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Linear nitramines are potentially carcinogenic environmental contaminants. The NnlA enzyme from Variovorax sp. strain JS1663 degrades the nitramine N-nitroglycine (NNG)-a natural product produced by some bacteria-to glyoxylate and nitrite (NO2-). Ammonium (NH4+) was predicted as the third product of this reaction. A source of nonheme FeII was shown to be required for initiation of NnlA activity. However, the role of this FeII for NnlA activity was unclear. This study reveals that NnlA contains a b-type heme cofactor. Reduction of this heme-either by a nonheme iron source or dithionite-is required to initiate NnlA activity. Therefore, FeII is not an essential substrate for holoenzyme activity. Our data show that reduced NnlA (FeII-NnlA) catalyzes at least 100 turnovers and does not require O2. Finally, NH4+ was verified as the third product, accounting for the complete nitrogen mass balance. Size exclusion chromatography showed that NnlA is a dimer in solution. Additionally, FeII-NnlA is oxidized by O2 and NO2- and stably binds carbon monoxide (CO) and nitric oxide (NO). These are characteristics shared with heme-binding PAS domains. Furthermore, a structural homology model of NnlA was generated using the PAS domain from Pseudomonas aeruginosa Aer2 as a template. The structural homology model suggested His73 is the axial ligand of the NnlA heme. Site-directed mutagenesis of His73 to alanine decreased the heme occupancy of NnlA and eliminated NNG activity, validating the homology model. We conclude that NnlA forms a homodimeric heme-binding PAS domain protein that requires reduction for initiation of the activity. IMPORTANCE Linear nitramines are potential carcinogens. These compounds result from environmental degradation of high-energy cyclic nitramines and as by-products of carbon capture technologies. Mechanistic understanding of the biodegradation of these compounds is critical to inform strategies for their remediation. Biodegradation of NNG by NnlA from Variovorax sp. strain JS 1663 requires nonheme iron, but its role is unclear. This study shows that nonheme iron is unnecessary. Instead, our study reveals that NnlA contains a heme cofactor, the reduction of which is critical for activating NNG degradation activity. These studies constrain the proposals for NnlA reaction mechanisms, thereby informing mechanistic studies of degradation of anthropogenic nitramine contaminants. In addition, these results will inform future work to design biocatalysts to degrade these nitramine contaminants.
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14
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Pati SG, Bopp CE, Kohler HPE, Hofstetter TB. Substrate-Specific Coupling of O 2 Activation to Hydroxylations of Aromatic Compounds by Rieske Non-heme Iron Dioxygenases. ACS Catal 2022; 12:6444-6456. [PMID: 35692249 PMCID: PMC9171724 DOI: 10.1021/acscatal.2c00383] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 04/09/2022] [Indexed: 02/07/2023]
Abstract
![]()
Rieske dioxygenases
catalyze the initial steps in the hydroxylation
of aromatic compounds and are critical for the metabolism of xenobiotic
substances. Because substrates do not bind to the mononuclear non-heme
FeII center, elementary steps leading to O2 activation
and substrate hydroxylation are difficult to delineate, thus making
it challenging to rationalize divergent observations on enzyme mechanisms,
reactivity, and substrate specificity. Here, we show for nitrobenzene
dioxygenase, a Rieske dioxygenase capable of transforming nitroarenes
to nitrite and substituted catechols, that unproductive O2 activation with the release of the unreacted substrate and reactive
oxygen species represents an important path in the catalytic cycle.
Through correlation of O2 uncoupling for a series of substituted
nitroaromatic compounds with 18O and 13C kinetic
isotope effects of dissolved O2 and aromatic substrates,
respectively, we show that O2 uncoupling occurs after the
rate-limiting formation of FeIII-(hydro)peroxo species
from which substrates are hydroxylated. Substituent effects on the
extent of O2 uncoupling suggest that the positioning of
the substrate in the active site rather than the susceptibility of
the substrate for attack by electrophilic oxygen species is responsible
for unproductive O2 uncoupling. The proposed catalytic
cycle provides a mechanistic basis for assessing the very different
efficiencies of substrate hydroxylation vs unproductive O2 activation and generation of reactive oxygen species in reactions
catalyzed by Rieske dioxygenases.
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Affiliation(s)
- Sarah G. Pati
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Charlotte E. Bopp
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
| | - Hans-Peter E. Kohler
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
| | - Thomas B. Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland
- Institute of Biogeochemistry and Pollutant Dynamics (IBP), ETH Zürich, 8092 Zürich, Switzerland
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15
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Monika, Ansari A. Effect of the ring size of TMC ligands in controlling C-H bond activation by metal-superoxo species. Dalton Trans 2022; 51:5878-5889. [PMID: 35347335 DOI: 10.1039/d2dt00491g] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Metal-superoxo species play a very important role in many metal-mediated catalytic transformation reactions. Their catalytic reactivity is affected by many factors such as the nature of metal ions and ring size of ligands. Herein, for the first time, we report DFT calculations on the electronic structures of a series of metal-superoxo species (M = V, Cr, Mn, Fe, and Co) with two ring size ligands, i.e., 13-TMC/14-TMC, and a detailed mechanistic study on the C-H bond activation of cyclohexa-1,4-diene followed by the effect of the ring size of ligands. Our DFT results showed that the electron density at the distal oxygen plays an important role in C-H bond activation. By computing the energetics of C-H bond activation and mapping the potential energy surface, it was found that the initial hydrogen abstraction is the rate-determining step with both TMC rings and all the studied metal-superoxo species. The significant electron density at the cyclohex-1,4-diene carbon indicates that the reaction proceeds via the proton-coupled electron transfer mechanism. By mapping the potential energy surfaces, we found that the 13-TMC ligated superoxo with the anti-isomer are more reactive than the 14-TMC superoxo species except for the iron-superoxo species where the 14-TMC ligated superoxo species is more reactive i.e. smaller ring size TMC is more reactive towards C-H bond activation. This is also supported by the structural correlation, i.e., the greater contraction in the smaller ring results in the metal being pushed out of plane along the z-axis, which reduces the steric hindrance. Thus, the ring size can help in designing catalysts with better efficiency for catalytic reactions.
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Affiliation(s)
- Monika
- Department of Chemistry, Central University of Haryana, India, 123031.
| | - Azaj Ansari
- Department of Chemistry, Central University of Haryana, India, 123031.
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16
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Shapterhasmi T, Palani N, Velusamy M, Bhuvanesh NS, Sundaravel K, Easwaramoorthi S. Iron(III) Complexes of Pyrrolidine and Piperidine Appended Tridentate 3N Donor Ligands as Models for Catechol Dioxygenase Enzymes. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.120924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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17
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Cook EN, Machan CW. Bioinspired mononuclear Mn complexes for O 2 activation and biologically relevant reactions. Dalton Trans 2021; 50:16871-16886. [PMID: 34730590 DOI: 10.1039/d1dt03178c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A general interest in harnessing the oxidizing power of dioxygen (O2) continues to motivate research efforts on bioinspired and biomimetic complexes to better understand how metalloenzymes mediate these reactions. The ubiquity of Fe- and Cu-based enzymes attracts significant attention and has resulted in many noteworthy developments for abiotic systems interested in direct O2 reduction and small molecule activation. However, despite the existence of Mn-based metalloenzymes with important O2-dependent activity, there has been comparatively less focus on the development of these analogues relative to Fe- and Cu-systems. In this Perspective, we summarize important contributions to the development of bioinspired mononuclear Mn complexes for O2 activation and studies on their reactivity, emphasizing important design parameters in the primary and secondary coordination spheres and outlining mechanistic trends.
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Affiliation(s)
- Emma N Cook
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, VA 22904-4319, USA.
| | - Charles W Machan
- Department of Chemistry, University of Virginia, PO Box 400319, Charlottesville, VA 22904-4319, USA.
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18
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Dedushko MA, Pikul JH, Kovacs JA. Superoxide Oxidation by a Thiolate-Ligated Iron Complex and Anion Inhibition. Inorg Chem 2021; 60:7250-7261. [PMID: 33900756 DOI: 10.1021/acs.inorgchem.1c00336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Superoxide (O2•-) is a toxic radical, generated via the adventitious reduction of dioxygen (O2), which has been implicated in a number of human disease states. Nonheme iron enzymes, superoxide reductase (SOR) and superoxide dismutase (SOD), detoxify O2•- via reduction to afford H2O2 and disproportionation to afford O2 and H2O2, respectively. The former contains a thiolate in the coordination sphere, which has been proposed to prevent O2•- oxidation to O2. The work described herein shows that, in contrast to this, oxidized thiolate-ligated [FeIII(SMe2N4(tren)(THF)]2+ (1ox-THF) is capable of oxidizing O2•- to O2. Coordinating anions, Cl- and OAc-, are shown to inhibit dioxygen evolution, implicating an inner-sphere mechanism. Previously we showed that the reduced thiolate-ligated [FeII(SMe2N4(tren))]+ (1) is capable of reducing O2•- via a proton-dependent inner-sphere mechanism involving a transient Fe(III)-OOH intermediate. A transient ferric-superoxo intermediate, [FeIII(SMe2N4(tren))(O2)]+ (3), is detected by electronic absorption spectroscopy at -130 °C in the reaction between 1ox-THF and KO2 and shown to evolve O2 upon slight warming to -115 °C. The DFT calculated O-O (1.306 Å) and Fe-O (1.943 Å) bond lengths of 3 are typical of ferric-superoxo complexes, and the time-dependent DFT calculated electronic absorption spectrum of 3 reproduces the experimental spectrum. The electronic structure of 3 is shown to consist of two antiferromagnetically coupled (Jcalc = -180 cm-1) unpaired electrons, one in a superoxo π*(O-O) orbital and the other in an antibonding π*(Fe(dyz)-S(py)) orbital.
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Affiliation(s)
- Maksym A Dedushko
- The Department of Chemistry, University of Washington: Box 351700, Seattle, Washington 98195-1700, United States
| | - Jessica H Pikul
- The Department of Chemistry, University of Washington: Box 351700, Seattle, Washington 98195-1700, United States
| | - Julie A Kovacs
- The Department of Chemistry, University of Washington: Box 351700, Seattle, Washington 98195-1700, United States
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19
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Schulz C, Castillo RG, Pantazis DA, DeBeer S, Neese F. Structure-Spectroscopy Correlations for Intermediate Q of Soluble Methane Monooxygenase: Insights from QM/MM Calculations. J Am Chem Soc 2021; 143:6560-6577. [PMID: 33884874 PMCID: PMC8154522 DOI: 10.1021/jacs.1c01180] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Indexed: 12/22/2022]
Abstract
The determination of the diiron core intermediate structures involved in the catalytic cycle of soluble methane monooxygenase (sMMO), the enzyme that selectively catalyzes the conversion of methane to methanol, has been a subject of intense interest within the bioinorganic scientific community. Particularly, the specific geometry and electronic structure of the intermediate that precedes methane binding, known as intermediate Q (or MMOHQ), has been debated for over 30 years. Some reported studies support a bis-μ-oxo-bridged Fe(IV)2O2 closed-core conformation Fe(IV)2O2 core, whereas others favor an open-core geometry, with a longer Fe-Fe distance. The lack of consensus calls for a thorough re-examination and reinterpretation of the spectroscopic data available on the MMOHQ intermediate. Herein, we report extensive simulations based on a hybrid quantum mechanics/molecular mechanics approach (QM/MM) approach that takes into account the complete enzyme to explore possible conformations for intermediates MMOHox and MMOHQ of the sMMOH catalytic cycle. High-level quantum chemical approaches are used to correlate specific structural motifs with geometric parameters for comparison with crystallographic and EXAFS data, as well as with spectroscopic data from Mössbauer spectroscopy, Fe K-edge high-energy resolution X-ray absorption spectroscopy (HERFD XAS), and resonance Raman 16O-18O difference spectroscopy. The results provide strong support for an open-core-type configuration in MMOHQ, with the most likely topology involving mono-oxo-bridged Fe ions and alternate terminal Fe-oxo and Fe-hydroxo groups that interact via intramolecular hydrogen bonding. The implications of an open-core intermediate Q on the reaction mechanism of sMMO are discussed.
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Affiliation(s)
- Christine
E. Schulz
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Rebeca G. Castillo
- Max
Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Dimitrios A. Pantazis
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max
Planck Institute for Chemical Energy Conversion, Stiftstr. 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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20
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Guo M, Lee YM, Fukuzumi S, Nam W. Biomimetic metal-oxidant adducts as active oxidants in oxidation reactions. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.213807] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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21
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Suzuki T, Sato A, Oshita H, Yajima T, Tani F, Abe H, Mieda-Higa K, Yanagisawa S, Ogura T, Shimazaki Y. Formation of Ni(II)-phenoxyl radical complexes by O 2: a mechanistic insight into the reaction of Ni(II)-phenol complexes with O 2. Dalton Trans 2021; 50:5161-5170. [PMID: 33881085 DOI: 10.1039/d1dt00105a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A reaction of Ni(ClO4)2·6H2O with a tripodal ligand having two di(tert-butyl)phenol moieties, H2tbuL, and 1 equivalent of triethylamine in CH2Cl2/CH3OH (1 : 1, v/v) under N2 gave a NiII-(phenol)(phenolate) complex, [Ni(HtbuL)(CH3OH)2]ClO4. The formation of the NiII-phenoxyl radical complex by O2 was observed in the reaction of this complex in the solid state. On the other hand, the NiII-phenoxyl radical complex [Ni(Me2NL)(CH3OH)2]ClO4 was obtained by the reaction of H2Me2NL having a p-(dimethylamino)phenol moiety with Ni(ClO4)2·6H2O in a similar procedure under O2, through the oxidation of the NiII-(phenol)(phenolate) complex. However, a direct redox reaction of the NiII ion could not be detected in the phenoxyl radical formation. The results of the reaction kinetics, XAS and X-ray structure analyses suggested that the O2 oxidation from the NiII-(phenol)(phenolate) complex to the NiII-phenoxyl radical complex occurs via the proton transfer-electron transfer (PT-ET) type mechanism of the phenol moiety weakly coordinated to the nickel ion.
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Affiliation(s)
- Takashi Suzuki
- Graduate School of Science and Engineering, Ibaraki University, Mito 310-8512, Japan.
| | - Akari Sato
- Graduate School of Science and Engineering, Ibaraki University, Mito 310-8512, Japan.
| | - Hiromi Oshita
- Faculty of Chemistry of Functional Molecules, Konan University, Higashinada-ku, Kobe 658-8501, Japan
| | - Tatsuo Yajima
- Faculty of Chemistry, Materials and Bioengineering, Kansai University, Suita, Osaka 564-8680, Japan
| | - Fumito Tani
- Institute for Materials Chemistry and Engineering, Kyushu University, Nishi-Ku, Fukuoka 819-0395, Japan
| | - Hitoshi Abe
- Graduate School of Science and Engineering, Ibaraki University, Mito 310-8512, Japan. and Institute of Materials Structure Science (IMSS), High Energy Accelerator Research Organization (KEK) 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan and Department of Materials Structure Science, School of High Energy Accelerator Science, SOKENDAI (the Graduate University for Advanced Studies), 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
| | - Kaoru Mieda-Higa
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Sachiko Yanagisawa
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Graduate School of Life Science, University of Hyogo, Kamigori, Hyogo 678-1297, Japan
| | - Yuichi Shimazaki
- Graduate School of Science and Engineering, Ibaraki University, Mito 310-8512, Japan.
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22
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Bagha UK, Satpathy JK, Mukherjee G, Sastri CV, de Visser SP. A comprehensive insight into aldehyde deformylation: mechanistic implications from biology and chemistry. Org Biomol Chem 2021; 19:1879-1899. [PMID: 33406196 DOI: 10.1039/d0ob02204g] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aldehyde deformylation is an important reaction in biology, organic chemistry and inorganic chemistry and the process has been widely applied and utilized. For instance, in biology, the aldehyde deformylation reaction has wide differences in biological function, whereby cyanobacteria convert aldehydes into alkanes or alkenes, which are used as natural products for, e.g., defense mechanisms. By contrast, the cytochromes P450 catalyse the biosynthesis of hormones, such as estrogen, through an aldehyde deformylation reaction step. In organic chemistry, the aldehyde deformylation reaction is a common process for replacing functional groups on a molecule, and as such, many different synthetic methods and procedures have been reported that involve an aldehyde deformylation step. In bioinorganic chemistry, a variety of metal(iii)-peroxo complexes have been synthesized as biomimetic models and shown to react efficiently with aldehydes through deformylation reactions. This review paper provides an overview of the various aldehyde deformylation reactions in organic chemistry, biology and biomimetic model systems, and shows a broad range of different chemical reaction mechanisms for this process. Although a nucleophilic attack at the carbonyl centre is the consensus reaction mechanism, several examples of an alternative electrophilic reaction mechanism starting with hydrogen atom abstraction have been reported as well. There is still much to learn and to discover on aldehyde deformylation reactions, as deciphered in this review paper.
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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.
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, Assam 781039, India.
| | - Sam P de Visser
- Manchester Institute of Biotechnology and the Department of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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23
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Schlagintweit JF, Altmann PJ, Böth AD, Hofmann BJ, Jandl C, Kaußler C, Nguyen L, Reich RM, Pöthig A, Kühn FE. Activation of Molecular Oxygen by a Cobalt(II) Tetra-NHC Complex*. Chemistry 2021; 27:1311-1315. [PMID: 33125815 PMCID: PMC7898330 DOI: 10.1002/chem.202004758] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Indexed: 11/24/2022]
Abstract
The first dicobalt(III) μ2 -peroxo N-heterocyclic carbene (NHC) complex is reported. It can be quantitatively generated from a cobalt(II) compound bearing a 16-membered macrocyclic tetra-NHC ligand via facile activation of dioxygen from air at ambient conditions. The reaction proceeds via an end-on superoxo intermediate as demonstrated by EPR studies and DFT. The peroxo moiety can be cleaved upon addition of acetic acid, yielding the corresponding CoIII acetate complex going along with H2 O2 formation. In contrast, both CoII and CoIII complexes are also studied as catalysts to utilize air for olefin and alkane oxidation reactions; however, not resulting in product formation. The observations are rationalized by DFT-calculations, suggesting a nucleophilic nature of the dicobalt(III) μ2 -peroxo complex. All isolated compounds are characterized by NMR, ESI-MS, elemental analysis, EPR and SC-XRD.
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Affiliation(s)
- Jonas F. Schlagintweit
- Molecular CatalysisCatalysis Research Center and Department of ChemistryTechnische Universität MünchenLichtenbergstraße 485747Garching bei MünchenGermany
| | - Philipp J. Altmann
- Molecular CatalysisCatalysis Research Center and Department of ChemistryTechnische Universität MünchenLichtenbergstraße 485747Garching bei MünchenGermany
- Single Crystal XRD Laboratory of the Catalysis Research CenterTechnische Universität MünchenErnst-Otto-Fischer-Str. 185747Garching bei MünchenGermany
| | - Alexander D. Böth
- Molecular CatalysisCatalysis Research Center and Department of ChemistryTechnische Universität MünchenLichtenbergstraße 485747Garching bei MünchenGermany
| | - Benjamin J. Hofmann
- Molecular CatalysisCatalysis Research Center and Department of ChemistryTechnische Universität MünchenLichtenbergstraße 485747Garching bei MünchenGermany
| | - Christian Jandl
- Single Crystal XRD Laboratory of the Catalysis Research CenterTechnische Universität MünchenErnst-Otto-Fischer-Str. 185747Garching bei MünchenGermany
| | - Clemens Kaußler
- Molecular CatalysisCatalysis Research Center and Department of ChemistryTechnische Universität MünchenLichtenbergstraße 485747Garching bei MünchenGermany
| | - Linda Nguyen
- Molecular CatalysisCatalysis Research Center and Department of ChemistryTechnische Universität MünchenLichtenbergstraße 485747Garching bei MünchenGermany
- Ausbildungszentrum der Technischen Universität MünchenTechnische Universität MünchenLichtenbergstraße 485747Garching bei MünchenGermany
| | - Robert M. Reich
- Molecular CatalysisCatalysis Research Center and Department of ChemistryTechnische Universität MünchenLichtenbergstraße 485747Garching bei MünchenGermany
| | - Alexander Pöthig
- Single Crystal XRD Laboratory of the Catalysis Research CenterTechnische Universität MünchenErnst-Otto-Fischer-Str. 185747Garching bei MünchenGermany
| | - Fritz E. Kühn
- Molecular CatalysisCatalysis Research Center and Department of ChemistryTechnische Universität MünchenLichtenbergstraße 485747Garching bei MünchenGermany
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24
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Shanmugam M, Quareshy M, Cameron AD, Bugg TDH, Chen Y. Light-Activated Electron Transfer and Catalytic Mechanism of Carnitine Oxidation by Rieske-Type Oxygenase from Human Microbiota. Angew Chem Int Ed Engl 2020; 60:4529-4534. [PMID: 33180358 PMCID: PMC7986066 DOI: 10.1002/anie.202012381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 10/23/2020] [Indexed: 01/18/2023]
Abstract
Oxidation of quaternary ammonium substrate, carnitine by non‐heme iron containing Acinetobacter baumannii (Ab) oxygenase CntA/reductase CntB is implicated in the onset of human cardiovascular disease. Herein, we develop a blue‐light (365 nm) activation of NADH coupled to electron paramagnetic resonance (EPR) measurements to study electron transfer from the excited state of NADH to the oxidized, Rieske‐type, [2Fe‐2S]2+ cluster in the AbCntA oxygenase domain with and without the substrate, carnitine. Further electron transfer from one‐electron reduced, Rieske‐type [2Fe‐2S]1+ center in AbCntA‐WT to the mono‐nuclear, non‐heme iron center through the bridging glutamate E205 and subsequent catalysis occurs only in the presence of carnitine. The electron transfer process in the AbCntA‐E205A mutant is severely affected, which likely accounts for the significant loss of catalytic activity in the AbCntA‐E205A mutant. The NADH photo‐activation coupled with EPR is broadly applicable to trap reactive intermediates at low temperature and creates a new method to characterize elusive intermediates in multiple redox‐centre containing proteins.
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Affiliation(s)
- Muralidharan Shanmugam
- Manchester Institute of Biotechnology (MIB) & Photon Science Institute (PSI), University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Mussa Quareshy
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Alexander D Cameron
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Timothy D H Bugg
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Yin Chen
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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25
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Shanmugam M, Quareshy M, Cameron AD, Bugg TDH, Chen Y. Light‐Activated Electron Transfer and Catalytic Mechanism of Carnitine Oxidation by Rieske‐Type Oxygenase from Human Microbiota. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202012381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Muralidharan Shanmugam
- Manchester Institute of Biotechnology (MIB) & Photon Science Institute (PSI) University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Mussa Quareshy
- School of Life Sciences University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Alexander D. Cameron
- School of Life Sciences University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Timothy D. H. Bugg
- Department of Chemistry University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
| | - Yin Chen
- School of Life Sciences University of Warwick Gibbet Hill Road Coventry CV4 7AL UK
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26
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Quareshy M, Shanmugam M, Townsend E, Jameson E, Bugg TDH, Cameron AD, Chen Y. Structural basis of carnitine monooxygenase CntA substrate specificity, inhibition, and intersubunit electron transfer. J Biol Chem 2020; 296:100038. [PMID: 33158989 PMCID: PMC7948474 DOI: 10.1074/jbc.ra120.016019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/27/2020] [Accepted: 11/06/2020] [Indexed: 12/27/2022] Open
Abstract
Microbial metabolism of carnitine to trimethylamine (TMA) in the gut can accelerate atherosclerosis and heart disease, and these TMA-producing enzymes are therefore important drug targets. Here, we report the first structures of the carnitine oxygenase CntA, an enzyme of the Rieske oxygenase family. CntA exists in a head-to-tail α3 trimeric structure. The two functional domains (the Rieske and the catalytic mononuclear iron domains) are located >40 Å apart in the same monomer but adjacent in two neighboring monomers. Structural determination of CntA and subsequent electron paramagnetic resonance measurements uncover the molecular basis of the so-called bridging glutamate (E205) residue in intersubunit electron transfer. The structures of the substrate-bound CntA help to define the substrate pocket. Importantly, a tyrosine residue (Y203) is essential for ligand recognition through a π-cation interaction with the quaternary ammonium group. This interaction between an aromatic residue and quaternary amine substrates allows us to delineate a subgroup of Rieske oxygenases (group V) from the prototype ring-hydroxylating Rieske oxygenases involved in bioremediation of aromatic pollutants in the environment. Furthermore, we report the discovery of the first known CntA inhibitors and solve the structure of CntA in complex with the inhibitor, demonstrating the pivotal role of Y203 through a π-π stacking interaction with the inhibitor. Our study provides the structural and molecular basis for future discovery of drugs targeting this TMA-producing enzyme in human gut.
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Affiliation(s)
- Mussa Quareshy
- School of Life Sciences, University of Warwick, Coventry, UK.
| | - Muralidharan Shanmugam
- Manchester Institute of Biotechnology & Photon Science Institute, The University of Manchester, Manchester, UK
| | | | - Eleanor Jameson
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | | | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, UK.
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27
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Li X, Zhu W, Liu Y. Mechanistic Insights into the Oxidative Rearrangement Catalyzed by the Unprecedented Dioxygenase ChaP Involved in Chartreusin Biosynthesis. Inorg Chem 2020; 59:13988-13999. [PMID: 32951427 DOI: 10.1021/acs.inorgchem.0c01706] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ChaP is a non-heme iron-dependent dioxygenase belonging to the vicinal oxygen chelate (VOC) enzyme superfamily that catalyzes the final α-pyrone ring formation in the biosynthesis of chartreusin. In contrast to other common dioxygenases, for example, 2,3-catechol dioxygenase which uses the dioxygen molecule as the oxidant, ChaP requires the flavin-activated oxygen (O22-) as the equivalent. Previous experiments showed that the ChaP-catalyzed ring rearrangement contains two successive C-C bond cleavages and one lactonization; however, the detailed reaction mechanism is unknown. In this work, on the basis of the recently obtained crystal structure of ChaP, the computational model was constructed and the catalytic mechanism of ChaP was explored by performing quantum mechanical/molecular mechanical (QM/MM) calculations. Our calculation results reveal that ChaP uses the proximal oxygen in iron-coordinated HOO- to attack the carbonyl carbon of the substrate, whereas the previous proposal that Asp49 acts as a base to deprotonate the iron-coordinated HOO- to generate O22- is unlikely. In the first stage reaction, owing to the coordination of the substrate with iron, the substrate is activated by accepting an electron from iron and the resulting oxy-radical intermediate formed by O-O cleavage can easily trigger the ring rearrangement. In the final decarboxylation, the phenolic anion of the substrate cooperatively accepts the proton of iron-coordinated HOO- to facilitate the attack of the distal oxygen, and the proton-coupled electron transfer (PCET) from the substrate to the FeIV═O plays a key role for the decarboxylation. These findings may provide useful information for understanding the ChaP-catalyzed oxidative rearrangement and other flavin-dependent non-heme dioxygenases.
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Affiliation(s)
- Xinyi Li
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Wenyou Zhu
- College of Chemistry and Chemical Engineering, Xuzhou Institute of Technology, Xuzhou, Jiangsu 221111, China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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28
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Tu N, Zhang D, Niu X, Du C, Zhang L, Xie W, Niu X, Liu Y, Li Y. A novel concept for the biodegradation mechanism of dianionic catechol with homoprotocatechuate 2,3-dioxygenase: A non-proton-assisted process. CHEMOSPHERE 2020; 246:125796. [PMID: 31918103 DOI: 10.1016/j.chemosphere.2019.125796] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 12/15/2019] [Accepted: 12/29/2019] [Indexed: 06/10/2023]
Abstract
The theory of "proton-assisted process" can well explain the catalytic mechanism of homoprotocatechuate 2,3-dioxygenase (2,3-HPCD) with a monoanionic substrate (homoprotocatechuate, HPCA). Here a "non-proton-assisted process" is presented to interpret catalytic mechanism of 2,3-HPCD with a dianionic substrate (4-nitrocatechol, 4NC). The ONIOM calculation is performed to investigate the reaction pathway of a wild-type 2,3-HPCD with 4NC (H200H-4NC system). The catalytic reaction is comprised of four steps: (1) A dioxygen attacks the aromatic ring to produce an alkylperoxo species. (2) O-O bond cleavage and the formation of an epoxide species occur. (3) A seven-membered O-heterocyclic compound is generated by the extinction of the epoxy structure. (4) The seven-membered ring undergoes ring opening to form the final product (C2-C3 cleavage product). The effective free energy barrier of the catalytic reaction of the H200H-4NC system is 26.2 kcal mol-1, which is much higher than that of the H200H-HPCA system. Furthermore, two calculated electronic configurations (Fe(III)-O2•- and Fe(III)-SQ•) have a high similarity to previously detected ones, which demonstrates that the Asn200 variant (H200N-4NC variant system) employs a C4 (para-carbon) pathway to produce a C4-C5 cleavage product. Our findings provide an in-depth understanding of the catalytic mechanisms of dianionic catechol and its derivatives.
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Affiliation(s)
- Ningyu Tu
- School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Dongmei Zhang
- School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Xianchun Niu
- School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Cheng Du
- School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Li Zhang
- School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Wenyu Xie
- School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming, 525000, China
| | - Xiaojun Niu
- School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming, 525000, China; School of Environment and Energy, South China University of Technology, Guangzhou, 510006, China
| | - Yang Liu
- School of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, Guangdong, 525000, China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Process and Control, Guangdong University of Petrochemical Technology, Maoming, 525000, China.
| | - Youming Li
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, 510640, China
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29
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Khan MS, Khalid M, Ahmad MS, Shahid M, Ahmad M. Catalytic activity of Mn(III) and Co(III) complexes: evaluation of catechol oxidase enzymatic and photodegradation properties. RESEARCH ON CHEMICAL INTERMEDIATES 2020. [DOI: 10.1007/s11164-020-04127-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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30
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Visser SP. Second‐Coordination Sphere Effects on Selectivity and Specificity of Heme and Nonheme Iron Enzymes. Chemistry 2020; 26:5308-5327. [DOI: 10.1002/chem.201905119] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 12/04/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Sam P. Visser
- The Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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31
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Chen F, Yang C, Hu X, Zhang X, Xie H, Jiang H, Jiang F, Zeng W. Photocatalyzed formal carbooxygenation of terminal alkynes. Org Chem Front 2020. [DOI: 10.1039/d0qo00020e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
An efficient visible-light-induced formal carbooxygenation of N-arylsulfonylamido alkynes with molecular oxygen has been developed.
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Affiliation(s)
- Fengjuan Chen
- Key Laboratory of Functional Molecular Engineering of Guangdong Province
- School of Chemistry and Chemical Engineering
- South China University of Technology
- Guangzhou 510641
- China
| | - Can Yang
- Key Laboratory of Functional Molecular Engineering of Guangdong Province
- School of Chemistry and Chemical Engineering
- South China University of Technology
- Guangzhou 510641
- China
| | - Xinwei Hu
- Key Laboratory of Functional Molecular Engineering of Guangdong Province
- School of Chemistry and Chemical Engineering
- South China University of Technology
- Guangzhou 510641
- China
| | - Xiaoqi Zhang
- Guangdong Provincial Engineering Research Center for Modernization of TCM
- College of Pharmacy
- Jinan University
- Guangzhou 510632
- China
| | - Haisheng Xie
- Key Laboratory of Functional Molecular Engineering of Guangdong Province
- School of Chemistry and Chemical Engineering
- South China University of Technology
- Guangzhou 510641
- China
| | - Huanfeng Jiang
- Key Laboratory of Functional Molecular Engineering of Guangdong Province
- School of Chemistry and Chemical Engineering
- South China University of Technology
- Guangzhou 510641
- China
| | - Fubin Jiang
- College of Chemistry
- Beijing Normal University
- Beijing
- China
| | - Wei Zeng
- Key Laboratory of Functional Molecular Engineering of Guangdong Province
- School of Chemistry and Chemical Engineering
- South China University of Technology
- Guangzhou 510641
- China
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32
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Mebs S, Srinivas V, Kositzki R, Griese JJ, Högbom M, Haumann M. Fate of oxygen species from O 2 activation at dimetal cofactors in an oxidase enzyme revealed by 57Fe nuclear resonance X-ray scattering and quantum chemistry. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:148060. [PMID: 31394094 DOI: 10.1016/j.bbabio.2019.148060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/30/2019] [Accepted: 08/02/2019] [Indexed: 10/26/2022]
Abstract
Oxygen (O2) activation is a central challenge in chemistry and catalyzed at prototypic dimetal cofactors in biological enzymes with diverse functions. Analysis of intermediates is required to elucidate the reaction paths of reductive O2 cleavage. An oxidase protein from the bacterium Geobacillus kaustophilus, R2lox, was used for aerobic in-vitro reconstitution with only 57Fe(II) or Mn(II) plus 57Fe(II) ions to yield [FeFe] or [MnFe] cofactors under various oxygen and solvent isotopic conditions including 16/18O and H/D exchange. 57Fe-specific X-ray scattering techniques were employed to collect nuclear forward scattering (NFS) and nuclear resonance vibrational spectroscopy (NRVS) data of the R2lox proteins. NFS revealed Fe/Mn(III)Fe(III) cofactor states and Mössbauer quadrupole splitting energies. Quantum chemical calculations of NRVS spectra assigned molecular structures, vibrational modes, and protonation patterns of the cofactors, featuring a terminal water (H2O) bound at iron or manganese in site 1 and a metal-bridging hydroxide (μOH-) ligand. A procedure for quantitation and correlation of experimental and computational NRVS difference signals due to isotope labeling was developed. This approach revealed that the protons of the ligands as well as the terminal water at the R2lox cofactors exchange with the bulk solvent whereas 18O from 18O2 cleavage is incorporated in the hydroxide bridge. In R2lox, the two water molecules from four-electron O2 reduction are released in a two-step reaction to the solvent. These results establish combined NRVS and QM/MM for tracking of iron-based oxygen activation in biological and chemical catalysts and clarify the reductive O2 cleavage route in an enzyme.
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Affiliation(s)
- Stefan Mebs
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16, 10691 Stockholm, Sweden
| | - Ramona Kositzki
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Julia J Griese
- Department of Cell and Molecular Biology, Structural Biology, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16, 10691 Stockholm, Sweden
| | - Michael Haumann
- Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
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33
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Zaitseva SV, Tyurin DV, Zdanovich SA, Koifman OI. Kinetics of the Formation of an Active Oxo Species of µ-Carbidodimeric Water-Soluble Iron(IV) Sulfophthalocyanine in the Reaction with tert-Butyl Hydroperoxide. RUSS J INORG CHEM+ 2019. [DOI: 10.1134/s0036023619060184] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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34
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Pattanayak S, Cantú Reinhard FG, Rana A, Gupta SS, de Visser SP. The Equatorial Ligand Effect on the Properties and Reactivity of Iron(V) Oxo Intermediates. Chemistry 2019; 25:8092-8104. [DOI: 10.1002/chem.201900708] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 12/23/2022]
Affiliation(s)
- Santanu Pattanayak
- Department of Chemical SciencesIndian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246 India
| | - Fabián G. Cantú Reinhard
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
| | - Atanu Rana
- Indian Association for the Cultivation of Sciences 2A Raja S. C. Mullick Road Kolkata 700032 India
| | - Sayam Sen Gupta
- Department of Chemical SciencesIndian Institute of Science Education and Research (IISER) Kolkata, Mohanpur 741246 India
| | - Sam P. de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical ScienceThe University of Manchester 131 Princess Street Manchester M1 7DN UK
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35
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Wang J, Chen J, Tang X, Li Y, Zhang R, Zhu L, Sun Y, Zhang Q, Wang W. Catalytic Mechanism for 2,3-Dihydroxybiphenyl Ring Cleavage by Nonheme Extradiol Dioxygenases BphC: Insights from QM/MM Analysis. J Phys Chem B 2019; 123:2244-2253. [DOI: 10.1021/acs.jpcb.8b11008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Junjie Wang
- Environment Research Institute, Shandong University, Qingdao 266237, P. R. China
| | - Jinfeng Chen
- Environment Research Institute, Shandong University, Qingdao 266237, P. R. China
| | - Xiaowen Tang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P. R. China
| | - Yanwei Li
- Environment Research Institute, Shandong University, Qingdao 266237, P. R. China
| | - Ruiming Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, P. R. China
| | - Ledong Zhu
- Environment Research Institute, Shandong University, Qingdao 266237, P. R. China
| | - Yanhui Sun
- College of Environment and Safety Engineering, Qingdao University of Science and Technology, Qingdao 266042, P. R. China
| | - Qingzhu Zhang
- Environment Research Institute, Shandong University, Qingdao 266237, P. R. China
| | - Wenxing Wang
- Environment Research Institute, Shandong University, Qingdao 266237, P. R. China
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36
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Hsieh CC, Liu YC, Tseng MC, Chiang MH, Horng YC. Dioxygen activation by a dinuclear thiolate-ligated Fe(ii) complex. Dalton Trans 2019; 48:379-386. [PMID: 30516213 DOI: 10.1039/c8dt04491k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Dioxygen activation by FeII thiolate complexes is relatively rare in biological and chemical systems because the sulfur site is at least as vulnerable as the iron site to oxidative modification. O2 activation by FeII-SR complexes with thiolate bound trans to the O2 binding site generally affords the FeIV[double bond, length as m-dash]O intermediate and oxidized thiolate. On the other hand, O2 activation by Fe(ii)-SR complexes with thiolate bound cis to the O2 binding site generates FeIII-O-FeIII or S-oxygenated complexes. The postulated FeIV[double bond, length as m-dash]O intermediate has only been identified in isopenicillin N synthase recently. We demonstrated here that O2 activation by a dinuclear FeII thiolate-rich complex produces a mononuclear FeIII complex and water with a supply of electron donors. The thiolate is bound cis to the postulated dioxygen binding site, and no FeIII-O-FeIII or S-oxygenated complex was observed. Although we have not detected the transient intermediate by spectroscopic measurements, the FeIV[double bond, length as m-dash]O intermediate is suggested to exist by theoretical calculation, and P-oxidation and hydride-transfer experiments. In addition, an unprecedented FeIII-O2-FeIII complex supported by thiolates was observed during the reaction by using a coldspray ionization time-of-flight mass (CSI-TOF MS) instrument. This is also supported by low-temperature UV-vis measurements. The intramolecular NHO[double bond, length as m-dash]FeIV hydrogen bonding, calculated by DFT, probably fine tunes the O2-activation process for intramolecular hydrogen abstraction, avoiding the S-oxygenation at cis-thiolate.
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Affiliation(s)
- Chang-Chih Hsieh
- Department of Chemistry, National Changhua University of Education, Changhua 50058, Taiwan.
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37
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Sarkar A, Chakraborty A, Adhikary A, Maity S, Mandal A, Samanta D, Ghosh P, Das D. Exploration of catecholase-like activity of a series of magnetically coupled transition metal complexes of Mn, Co and Ni: new insights into the solution state behavior of Mn complexes. Dalton Trans 2019; 48:14164-14177. [DOI: 10.1039/c9dt02399b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Oxidation state dependent catecholase activity has been explored with Mn-Schiff-base complex which transform oxidation state from +ii to +iii in solution with time by combined experimental and theoretical investigations.
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Affiliation(s)
- Abani Sarkar
- Department of Chemistry
- University College of Science
- University of Calcutta
- Kolkata 700009
- India
| | - Aratrika Chakraborty
- Department of Chemistry
- University College of Science
- University of Calcutta
- Kolkata 700009
- India
| | - Amit Adhikary
- Department of Chemistry
- University College of Science
- University of Calcutta
- Kolkata 700009
- India
| | - Suvendu Maity
- Department of Chemistry
- R. K. Mission Residential College
- Kolkata 700 103
- India
| | - Arnab Mandal
- Department of Chemistry
- University College of Science
- University of Calcutta
- Kolkata 700009
- India
| | - Debabrata Samanta
- Department of Chemistry
- Indian Institute of Technology
- Kanpur-208016
- India
| | - Prasanta Ghosh
- Department of Chemistry
- R. K. Mission Residential College
- Kolkata 700 103
- India
| | - Debasis Das
- Department of Chemistry
- University College of Science
- University of Calcutta
- Kolkata 700009
- India
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38
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X-Ray Crystallography of Carbon Monoxide Dehydrogenases. Methods Mol Biol 2018. [PMID: 30317481 DOI: 10.1007/978-1-4939-8864-8_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Carbon monoxide dehydrogenases (CODHs) are central players in the biogeochemical carbon monoxide (CO) cycle and have been extensively studied from the ecological level to the structural/molecular level. Of the two types of CODHs, the oxygen-tolerant CODHs use a bimetallic [CuSMo(=O)OH] center connected to the protein via a pyranopterin cofactor, whereas the oxygen-sensitive CODHs contain a [NiFe4S4-OHx]-cluster. Despite the fact that we have a basic understanding of how both types of CODHs use distinct active sites to catalyze the oxidation of CO with water to CO2, two protons, and two electrons (a reversible reaction in the cases of the oxygen-sensitive CODHs), many questions remain unanswered, especially concerning the electronic structures of the intermediate states. Since these states will likely be only revealed by the interplay of experimental and theoretical methods, there is a need to obtain accurate descriptions of the active site architectures in various states and, consequently, a need to generate crystals with good diffraction quality and collect data at element-specific wavelengths in order to determine the identity of elements in the case of mixed states. This chapter provides a description of the general working protocols for the crystallization and structural analysis of Cu,Mo-CODH and Ni,Fe-CODH that facilitates the mechanistic investigations of these important metalloenzymes.
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39
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Tian G, Su H, Liu Y. Mechanism of Sulfoxidation and C–S Bond Formation Involved in the Biosynthesis of Ergothioneine Catalyzed by Ergothioneine Synthase (EgtB). ACS Catal 2018. [DOI: 10.1021/acscatal.8b01473] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ge Tian
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, People’s Republic of China
| | - Hao Su
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, People’s Republic of China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, People’s Republic of China
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40
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Yang Y, Liu F, Liu A. Adapting to oxygen: 3-Hydroxyanthrinilate 3,4-dioxygenase employs loop dynamics to accommodate two substrates with disparate polarities. J Biol Chem 2018; 293:10415-10424. [PMID: 29784877 DOI: 10.1074/jbc.ra118.002698] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 05/18/2018] [Indexed: 11/06/2022] Open
Abstract
3-Hydroxyanthranilate 3,4-dioxygenase (HAO) is an iron-dependent protein that activates O2 and inserts both oxygen atoms into 3-hydroxyanthranilate (3-HAA). An intriguing question is how HAO can rapidly bind O2, even though local O2 concentrations and diffusion rates are relatively low. Here, a close inspection of the HAO structures revealed that substrate- and inhibitor-bound structures exhibit a closed conformation with three hydrophobic loop regions moving toward the catalytic iron center, whereas the ligand-free structure is open. We hypothesized that these loop movements enhance O2 binding to the binary complex of HAO and 3-HAA. We found that the carboxyl end of 3-HAA triggers changes in two loop regions and that the third loop movement appears to be driven by an H-bond interaction between Asn27 and Ile142 Mutational analyses revealed that N27A, I142A, and I142P variants cannot form a closed conformation, and steady-state kinetic assays indicated that these variants have a substantially higher Km for O2 than WT HAO. This observation suggested enhanced hydrophobicity at the iron center resulting from the concerted loop movements after the binding of the primary substrate, which is hydrophilic. Given that O2 is nonpolar, the increased hydrophobicity at the iron center of the binary complex appears to be essential for rapid O2 binding and activation, explaining the reason for the 3-HAA-induced loop movements. Because substrate binding-induced open-to-closed conformational changes are common, the results reported here may help further our understanding of how oxygen is enriched in nonheme iron-dependent dioxygenases.
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Affiliation(s)
- Yu Yang
- From the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249 and
| | - Fange Liu
- the Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Aimin Liu
- From the Department of Chemistry, University of Texas at San Antonio, San Antonio, Texas 78249 and
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41
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Zhang LL, Wang XY, Jiang KY, Zhao BY, Yan HM, Zhang XY, Zhang ZX, Guo Z, Che CM. A theoretical study on the oxidation of alkenes to aldehydes catalyzed by ruthenium porphyrins using O 2 as the sole oxidant. Dalton Trans 2018; 47:5286-5297. [PMID: 29569676 DOI: 10.1039/c8dt00614h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Density functional theory (DFT) calculations were used to study the ruthenium porphyrin-catalyzed oxidation of styrene to generate an aldehyde. The results indicate that two reactive oxidants, dioxoruthenium and monooxoruthenium-superoxo porphyrins, participate in the catalytic oxidation. In the mechanism, the resultant monooxoruthenium porphyrin acts in the tandem epoxide isomerization (E-I) to selectively yield an aldehyde and generate a dioxoruthenium porphyrin, thereby triggering new oxidation reaction cycles. In this calculation, several key elements responsible for the observed oxidative ability have been established by using Frontier molecular orbital (FMO) theory, natural bond orbital (NBO) analysis, etc., which include the reaction energy, the spin exchange effect, the spin-state conversion process, and the energy level of the lowest unoccupied molecular orbitals (LUMOs) of the reactive oxidants. The comparative oxidative abilities of the ruthenium-oxo/superoxo compounds with different axial ligands are also investigated. The results suggest that the ruthenium-oxo/superoxo species featuring a chlorine axial ligand is more reactive than that substituted with oxygen. This tuneable reactivity can be understood when considering the different electronic characters of the two ligands and the effective atomic number rule (EAN).
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Affiliation(s)
- Lin-Lin Zhang
- College of Material Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Shanxi, 030024, P. R. China.
| | - Xiang-Yun Wang
- College of Material Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Shanxi, 030024, P. R. China.
| | - Kun-Yao Jiang
- College of Material Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Shanxi, 030024, P. R. China.
| | - Bing-Yuan Zhao
- College of Material Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Shanxi, 030024, P. R. China.
| | - Hui-Min Yan
- College of Material Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Shanxi, 030024, P. R. China.
| | - Xiao-Yun Zhang
- College of Material Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Shanxi, 030024, P. R. China.
| | - Zhu-Xia Zhang
- College of Material Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Shanxi, 030024, P. R. China.
| | - Zhen Guo
- College of Material Science & Engineering, Key Laboratory of Interface Science and Engineering in Advanced Materials, Ministry of Education, Taiyuan University of Technology, Shanxi, 030024, P. R. China.
| | - Chi-Ming Che
- Department of Chemistry, the University of Hong Kong, Hong Kong, P. R. China.
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42
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Stepanović S, Angelone D, Gruden M, Swart M. The role of spin states in the catalytic mechanism of the intra- and extradiol cleavage of catechols by O 2. Org Biomol Chem 2018; 15:7860-7868. [PMID: 28880037 DOI: 10.1039/c7ob01814b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Iron-dependent enzymes and biomimetic iron complexes can catalyze the ring cleavage of very inert, aromatic compounds. The mechanisms of these transformations and the factors that lead either to extradiol cleavage or intradiol cleavage have not been fully understood. By using density functional theory we have elucidated the mechanism of the catalytic cycle for two biomimetic complexes, and explained the difference in the experimentally obtained products.
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Affiliation(s)
- S Stepanović
- Center for Chemistry, Institute of Chemistry, Technology and Metallurgy, University of Belgrade Njegoseva 12, 11001 Belgrade, Serbia
| | - D Angelone
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi (Ciències), 17003 Girona, Spain
| | - M Gruden
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, 11001 Belgrade, Serbia.
| | - M Swart
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi (Ciències), 17003 Girona, Spain and ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
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43
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Jasniewski AJ, Que L. Dioxygen Activation by Nonheme Diiron Enzymes: Diverse Dioxygen Adducts, High-Valent Intermediates, and Related Model Complexes. Chem Rev 2018; 118:2554-2592. [PMID: 29400961 PMCID: PMC5920527 DOI: 10.1021/acs.chemrev.7b00457] [Citation(s) in RCA: 316] [Impact Index Per Article: 52.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A growing subset of metalloenzymes activates dioxygen with nonheme diiron active sites to effect substrate oxidations that range from the hydroxylation of methane and the desaturation of fatty acids to the deformylation of fatty aldehydes to produce alkanes and the six-electron oxidation of aminoarenes to nitroarenes in the biosynthesis of antibiotics. A common feature of their reaction mechanisms is the formation of O2 adducts that evolve into more reactive derivatives such as diiron(II,III)-superoxo, diiron(III)-peroxo, diiron(III,IV)-oxo, and diiron(IV)-oxo species, which carry out particular substrate oxidation tasks. In this review, we survey the various enzymes belonging to this unique subset and the mechanisms by which substrate oxidation is carried out. We examine the nature of the reactive intermediates, as revealed by X-ray crystallography and the application of various spectroscopic methods and their associated reactivity. We also discuss the structural and electronic properties of the model complexes that have been found to mimic salient aspects of these enzyme active sites. Much has been learned in the past 25 years, but key questions remain to be answered.
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Affiliation(s)
- Andrew J. Jasniewski
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455, United States
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44
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Abstract
Aerobic organisms have evolved to activate oxygen from the atmosphere, which allows them to catalyze the oxidation of different kinds of substrates. This activation of oxygen is achieved by a metal center (usually iron or copper) buried within a metalloprotein. In the case of iron-containing heme enzymes, the activation of oxygen is achieved by formation of transient iron-oxo (ferryl) intermediates; these intermediates are called Compound I and Compound II. The Compound I and II intermediates were first discovered in the 1930s in horseradish peroxidase, and it is now known that these same species are used across the family of heme enzymes, which include all of the peroxidases, the heme catalases, the P450s, cytochrome c oxidase, and NO synthase. Many years have passed since the first observations, but establishing the chemical nature of these transient ferryl species remains a fundamental question that is relevant to the reactivity, and therefore the usefulness, of these species in biology. This Account summarizes experiments that were conceived and conducted at Leicester and presents our ideas on the chemical nature, stability, and reactivity of these ferryl heme species. We begin by briefly summarizing the early milestones in the field, from the 1940s and 1950s. We present comparisons between the nature and reactivity of the ferryl species in horseradish peroxidase, cytochrome c peroxidase, and ascorbate peroxidase; and we consider different modes of electron delivery to ferryl heme, from different substrates in different peroxidases. We address the question of whether the ferryl heme is best formulated as an (unprotonated) FeIV═O or as a (protonated) FeIV-OH species. A range of spectroscopic approaches (EXAFS, resonance Raman, Mossbauer, and EPR) have been used over many decades to examine this question, and in the last ten years, X-ray crystallography has also been employed. We describe how information from all of these studies has blended together to create an overall picture, and how the recent application of neutron crystallography has directly identified protonation states and has helped to clarify the precise nature of the ferryl heme in cytochrome c peroxidase and ascorbate peroxidase. We draw comparisons between the Compound I and Compound II species that we have observed in peroxidases with those found in other heme systems, notably the P450s, highlighting possible commonality across these heme ferryl systems. The identification of proton locations from neutron structures of these ferryl species opens the door for understanding the proton translocations that need to occur during O-O bond cleavage.
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Affiliation(s)
- Peter C. E. Moody
- Department
of Molecular and Cell Biology and Leicester Institute of Structural
and Chemical Biology, University of Leicester, Lancaster Road, Leicester LE1 9HN, England
| | - Emma L. Raven
- Department
of Chemistry and Leicester Institute of Structural and Chemical Biology, University of Leicester, University Road, Leicester LE1 7RH, U.K
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45
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Leipzig BK, Rees JA, Kowalska JK, Theisen RM, Kavčič M, Poon PCY, Kaminsky W, DeBeer S, Bill E, Kovacs JA. How Do Ring Size and π-Donating Thiolate Ligands Affect Redox-Active, α-Imino-N-heterocycle Ligand Activation? Inorg Chem 2018; 57:1935-1949. [PMID: 29411979 PMCID: PMC8312276 DOI: 10.1021/acs.inorgchem.7b02748] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Considerable effort has been devoted to the development of first-row transition-metal catalysts containing redox-active imino-pyridine ligands that are capable of storing multiple reducing equivalents. This property allows abundant and inexpensive first-row transition metals, which favor sequential one-electron redox processes, to function as competent catalysts in the concerted two-electron reduction of substrates. Herein we report the syntheses and characterization of a series of iron complexes that contain both π-donating thiolate and π-accepting (α-imino)-N-heterocycle redox-active ligands, with progressively larger N-heterocycle rings (imidazole, pyridine, and quinoline). A cooperative interaction between these complementary redox-active ligands is shown to dictate the properties of these complexes. Unusually intense charge-transfer (CT) bands, and intraligand metrical parameters, reminiscent of a reduced (α-imino)-N-heterocycle ligand (L•-), initially suggested that the electron-donating thiolate had reduced the N-heterocycle. Sulfur K-edge X-ray absorption spectroscopic (XAS) data, however, provides evidence for direct communication, via backbonding, between the thiolate sulfur and the formally orthogonal (α-imino)-N-heterocycle ligand π*-orbitals. DFT calculations provide evidence for extensive delocalization of bonds over the sulfur, iron, and (α-imino)-N-heterocycle, and TD-DFT shows that the intense optical CT bands involve transitions between a mixed Fe/S donor, and (α-imino)-N-heterocycle π*-acceptor orbital. The energies and intensities of the optical and S K-edge pre-edge XAS transitions are shown to correlate with N-heterocycle ring size, as do the redox potentials. When the thiolate is replaced with a thioether, or when the low-spin S = 0 Fe(II) is replaced with a high-spin S = 3/2 Co(II), the N-heterocycle ligand metrical parameters and electronic structure do not change relative to the neutral L0 ligand. With respect to the development of future catalysts containing redox-active ligands, the energy cost of storing reducing equivalents is shown to be lowest when a quinoline, as opposed to imidazole or pyridine, is incorporated into the ligand backbone of the corresponding Fe complex.
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Affiliation(s)
- Benjamin K. Leipzig
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Julian A. Rees
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Joanna K. Kowalska
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34–36, D–45470 Mülheim an der Ruhr, Germany
| | - Roslyn M. Theisen
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | | | | | - Werner Kaminsky
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34–36, D–45470 Mülheim an der Ruhr, Germany
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34–36, D–45470 Mülheim an der Ruhr, Germany
| | - Julie A. Kovacs
- The Department of Chemistry, University of Washington, Box 351700, Seattle, Washington 98195-1700, United States
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46
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Miłaczewska A, Kot E, Amaya JA, Makris TM, Zając M, Korecki J, Chumakov A, Trzewik B, Kędracka-Krok S, Minor W, Chruszcz M, Borowski T. On the Structure and Reaction Mechanism of Human Acireductone Dioxygenase. Chemistry 2018; 24:5225-5237. [PMID: 29193386 DOI: 10.1002/chem.201704617] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Indexed: 12/24/2022]
Abstract
Acireductone dioxygenase (ARD) is an intriguing enzyme from the methionine salvage pathway that is capable of catalysing two different oxidation reactions with the same substrate depending on the type of the metal ion in the active site. To date, the structural information regarding the ARD-acireductone complex is limited and possible reaction mechanisms are still under debate. The results of joint experimental and computational studies undertaken to advance knowledge about ARD are reported. The crystal structure of an ARD from Homo sapiens was determined with selenomethionine. EPR spectroscopy suggested that binding acireductone triggers one protein residue to dissociate from Fe2+ , which allows NO (and presumably O2 ) to bind directly to the metal. Mössbauer spectroscopic data (interpreted with the aid of DFT calculations) was consistent with bidentate binding of acireductone to Fe2+ and concomitant dissociation of His88 from the metal. Major features of Fe vibrational spectra obtained for the native enzyme and upon addition of acireductone were reproduced by QM/MM calculations for the proposed models. A computational (QM/MM) study of the reaction mechanisms suggests that Fe2+ promotes O-O bond homolysis, which elicits cleavage of the C1-C2 bond of the substrate. Higher M3+ /M2+ redox potentials of other divalent metals do not support this pathway, and instead the reaction proceeds similarly to the key reaction step in the quercetin 2,3-dioxygenase mechanism.
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Affiliation(s)
- Anna Miłaczewska
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland.,University of Virginia, Department of Molecular Physiology and Biological Physics, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Ewa Kot
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland
| | - José A Amaya
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Thomas M Makris
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Marcin Zając
- National Synchrotron Radiation Centre Solaris, Jagiellonian University, ul. Czerwone Maki 98, 30-392, Kraków, Poland
| | - Józef Korecki
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland.,AGH University of Science and Technology, Faculty of Physics and Applied Computer Science, al. Mickiewicza 30, 30-059, Kraków, Poland
| | - Aleksandr Chumakov
- European Synchrotron Radiation Facility (ESRF), P.O. Box 220, F-, 38043, Grenoble, France
| | - Bartosz Trzewik
- Jagiellonian University, Faculty of Chemistry, ul. Romana Ingardena 3, 30-060, Kraków, Poland
| | - Sylwia Kędracka-Krok
- Department of Physical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Krakow, Poland.,Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387, Krakow, Poland
| | - Władek Minor
- University of Virginia, Department of Molecular Physiology and Biological Physics, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Maksymilian Chruszcz
- University of South Carolina, Department of Chemistry and Biochemistry, 631 Sumter Street, Columbia, SC, 29208, USA
| | - Tomasz Borowski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239, Krakow, Poland
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47
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Castillo RG, Banerjee R, Allpress CJ, Rohde GT, Bill E, Que L, Lipscomb JD, DeBeer S. High-Energy-Resolution Fluorescence-Detected X-ray Absorption of the Q Intermediate of Soluble Methane Monooxygenase. J Am Chem Soc 2017; 139:18024-18033. [PMID: 29136468 PMCID: PMC5729100 DOI: 10.1021/jacs.7b09560] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Kα high-energy-resolution fluorescence detected X-ray absorption spectroscopy (HERFD XAS) provides a powerful tool for overcoming the limitations of conventional XAS to identify the electronic structure and coordination environment of metalloprotein active sites. Herein, Fe Kα HERFD XAS is applied to the diiron active site of soluble methane monooxygenase (sMMO) and to a series of high-valent diiron model complexes, including diamond-core [FeIV2(μ-O)2(L)2](ClO4)4] (3) and open-core [(O═FeIV-O-FeIV(OH)(L)2](ClO4)3 (4) models (where, L = tris(3,5-dimethyl-4-methoxypyridyl-2-methyl)amine) (TPA*)). Pronounced differences in the HERFD XAS pre-edge energies and intensities are observed for the open versus closed Fe2O2 cores in the model compounds. These differences are reproduced by time-dependent density functional theory (TDDFT) calculations and allow for the pre-edge energies and intensity to be directly correlated with the local active site geometric and electronic structure. A comparison of the model complex HERFD XAS data to that of MMOHQ (the key intermediate in methane oxidation) is supportive of an open-core structure. Specifically, the large pre-edge area observed for MMOHQ may be rationalized by invoking an open-core structure with a terminal FeIV═O motif, though further modulations of the core structure due to the protein environment cannot be ruled out. The present study thus motivates the need for additional experimental and theoretical studies to unambiguously assess the active site conformation of MMOHQ.
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Affiliation(s)
- Rebeca G. Castillo
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34, D-45470 Mülheim an der Ruhr, Germany
| | - Rahul Banerjee
- Department of Biochemistry, Molecular Biology and Biophysics, 321 Church St. SE, Minneapolis, MN 55455
| | - Caleb J. Allpress
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455
| | - Gregory T. Rohde
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455
| | - Eckhard Bill
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34, D-45470 Mülheim an der Ruhr, Germany
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, MN 55455
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, 321 Church St. SE, Minneapolis, MN 55455
| | - Serena DeBeer
- Max Planck Institute for Chemical Energy Conversion, Stiftstrasse 34, D-45470 Mülheim an der Ruhr, Germany
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48
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Garai M, Dey D, Yadav HR, Choudhury AR, Maji M, Biswas B. Catalytic Fate of Two Copper Complexes towards Phenoxazinone Synthase and Catechol Dioxygenase Activity. ChemistrySelect 2017. [DOI: 10.1002/slct.201702113] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mamoni Garai
- Department of Chemistry; Raghunathpur College; Purulia 723 133,West Bengal India
| | - Dhananjay Dey
- Department of Chemistry; Raghunathpur College; Purulia 723 133,West Bengal India
| | - Hare Ram Yadav
- Department of Chemical Sciences; Indian Institute of Science Education and Research, S.A.S. Nagar, Sector 81, Manauli PO; Mohali 140 306 India
| | - Angshuman Roy Choudhury
- Department of Chemical Sciences; Indian Institute of Science Education and Research, S.A.S. Nagar, Sector 81, Manauli PO; Mohali 140 306 India
| | - Milan Maji
- Department of Chemistry; National Institute of Technology; Durgapur 713209, West Bengal India
| | - Bhaskar Biswas
- Department of Chemistry; Raghunathpur College; Purulia 723 133,West Bengal India
- Present Address: Department of Chemistry; Surendranath College; 24/2 M.G. Road, Kolkata 700009, West Bengal India
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49
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Roy S, Kästner J. Catalytic Mechanism of Salicylate Dioxygenase: QM/MM Simulations Reveal the Origin of Unexpected Regioselectivity of the Ring Cleavage. Chemistry 2017; 23:8949-8962. [DOI: 10.1002/chem.201701286] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Subhendu Roy
- Institute for Theoretical Chemistry; University of Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Germany
| | - Johannes Kästner
- Institute for Theoretical Chemistry; University of Stuttgart; Pfaffenwaldring 55 70569 Stuttgart Germany
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50
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Bernasconi L, Kazaryan A, Belanzoni P, Baerends EJ. Catalytic Oxidation of Water with High-Spin Iron(IV)–Oxo Species: Role of the Water Solvent. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00568] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Leonardo Bernasconi
- STFC
Rutherford Appleton Laboratory, Harwell Oxford, Didcot OX11 0QX, United Kingdom
| | - Andranik Kazaryan
- Theoretical
Chemistry Section, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Paola Belanzoni
- Department
of Chemistry, Biology and Biotechnology, University of Perugia and Institute of Molecular Science and Technologies (ISTM-CNR), Via Elce
di Sotto 8, I-06123 Perugia, Italy
| | - Evert Jan Baerends
- Theoretical
Chemistry Section, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
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