1
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Hota PK, Panda S, Phan H, Kim B, Siegler MA, Karlin KD. Dioxygenase Chemistry in Nucleophilic Aldehyde Deformylations Utilizing Dicopper O 2-Derived Peroxide Complexes. J Am Chem Soc 2024; 146:23854-23871. [PMID: 39141923 DOI: 10.1021/jacs.4c06243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/16/2024]
Abstract
The chemistry of copper-dioxygen complexes is relevant to copper enzymes in biology as well as in (ligand)Cu-O2 (or Cu2-O2) species utilized in oxidative transformations. For overall energy considerations, as applicable in chemical synthesis, it is beneficial to have an appropriate atom economy; both O-atoms of O2(g) are transferred to the product(s). However, examples of such dioxygenase-type chemistry are extremely rare or not well documented. Herein, we report on nucleophilic oxidative aldehyde deformylation reactivity by the peroxo-dicopper(II) species [Cu2II(BPMPO-)(O22-)]1+ {BPMPO-H = 2,6-bis{[(bis(2-pyridylmethyl)amino]methyl}-4-methylphenol)} and [Cu2II(XYLO-)(O22-)]1+ (XYLO- = a BPMPO- analogue possessing bis(2-{2-pyridyl}ethyl)amine chelating arms). Their dicopper(I) precursors are dioxygenase catalysts. The O2(g)-derived peroxo-dicopper(II) intermediates react rapidly with aldehydes like 2-phenylpropionaldehyde (2-PPA) and cyclohexanecarboxaldehyde (CCA) in 2-methyltetrahydrofuran at -90 °C. Warming to room temperature (RT) followed by workup results in good yields of formate (HC(O)O-) along with ketones (acetophenone or cyclohexanone). Mechanistic investigation shows that [Cu2II(BPMPO-)(O22-)]1+ species initially reacts reversibly with the aldehydes to form detectable dicopper(II) peroxyhemiacetal intermediates, for which optical titrations provide the Keq (at -90 °C) of 73.6 × 102 M-1 (2-PPA) and 10.4 × 102 M-1 (CCA). In the reaction of [Cu2II(XYLO-)(O22-)]1+ with 2-PPA, product complexes characterized by single-crystal X-ray crystallography are the anticipated dicopper(I) complex, [Cu2I(XYLO-)]1+ plus a mixed-valent Cu(I)Cu(II)-formate species. Formate was further identified and confirmed by 1H NMR spectroscopy and electrospray ionization mass spectrometry (ESI-MS) analysis. Using 18O2(g)-isotope labeling the reaction produced a high yield of 18-O incorporated acetophenone as well as formate. The overall results signify that true dioxygenase reactions have occurred, supported by a thorough mechanistic investigation.
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Affiliation(s)
- Pradip Kumar Hota
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Sanjib Panda
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Hai Phan
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Bohee Kim
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Kenneth D Karlin
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
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2
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Mukherjee G, Velmurugan G, Kerscher M, Kumar Satpathy J, Sastri CV, Comba P. Mechanistic Insights into Amphoteric Reactivity of an Iron-Bispidine Complex. Chemistry 2024; 30:e202303127. [PMID: 37942658 DOI: 10.1002/chem.202303127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 11/10/2023]
Abstract
The reactivity of FeIII -alkylperoxido complexes has remained a riddle to inorganic chemists owing to their thermal instability and impotency towards organic substrates. These iron-oxygen adducts have been known as sluggish oxidants towards oxidative electrophilic and nucleophilic reactions. Herein, we report the synthesis and spectroscopic characterization of a relatively stable mononuclear high-spin FeIII -alkylperoxido complex supported by an engineered bispidine framework. Against the notion, this FeIII -alkylperoxido complex serves as a rare example of versatile reactivity in both electrophilic and nucleophilic reactions. Detailed mechanistic studies and computational calculations reveal a novel reaction mechanism, where a putative superoxido intermediate orchestrates the amphoteric property of the oxidant. The design of the backbone is pivotal to convey stability and reactivity to alkylperoxido and superoxido intermediates. Contrary to the well-known O-O bond cleavage that generates an FeIV -oxido species, the FeIII -alkylperoxido complex reported here undergoes O-C bond scission to generate a superoxido moiety that is responsible for the amphiphilic reactivity.
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Affiliation(s)
- Gourab Mukherjee
- Department of Catalysis & Fine Chemicals, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad, 500007, India
| | - Gunasekaran Velmurugan
- Anorganisch-Chemisches Institut and, Interdisciplinary Center for Scientific Computing (IWR), Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany)
| | - Marion Kerscher
- Anorganisch-Chemisches Institut and, Interdisciplinary Center for Scientific Computing (IWR), Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany)
| | - Jagnyesh Kumar Satpathy
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Peter Comba
- Anorganisch-Chemisches Institut and, Interdisciplinary Center for Scientific Computing (IWR), Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany)
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3
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Jeong D, Selverstone Valentine J, Cho J. Bio-inspired mononuclear nonheme metal peroxo complexes: Synthesis, structures and mechanistic studies toward understanding enzymatic reactions. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2023.215021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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4
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Jeong D, Kim H, Cho J. Oxidation of Aldehydes into Carboxylic Acids by a Mononuclear Manganese(III) Iodosylbenzene Complex through Electrophilic C-H Bond Activation. J Am Chem Soc 2023; 145:888-897. [PMID: 36598425 DOI: 10.1021/jacs.2c09274] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The oxidation of aldehyde is one of the fundamental reactions in the biological system. Various synthetic procedures and catalysts have been developed to convert aldehydes into corresponding carboxylic acids efficiently under ambient conditions. In this work, we report the oxidation of aldehydes by a mononuclear manganese(III) iodosylbenzene complex, [MnIII(TBDAP)(OIPh)(OH)]2+ (1), with kinetic and mechanistic studies in detail. The reaction of 1 with aldehydes resulted in the formation of corresponding carboxylic acids via a pre-equilibrium state. Hammett plot and reaction rates of 1 with 1°-, 2°-, and 3°-aldehydes revealed the electrophilicity of 1 in the aldehyde oxidation. A kinetic isotope effect experiment and reactivity of 1 toward cyclohexanecarboxaldehyde (CCA) analogues indicate that the reaction of 1 with aldehyde occurs through the rate-determining C-H bond activation at the formyl group. The reaction rate of 1 with CCA is correlated to the bond dissociation energy of the formyl group plotting a linear correlation with other aliphatic C-H bonds. Density functional theory calculations found that 1 electrostatically interacts with CCA at the pre-equilibrium state in which the C-H bond activation of the formyl group is performed as the most feasible pathway. Surprisingly, the rate-determining step is characterized as hydride transfer from CCA to 1, affording an (oxo)methylium intermediate. At the fundamental level, it is revealed that the hydride transfer is composed of H atom abstraction followed by a fast electron transfer. Catalytic reactions of aldehydes by 1 are also presented with a broad substrate scope. This novel mechanistic study gives better insights into the metal oxygen chemistry and would be prominently valuable for development of transition metal catalysts.
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Affiliation(s)
- Donghyun Jeong
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan44919, Republic of Korea
| | - Hyokyung Kim
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan44919, Republic of Korea
| | - Jaeheung Cho
- Department of Chemistry, Ulsan National Institute of Science and Technology (UNIST), Ulsan44919, Republic of Korea.,Graduate School of Carbon Neutrality, Ulsan National Institute of Science and Technology (UNIST), Ulsan44919, Republic of Korea
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5
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Wang L, Chen Z, Fan G, Liu X, Liu P. Organophotoredox and Hydrogen Atom Transfer Cocatalyzed C-H Alkylation of Quinoxalin-2(1 H)-ones with Aldehydes, Amides, Alcohols, Ethers, or Cycloalkanes. J Org Chem 2022; 87:14580-14587. [PMID: 36206555 DOI: 10.1021/acs.joc.2c01967] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Described is a mild method that merges organophotoredox catalysis with hydrogen atom transfer to enable C-H alkylation of quinoxalin-2(1H)-ones with feedstock aldehydes, amides, alcohols, ethers, or cycloalkanes. This reaction occurred under environmentally benign and external oxidant-free reaction conditions, providing a general and sustainable access to various C3-alkylated quinoxalinone derivatives with broad substituent diversity and good functional group compatibility.
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Affiliation(s)
- Liling Wang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Zhaoxing Chen
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Guohua Fan
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China
| | - Xiaozu Liu
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
| | - Peijun Liu
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, School of Pharmacy, Zunyi Medical University, Zunyi 563000, China.,Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563000, China
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6
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Lueckheide MJ, Ertem MZ, Michon MA, Chmielniak P, Robinson JR. Peroxide-Selective Reduction of O 2 at Redox-Inactive Rare-Earth(III) Triflates Generates an Ambiphilic Peroxide. J Am Chem Soc 2022; 144:17295-17306. [PMID: 36083877 DOI: 10.1021/jacs.2c08140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Metal peroxides are key species involved in a range of critical biological and synthetic processes. Rare-earth (group III and the lanthanides; Sc, Y, La-Lu) peroxides have been implicated as reactive intermediates in catalysis; however, reactivity studies of isolated, structurally characterized rare-earth peroxides have been limited. Herein, we report the peroxide-selective (93-99% O22-) reduction of dioxygen (O2) at redox-inactive rare-earth triflates in methanol using a mild metallocene reductant, decamethylferrocene (Fc*). The first molecular praseodymium peroxide ([PrIII2(O22-)(18C6)2(EG)2][OTf]4; 18C6 = 18-crown-6, EG = ethylene glycol, -OTf = -O3SCF3; 2-Pr) was isolated and characterized by single-crystal X-ray diffraction, Raman spectroscopy, and NMR spectroscopy. 2-Pr displays high thermal stability (120 °C, 50 mTorr), is protonated by mild organic acids [pKa1(MeOH) = 5.09 ± 0.23], and engages in electrophilic (e.g., oxygen atom transfer) and nucleophilic (e.g., phosphate-ester cleavage) reactivity. Our mechanistic studies reveal that the rate of oxygen reduction is dictated by metal-ion accessibility, rather than Lewis acidity, and suggest new opportunities for differentiated reactivity of redox-inactive metal ions by leveraging weak metal-ligand binding events preceding electron transfer.
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Affiliation(s)
- Matthew J Lueckheide
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Mehmed Z Ertem
- Chemistry Division, Energy & Photon Sciences, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Michael A Michon
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Pawel Chmielniak
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Jerome R Robinson
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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7
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Zhao R, Zhang BB, Liu Z, Cheng GJ, Wang ZX. DFT Mechanistic Insights into Aldehyde Deformylations with Biomimetic Metal-Dioxygen Complexes: Distinct Mechanisms and Reaction Rules. JACS AU 2022; 2:745-761. [PMID: 35373207 PMCID: PMC8970012 DOI: 10.1021/jacsau.2c00014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Indexed: 05/12/2023]
Abstract
Aldehyde deformylations occurring in organisms are catalyzed by metalloenzymes through metal-dioxygen active cores, attracting great interest to study small-molecule metal-dioxygen complexes for understanding relevant biological processes and developing biomimetic catalysts for aerobic transformations. As the known deformylation mechanisms, including nucleophilic attack, aldehyde α-H-atom abstraction, and aldehyde hydrogen atom abstraction, undergo outer-sphere pathways, we herein report a distinct inner-sphere mechanism based on density functional theory (DFT) mechanistic studies of aldehyde deformylations with a copper (II)-superoxo complex. The inner-sphere mechanism proceeds via a sequence mainly including aldehyde end-on coordination, homolytic aldehyde C-C bond cleavage, and dioxygen O-O bond cleavage, among which the C-C bond cleavage is the rate-determining step with a barrier substantially lower than those of outer-sphere pathways. The aldehyde C-C bond cleavage, enabled through the activation of the dioxygen ligand radical in a second-order nucleophilic substitution (SN2)-like fashion, leads to an alkyl radical and facilitates the subsequent dioxygen O-O bond cleavage. Furthermore, we deduced the rules for the reactions of metal-dioxygen complexes with aldehydes and nitriles via the inner-sphere mechanism. Expectedly, our proposed inner-sphere mechanisms and the reaction rules offer another perspective to understand relevant biological processes involving metal-dioxygen cores and to discover metal-dioxygen catalysts for aerobic transformations.
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Affiliation(s)
- Ruihua Zhao
- School
of Chemical Sciences, University of Chinese
Academy of Sciences, Beijing 100039, China
- Warshel
Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
| | - Bei-Bei Zhang
- School
of Chemical Sciences, University of Chinese
Academy of Sciences, Beijing 100039, China
| | - Zheyuan Liu
- College
of Materials Science and Engineering, Fuzhou
University, Fuzhou 350108, China
| | - Gui-Juan Cheng
- Warshel
Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
| | - Zhi-Xiang Wang
- School
of Chemical Sciences, University of Chinese
Academy of Sciences, Beijing 100039, China
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8
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Henry Martínez Q, Valezi DF, Di Mauro E, Páez-Mozo EA, Fernando Martínez O. Characterization of peroxo-Mo and superoxo-Mo intermediate adducts in Photo-Oxygen Atom Transfer with O2. Catal Today 2022. [DOI: 10.1016/j.cattod.2022.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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9
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Oloo WN, Szávuly M, Kaizer J, Que L. Nonheme Diiron Oxygenase Mimic That Generates a Diferric-Peroxo Intermediate Capable of Catalytic Olefin Epoxidation and Alkane Hydroxylation Including Cyclohexane. Inorg Chem 2022; 61:37-41. [PMID: 34894683 PMCID: PMC8958355 DOI: 10.1021/acs.inorgchem.1c03468] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Herein are described substrate oxidations with H2O2 catalyzed by [FeII(IndH)(CH3CN)3](ClO4)2 [IndH = 1,3-bis(2'-pyridylimino)isoindoline], involving a spectroscopically characterized (μ-oxo)(μ-1,2-peroxo)diiron(III) intermediate (2) that is capable of olefin epoxidation and alkane hydroxylation including cyclohexane. Species 2 also converts ketones to lactones with a decay rate dependent on [ketone], suggesting direct nucleophilic attack of the substrate carbonyl group by the peroxo species. In contrast, peroxo decay is unaffected by the addition of olefins or alkanes, but the label from H218O is incorporated into the the epoxide and alcohol products, implicating a high-valent iron-oxo oxidant that derives from O-O bond cleavage of the peroxo intermediate. These results demonstrate an ambiphilic diferric-peroxo intermediate that mimics the range of oxidative reactivities associated with O2-activating nonheme diiron enzymes.
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Affiliation(s)
- Williamson N Oloo
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Miklós Szávuly
- Research Group of Bioorganic and Biocoordination Chemistry, University of Pannonia, 8200 Veszprém, Hungary
| | - József Kaizer
- Research Group of Bioorganic and Biocoordination Chemistry, University of Pannonia, 8200 Veszprém, Hungary
| | - Lawrence Que
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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10
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Winslow C, Lee HB, Field MJ, Teat SJ, Rittle J. Structure and Reactivity of a High-Spin, Nonheme Iron(III)- Superoxo Complex Supported by Phosphinimide Ligands. J Am Chem Soc 2021; 143:13686-13693. [PMID: 34424708 DOI: 10.1021/jacs.1c05276] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonheme iron oxygenases utilize dioxygen to accomplish challenging chemical oxidations. A further understanding of the Fe-O2 intermediates implicated in these processes is challenged by their highly transient nature. To that end, we have developed a ligand platform featuring phosphinimide donors intended to stabilize oxidized, high-spin iron complexes. O2 exposure of single crystals of a three-coordinate Fe(II) complex of this framework allowed for in crystallo trapping of a terminally bound Fe-O2 complex suitable for XRD characterization. Spectroscopic and computational studies of this species support a high-spin Fe(III) center antiferromagnetically coupled to a superoxide ligand, similar to that proposed for numerous nonheme iron oxygenases. In addition to the apparent stability of this synthetic Fe-O2 complex, its ability to engage in a range of stoichiometric and catalytic oxidation processes demonstrates that this iron-phosphinimide system is primed for development in modeling oxidizing bioinorganic intermediates and green oxidation chemistry.
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Affiliation(s)
- Charles Winslow
- College of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Heui Beom Lee
- College of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Mackenzie J Field
- Department of Chemistry, University of California Irvine, Irvine, California 92697, United States
| | - Simon J Teat
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jonathan Rittle
- College of Chemistry, University of California Berkeley, Berkeley, California 94720, United States
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11
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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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12
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Basri RS, Rahman RNZRA, Kamarudin NHA, Ali MSM. Cyanobacterial aldehyde deformylating oxygenase: Structure, function, and potential in biofuels production. Int J Biol Macromol 2020; 164:3155-3162. [PMID: 32841666 DOI: 10.1016/j.ijbiomac.2020.08.162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/04/2020] [Accepted: 08/20/2020] [Indexed: 11/27/2022]
Abstract
The conversion of aldehydes to valuable alkanes via cyanobacterial aldehyde deformylating oxygenase is of great interest. The availability of fossil reserves that keep on decreasing due to human exploitation is worrying, and even more troubling is the combustion emission from the fuel, which contributes to the environmental crisis and health issues. Hence, it is crucial to use a renewable and eco-friendly alternative that yields compound with the closest features as conventional petroleum-based fuel, and that can be used in biofuels production. Cyanobacterial aldehyde deformylating oxygenase (ADO) is a metal-dependent enzyme with an α-helical structure that contains di‑iron at the active site. The substrate enters the active site of every ADO through a hydrophobic channel. This enzyme exhibits catalytic activity toward converting Cn aldehyde to Cn-1 alkane and formate as a co-product. These cyanobacterial enzymes are small and easy to manipulate. Currently, ADOs are broadly studied and engineered for improving their enzymatic activity and substrate specificity for better alkane production. This review provides a summary of recent progress in the study of the structure and function of ADO, structural-based engineering of the enzyme, and highlight its potential in producing biofuels.
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Affiliation(s)
- Rose Syuhada Basri
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
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13
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Mak WS, Wang X, Arenas R, Cui Y, Bertolani S, Deng WQ, Tagkopoulos I, Wilson DK, Siegel JB. Discovery, Design, and Structural Characterization of Alkane-Producing Enzymes across the Ferritin-like Superfamily. Biochemistry 2020; 59:3834-3843. [PMID: 32935984 DOI: 10.1021/acs.biochem.0c00665] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
To complement established rational and evolutionary protein design approaches, significant efforts are being made to utilize computational modeling and the diversity of naturally occurring protein sequences. Here, we combine structural biology, genomic mining, and computational modeling to identify structural features critical to aldehyde deformylating oxygenases (ADOs), an enzyme family that has significant implications in synthetic biology and chemoenzymatic synthesis. Through these efforts, we discovered latent ADO-like function across the ferritin-like superfamily in various species of Bacteria and Archaea. We created a machine learning model that uses protein structural features to discriminate ADO-like activity. Computational enzyme design tools were then utilized to introduce ADO-like activity into the small subunit of Escherichia coli class I ribonucleotide reductase. The integrated approach of genomic mining, structural biology, molecular modeling, and machine learning has the potential to be utilized for rapid discovery and modulation of functions across enzyme families.
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Affiliation(s)
- Wai Shun Mak
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - XiaoKang Wang
- Department of Biomedical Engineering, University of California, Davis, Davis, California 95616, United States
| | - Rigoberto Arenas
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States.,Chemistry Graduate Group, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Youtian Cui
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Steve Bertolani
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Wen Qiao Deng
- California College of Arts, 1111 Eighth Street, San Francisco, California 94107, United States
| | - Ilias Tagkopoulos
- Department of Biomedical Engineering, University of California, Davis, Davis, California 95616, United States.,Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616, United States.,Department of Computer Science, University of California, Davis, Davis, California 95616, United States
| | - David K Wilson
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, California 95616, United States.,Chemistry Graduate Group, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Justin B Siegel
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States.,Department of Biochemistry and Molecular Medicine, University of California, Davis, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States.,Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, California 95616, United States
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14
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Isomerization of n-C5/C6 Bioparaffins to Gasoline Components with High Octane Number. ENERGIES 2020. [DOI: 10.3390/en13071672] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The thermal and catalytic conversion processes of alternative feedstocks (e.g., waste and biomass) to different engine fuels can result in the formation of a significant amount of light hydrocarbons as by-products in the boiling range of gasoline. The properties of these C5/C6 hydrocarbons need to be improved due to many reasons, e.g., their benzene content, and/or poor oxidation stability (high olefin content) and low octane number (<60). The aim of the research work was to increase the octane number of benzene containing C5/C6 bioparaffin fractions by catalytic isomerization. These by-products were obtained from special hydrocracking of waste cooking oil to hydrocarbons in the boiling range of aviation turbine fuels (JET fuels)/diesel fuels. Experiments were carried out in a reactor system containing down-flow tubular reactors over Pt/Al2O3/Cl and Pt/H-Mordenite/Al2O3 catalysts at 115–145 °C and 230–270 °C, respectively. Based on the results obtained at different process parameter combinations, it was concluded that the hydrogenation of benzene was complete over both catalysts, and the liquid yields were higher (ca. 98% > ca. 93 %) in the case of Pt/Al2O3/Cl. In addition, the octane number was also enhanced (ca. 32 > ca. 27 unit) in the products compared to the feedstock. This was because a higher isoparaffin content can be obtained at a lower operating temperature. Moreover, cracking side reactions take place to a lesser extent. The utilization of these isomerized bio-origin light fractions can contribute to the competitiveness of second-generation biofuels.
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15
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Barman P, Cantú Reinhard FG, Bagha UK, Kumar D, Sastri CV, de Visser SP. Hydrogen by Deuterium Substitution in an Aldehyde Tunes the Regioselectivity by a Nonheme Manganese(III)-Peroxo Complex. Angew Chem Int Ed Engl 2019; 58:10639-10643. [PMID: 31108009 DOI: 10.1002/anie.201905416] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Indexed: 12/31/2022]
Abstract
Mononuclear nonheme MnIII -peroxo complexes are important intermediates in biology, and take part in oxygen activation by photosystem II. Herein, we present work on two isomeric biomimetic side-on MnIII -peroxo intermediates with bispidine ligand system and reactivity patterns with aldehydes. The complexes are characterized with UV/Vis and mass spectrometric techniques and reaction rates with cyclohexane carboxaldehyde (CCA) are measured. The reaction gives an unusual regioselectivity switch from aliphatic to aldehyde hydrogen atom abstraction upon deuteration of the substrate, leading to the corresponding carboxylic acid product for the latter, while the former gives a deformylation reaction. Mechanistic details are established from kinetic isotope effect studies and density functional theory calculations. Thus, replacement of C-H by C-D raises the hydrogen atom abstraction barriers and enables a regioselectivity switch to a competitive pathway that is slightly higher in energy.
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Affiliation(s)
- Prasenjit Barman
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Fabián G Cantú Reinhard
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Umesh Kumar Bagha
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Devesh Kumar
- Department of Physics, School of Physical and Decision Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, 226025, India
| | - Chivukula V Sastri
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, 781039, India
| | - Sam P de Visser
- Manchester Institute of Biotechnology and School of Chemical Engineering and Analytical Science, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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16
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Barman P, Cantú Reinhard FG, Bagha UK, Kumar D, Sastri CV, de Visser SP. Hydrogen by Deuterium Substitution in an Aldehyde Tunes the Regioselectivity by a Nonheme Manganese(III)–Peroxo Complex. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905416] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Prasenjit Barman
- Department of ChemistryIndian Institute of Technology Guwahati Guwahati Assam 781039 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
| | - Umesh Kumar Bagha
- Department of ChemistryIndian Institute of Technology Guwahati Guwahati Assam 781039 India
| | - Devesh Kumar
- Department of PhysicsSchool of Physical and Decision SciencesBabasaheb Bhimrao Ambedkar University Lucknow 226025 India
| | - Chivukula V. Sastri
- Department of ChemistryIndian Institute of Technology Guwahati Guwahati Assam 781039 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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17
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Liang S, Kumon T, Angnes RA, Sanchez M, Xu B, Hammond GB. Synthesis of Alkyl Halides from Aldehydes via Deformylative Halogenation. Org Lett 2019; 21:3848-3854. [PMID: 31050440 PMCID: PMC6525078 DOI: 10.1021/acs.orglett.9b01337] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An unprecedented deformylative halogenation of aldehydes to alkyl halides is presented. Under oxidative conditions, 1,4-dihydropyridine (DHP), derived from an aldehyde, generated a C(sp3)- radical that coupled with a halogen radical that was generated from inexpensive and atom-economical halogen sources (NaBr, NaI, or HCl), to yield an alkyl halide. Because of the mild conditions, a wide range of functional groups were tolerated, and excellent site selectivity was achieved.
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Affiliation(s)
- Shengzong Liang
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
| | - Tatsuya Kumon
- Faculty of Molecular Chemistry and Engineering, Kyoto Institute of Technology, Matsugasaki, Kyoto 606-8585, Japan
| | - Ricardo A. Angnes
- Chemistry Institute, State University of Campinas - Unicamp C.P. 6154, CEP.13083-970, Campinas, São Paulo, Brazil
| | - Melissa Sanchez
- California State University Fresno, 2555 East San Ramon Avenue M/S SB70, Fresno, California 93740, United States
| | - Bo Xu
- Key Laboratory of Science and Technology of Eco-Textiles, Ministry of Education, College of Chemistry, Chemical Engineering and Biotechnology, Donghua University, Shanghai 201620, China
| | - Gerald B. Hammond
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292, United States
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18
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Wei W, Siegbahn PEM, Liao R. Mechanism of the Dinuclear Iron Enzymep‐Aminobenzoate N‐oxygenase from Density Functional Calculations. ChemCatChem 2018. [DOI: 10.1002/cctc.201801072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wen‐Jie Wei
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Hubei Key Laboratory of Materials Chemistry and Service Failure School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 P. R. China
| | - Per E. M. Siegbahn
- Department of Organic Chemistry, Arrhenius LaboratoryStockholm University Stockholm SE-10691 Sweden
| | - Rong‐Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Hubei Key Laboratory of Materials Chemistry and Service Failure School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 P. R. China
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19
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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: 304] [Impact Index Per Article: 50.7] [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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20
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Shipilovskikh SA, Rubtsov AE, Malkov AV. Oxidative Dehomologation of Aldehydes with Oxygen as a Terminal Oxidant. Org Lett 2017; 19:6760-6762. [DOI: 10.1021/acs.orglett.7b03512] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Aleksandr E. Rubtsov
- Department
of Chemistry, Perm State University, Bukireva 15, Perm 614990, Russia
| | - Andrei V. Malkov
- Department
of Chemistry, Loughborough University, Loughborough, Leics LE11
3TU, U.K
- Department
of Organic Chemistry, RUDN University, 6 Miklukho-Maklaya Street, Moscow 117198, Russia
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21
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Mazziotta A, Makarov IS, Fristrup P, Madsen R. Synthetic Applications and Mechanistic Studies of the Hydroxide-Mediated Cleavage of Carbon-Carbon Bonds in Ketones. J Org Chem 2017; 82:5890-5897. [PMID: 28499339 DOI: 10.1021/acs.joc.7b00802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The hydroxide-mediated cleavage of ketones into alkanes and carboxylic acids has been reinvestigated and the substrate scope extended to benzyl carbonyl compounds. The transformation is performed with a 0.05 M ketone solution in refluxing xylene in the presence of 10 equiv of potassium hydroxide. The reaction constitutes a straightforward protocol for the synthesis of certain phenyl-substituted carboxylic acids from 2-phenylcycloalkanones. The mechanism was investigated by kinetic experiments which indicated a first order reaction in hydroxide and a full negative charge in the rate-determining step. The studies were complemented by a theoretical investigation where two possible pathways were characterized by DFT/M06-2X. The calculations showed that the scission takes place by nucleophilic attack of hydroxide on the ketone followed by fragmentation of the resulting oxyanion into the carboxylic acid and a benzyl anion.
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Affiliation(s)
- Andrea Mazziotta
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - Ilya S Makarov
- Department of Chemistry, Ludwig-Maximilians-Universität , Butenandtstrasse 5-13, 81377 Munich, Germany
| | - Peter Fristrup
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - Robert Madsen
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
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22
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Ding K, Xu S, Alotaibi R, Paudel K, Reinheimer EW, Weatherly J. Nickel-Catalyzed Decarbonylation of Aromatic Aldehydes. J Org Chem 2017; 82:4924-4929. [DOI: 10.1021/acs.joc.7b00284] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Keying Ding
- Department
of Chemistry, Middle Tennessee State University, Murfreesboro, Tennessee 37132, United States
| | - Shi Xu
- Department
of Chemistry, Middle Tennessee State University, Murfreesboro, Tennessee 37132, United States
| | - Rajeh Alotaibi
- Department
of Chemistry, Middle Tennessee State University, Murfreesboro, Tennessee 37132, United States
| | - Keshav Paudel
- Department
of Chemistry, Middle Tennessee State University, Murfreesboro, Tennessee 37132, United States
| | | | - Jessie Weatherly
- Department
of Chemistry, Middle Tennessee State University, Murfreesboro, Tennessee 37132, United States
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23
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Wise CE, Grant JL, Amaya JA, Ratigan SC, Hsieh CH, Manley OM, Makris TM. Divergent mechanisms of iron-containing enzymes for hydrocarbon biosynthesis. J Biol Inorg Chem 2016; 22:221-235. [DOI: 10.1007/s00775-016-1425-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 12/09/2016] [Indexed: 12/22/2022]
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24
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Gutiérrez-Bonet Á, Tellis JC, Matsui JK, Vara BA, Molander GA. 1,4-Dihydropyridines as Alkyl Radical Precursors: Introducing the Aldehyde Feedstock to Nickel/Photoredox Dual Catalysis. ACS Catal 2016; 6:8004-8008. [PMID: 27990318 PMCID: PMC5152669 DOI: 10.1021/acscatal.6b02786] [Citation(s) in RCA: 184] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 10/20/2016] [Indexed: 01/05/2023]
Abstract
![]()
A Ni/photoredox dual catalytic cross-coupling
is disclosed in which
a diverse range of (hetero)aryl bromides are used as electrophiles,
with 1,4-dihydropyridines serving as precursors to Csp3-centered alkyl radical coupling partners. The reported method
is characterized by its extremely mild reaction conditions, enabling
access to underexplored cores.
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Affiliation(s)
- Álvaro Gutiérrez-Bonet
- Roy and Diana Vagelos Laboratories,
Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - John C. Tellis
- Roy and Diana Vagelos Laboratories,
Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Jennifer K. Matsui
- Roy and Diana Vagelos Laboratories,
Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Brandon A. Vara
- Roy and Diana Vagelos Laboratories,
Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Gary A. Molander
- Roy and Diana Vagelos Laboratories,
Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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25
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Wang C, Zhao C, Hu L, Chen H. Calculated Mechanism of Cyanobacterial Aldehyde-Deformylating Oxygenase: Asymmetric Aldehyde Activation by a Symmetric Diiron Cofactor. J Phys Chem Lett 2016; 7:4427-4432. [PMID: 27775357 DOI: 10.1021/acs.jpclett.6b02061] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cyanobacterial aldehyde-deformylating oxygenase (cADO) is a nonheme diiron enzyme that catalyzes the conversion of aldehyde to alk(a/e)ne, an important transformation in biofuel research. In this work, we report a highly desired computational study for probing the mechanism of cADO. By combining our QM/MM results with the available 57Fe Mössbauer spectroscopic data, the gained detailed structural information suggests construction of asymmetry from the symmetric diiron cofactor in an aldehyde substrate and O2 activation. His160, one of the two iron-coordinate histidine residues in cADO, plays a pivotal role in this asymmetric aldehyde activation process by unprecedented reversible dissociation from the diiron cofactor, a behavior unknown in any other nonheme dinuclear or mononuclear enzymes. The revealed intrinsically asymmetric interactions of the substrate/O2 with the symmetric cofactor in cADO are inspirational for exploring diiron subsite resolution in other nonheme diiron enzymes.
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Affiliation(s)
- Chao Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China
| | - Chongyang Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China
| | - Lianrui Hu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
- University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China
| | - Hui Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
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26
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Sutherlin KD, Liu LV, Lee YM, Kwak Y, Yoda Y, Saito M, Kurokuzu M, Kobayashi Y, Seto M, Que L, Nam W, Solomon EI. Nuclear Resonance Vibrational Spectroscopic Definition of Peroxy Intermediates in Nonheme Iron Sites. J Am Chem Soc 2016; 138:14294-14302. [PMID: 27726349 DOI: 10.1021/jacs.6b07227] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
FeIII-(hydro)peroxy intermediates have been isolated in two classes of mononuclear nonheme Fe enzymes that are important in bioremediation: the Rieske dioxygenases and the extradiol dioxygenases. The binding mode and protonation state of the peroxide moieties in these intermediates are not well-defined, due to a lack of vibrational structural data. Nuclear resonance vibrational spectroscopy (NRVS) is an important technique for obtaining vibrational information on these and other intermediates, as it is sensitive to all normal modes with Fe displacement. Here, we present the NRVS spectra of side-on FeIII-peroxy and end-on FeIII-hydroperoxy model complexes and assign these spectra using calibrated DFT calculations. We then use DFT calculations to define and understand the changes in the NRVS spectra that arise from protonation and from opening the Fe-O-O angle. This study identifies four spectroscopic handles that will enable definition of the binding mode and protonation state of FeIII-peroxy intermediates in mononuclear nonheme Fe enzymes. These structural differences are important in determining the frontier molecular orbitals available for reactivity.
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Affiliation(s)
- Kyle D Sutherlin
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Lei V Liu
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Yong-Min Lee
- Department of Bioinspired Science, Department of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University , Seoul 120-750, Korea
| | - Yeonju Kwak
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | | | - Makina Saito
- Research Reactor Institute, Kyoto University , Osaka 590-0494, Japan
| | - Masayuki Kurokuzu
- Research Reactor Institute, Kyoto University , Osaka 590-0494, Japan
| | | | - Makoto Seto
- Research Reactor Institute, Kyoto University , Osaka 590-0494, Japan
| | - Lawrence Que
- Department of Chemistry, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Wonwoo Nam
- Department of Bioinspired Science, Department of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University , Seoul 120-750, Korea
| | - Edward I Solomon
- Department of Chemistry, Stanford University , Stanford, California 94305, United States.,SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
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27
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Rana S, Pandey B, Dey A, Haque R, Rajaraman G, Maiti D. A Doubly Biomimetic Synthetic Transformation: Catalytic Decarbonylation and Halogenation at Room Temperature by Vanadium Pentoxide. ChemCatChem 2016. [DOI: 10.1002/cctc.201600843] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Sujoy Rana
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
| | - Bhawana Pandey
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
| | - Aniruddha Dey
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
| | - Rameezul Haque
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
| | - Gopalan Rajaraman
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
| | - Debabrata Maiti
- Department of Chemistry; Indian Institute of Technology Bombay, Powai; Mumbai- 400076 India
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28
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A growing family of O2 activating dinuclear iron enzymes with key catalytic diiron(III)-peroxo intermediates: Biological systems and chemical models. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.05.014] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Ellington BR, Paul B, Das D, Vitek AK, Zimmerman PM, Marsh ENG. An Unusual Iron-Dependent Oxidative Deformylation Reaction Providing Insight into Hydrocarbon Biosynthesis in Nature. ACS Catal 2016. [DOI: 10.1021/acscatal.6b00592] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Benjamin R. Ellington
- Department of Biological Chemistry and ‡Department of
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Bishwajit Paul
- Department of Biological Chemistry and ‡Department of
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Debasis Das
- Department of Biological Chemistry and ‡Department of
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Andrew K. Vitek
- Department of Biological Chemistry and ‡Department of
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Paul M. Zimmerman
- Department of Biological Chemistry and ‡Department of
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - E. Neil G. Marsh
- Department of Biological Chemistry and ‡Department of
Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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30
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Sekino M, Furutachi H, Tasaki K, Ishikawa T, Mori S, Fujinami S, Akine S, Sakata Y, Nomura T, Ogura T, Kitagawa T, Suzuki M. New mechanistic insight into intramolecular arene hydroxylation initiated by (μ-1,2-peroxo)diiron(III) complexes with dinucleating ligands. Dalton Trans 2016; 45:469-73. [PMID: 26646073 DOI: 10.1039/c5dt04088d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
(μ-1,2-Peroxo)diiron(iii) complexes (-R) with dinucleating ligands (R-L) generated from the reaction of bis(μ-hydroxo)diiron(ii) complexes [Fe2(R-L)(OH)2](2+) (-R) with dioxygen in acetone at -20 °C provide a diiron-centred electrophilic oxidant, presumably diiron(iv)-oxo species, which is involved in aromatic ligand hydroxylation.
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Affiliation(s)
- Mio Sekino
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Hideki Furutachi
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Kyosuke Tasaki
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Takanao Ishikawa
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Shigeki Mori
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Shuhei Fujinami
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Shigehisa Akine
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Yoko Sakata
- Department of Chemistry, Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan.
| | - Takashi Nomura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Takashi Ogura
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Teizo Kitagawa
- Picobiology Institute, Graduate School of Life Science, University of Hyogo, Ako-gun, Hyogo 678-1297, Japan
| | - Masatatsu Suzuki
- Department of Chemistry and Biochemistry, Graduate Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
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31
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Corcos AR, Villanueva O, Walroth RC, Sharma SK, Bacsa J, Lancaster KM, MacBeth CE, Berry JF. Oxygen Activation by Co(II) and a Redox Non-Innocent Ligand: Spectroscopic Characterization of a Radical–Co(II)–Superoxide Complex with Divergent Catalytic Reactivity. J Am Chem Soc 2016; 138:1796-9. [DOI: 10.1021/jacs.5b12643] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Amanda R. Corcos
- Department
of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
| | - Omar Villanueva
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Richard C. Walroth
- Department
of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Savita K. Sharma
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - John Bacsa
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - Kyle M. Lancaster
- Department
of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Cora E. MacBeth
- Department
of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, United States
| | - John F. Berry
- Department
of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin 53706, United States
| |
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