101
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Liu J, Wu P, Yan S, Li Y, Cao Z, Wang B. Spin-Regulated Inner-Sphere Electron Transfer Enables Efficient O—O Bond Activation in Nonheme Diiron Monooxygenase MIOX. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jia Liu
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Peng Wu
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Shengheng Yan
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Yuanyuan Li
- College of Chemistry and Chemical Engineering, Henan University, Kaifeng, Henan 475004, China
| | - Zexing Cao
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, People’s Republic of China
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102
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Ottenbacher RV, Bryliakova AA, Shashkov MV, Talsi EP, Bryliakov KP. To Rebound or...Rebound? Evidence for the “Alternative Rebound” Mechanism in C–H Oxidations by the Systems Nonheme Mn Complex/H 2O 2/Carboxylic Acid. ACS Catal 2021. [DOI: 10.1021/acscatal.1c00811] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Roman V. Ottenbacher
- Novosibirsk State University, Pirogova 1, Novosibirsk 630090, Russian Federation
- Boreskov Institute of Catalysis, Pr. Lavrentieva 5, Novosibirsk 630090, Russian Federation
| | - Anna A. Bryliakova
- Novosibirsk State University, Pirogova 1, Novosibirsk 630090, Russian Federation
| | - Mikhail V. Shashkov
- Novosibirsk State University, Pirogova 1, Novosibirsk 630090, Russian Federation
- Boreskov Institute of Catalysis, Pr. Lavrentieva 5, Novosibirsk 630090, Russian Federation
| | - Evgenii P. Talsi
- Boreskov Institute of Catalysis, Pr. Lavrentieva 5, Novosibirsk 630090, Russian Federation
| | - Konstantin P. Bryliakov
- Novosibirsk State University, Pirogova 1, Novosibirsk 630090, Russian Federation
- Boreskov Institute of Catalysis, Pr. Lavrentieva 5, Novosibirsk 630090, Russian Federation
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103
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Xu Y, Yuan X, Chen M, Dong A, Liu B, Jiang F, Yang S, Liu X. Identification of atomically dispersed Fe-oxo species as new active sites in HZSM-5 for efficient non-oxidative methane dehydroaromatization. J Catal 2021. [DOI: 10.1016/j.jcat.2021.02.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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104
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Han SB, Ali HS, de Visser SP. Glutarate Hydroxylation by the Carbon Starvation-Induced Protein D: A Computational Study into the Stereo- and Regioselectivities of the Reaction. Inorg Chem 2021; 60:4800-4815. [DOI: 10.1021/acs.inorgchem.0c03749] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Sungho Bosco Han
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Hafiz Saqib Ali
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
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105
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Chalupský J, Srnec M. Beyond the Classical Contributions to Exchange Coupling in Binuclear Transition Metal Complexes. J Phys Chem A 2021; 125:2276-2283. [PMID: 33724818 DOI: 10.1021/acs.jpca.0c11237] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Complexes with two or more magnetically coupled metal ions have attracted considerable attention as catalysts of many vital processes, single-molecule magnets, or spin-crossover compounds. Elucidation of their electronic structures is essential for understanding their catalytic and magnetic properties. Here, we provide an unprecedented insight into exchange-coupling mechanisms between the magnetic centers in six prototypical bis-μ-oxo bimetallic M2O2 complexes, including two biologically relevant models of non-heme iron enzymes. Employing multiconfigurational/multireference methods and related orbital entanglement analysis, we revealed the essential and counterintuitive role of predominantly unoccupied valence metal d orbitals in their strong antiferromagnetic coupling. We found that the participation of these orbitals is twofold. First, they enhance the superexchange between the singly occupied d orbitals. Second, they become substantially occupied and thus directly magnetically active, which we perceive as a new mechanism of the exchange interaction between the magnetic transition metal centers.
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Affiliation(s)
- Jakub Chalupský
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, Prague 6 16610, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences, Dolejškova 3, Prague 8 18223, Czech Republic
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106
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Kerbib W, Singh S, Nautiyal D, Kumar A, Kumar S. Ni(II) complexes of tripodal N4 ligands as catalysts for alkane hydroxylation and O-arylation of phenol: Structural and reactivity effects induced by fluoro substitution. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2020.120191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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107
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Ali HS, Henchman RH, Warwicker J, de Visser SP. How Do Electrostatic Perturbations of the Protein Affect the Bifurcation Pathways of Substrate Hydroxylation versus Desaturation in the Nonheme Iron-Dependent Viomycin Biosynthesis Enzyme? J Phys Chem A 2021; 125:1720-1737. [DOI: 10.1021/acs.jpca.1c00141] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Richard H. Henchman
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemistry, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Jim Warwicker
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
| | - Sam P. de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, U.K
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108
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Chalupský J, Srnec M, Yanai T. Interpretation of Exchange Interaction through Orbital Entanglement. J Phys Chem Lett 2021; 12:1268-1274. [PMID: 33497240 DOI: 10.1021/acs.jpclett.0c03652] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recently, the analysis of single-orbital entropy and mutual information has been introduced as a tool for the investigation of contributions to the exchange (J) coupling between open-shell metal ions [Stein et al. J. Phys. Chem. Lett. 2019, 10, 6762-6770]. Here, we show that this analysis may lead to an incorrect interpretation of the J-coupling mechanism. Instead, we propose an orbital-entanglement analysis that is based on the two-electron density and that provides a coherent picture of the contributing exchange pathways, which seems fully consistent with the available J values. For this purpose, we used a prototypical bis-μ-oxo binuclear manganese complex ([Mn2O2(NH3)8]4+) and demonstrated that its antiferromagnetism (J < 0), calculated by using the active space composed of all valence pO and dMn orbitals, correlates well with the largest elements in the differential low-spin vs high-spin entanglement map. These elements correspond to interactions between the pairs of dMn orbitals mediated by the oxo-bridging out-of-plane p orbitals, representing the π superexchange pathway. We also show that the reduction of active space to manifold of the singly occupied magnetic orbitals does not lead to discrepancy between the calculated J values and entanglement maps. This contrasts to analysis of mutual information, which suggests the "direct" dMn-dMn interactions to play a dominant role for the J coupling, irrespective of the size of active space as well as of the antiferromagnetism expected. The failure is attributed to the large contribution of spin entanglement contained in the mutual information of the low-spin state, which may be regarded as the origin of the different complexity of its wave function and electron density.
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Affiliation(s)
- Jakub Chalupský
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Prague 6, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague 8, Czech Republic
| | - Takeshi Yanai
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusa Ward, Nagoya, Aichi 464-8601, Japan
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furocho, Chikusa Ward, Nagoya, Aichi 464-8601, Japan
- Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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109
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Study of the catalytic mechanism of a non-heme Fe catalyst: The role of the spin state of the iron. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2020.138282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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110
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Copeland RA, Davis KM, Shoda TKC, Blaesi EJ, Boal AK, Krebs C, Bollinger JM. An Iron(IV)-Oxo Intermediate Initiating l-Arginine Oxidation but Not Ethylene Production by the 2-Oxoglutarate-Dependent Oxygenase, Ethylene-Forming Enzyme. J Am Chem Soc 2021; 143:2293-2303. [PMID: 33522811 DOI: 10.1021/jacs.0c10923] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Ethylene-forming enzyme (EFE) is an ambifunctional iron(II)- and 2-oxoglutarate-dependent (Fe/2OG) oxygenase. In its major (EF) reaction, it converts carbons 1, 2, and 5 of 2OG to CO2 and carbons 3 and 4 to ethylene, a four-electron oxidation drastically different from the simpler decarboxylation of 2OG to succinate mediated by all other Fe/2OG enzymes. EFE also catalyzes a minor reaction, in which the normal decarboxylation is coupled to oxidation of l-arginine (a required activator for the EF pathway), resulting in its conversion to l-glutamate semialdehyde and guanidine. Here we show that, consistent with precedent, the l-Arg-oxidation (RO) pathway proceeds via an iron(IV)-oxo (ferryl) intermediate. Use of 5,5-[2H2]-l-Arg slows decay of the ferryl complex by >16-fold, implying that RO is initiated by hydrogen-atom transfer (HAT) from C5. That this large substrate deuterium kinetic isotope effect has no impact on the EF:RO partition ratio implies that the same ferryl intermediate cannot be on the EF pathway; the pathways must diverge earlier. Consistent with this conclusion, the variant enzyme bearing the Asp191Glu ligand substitution accumulates ∼4 times as much of the ferryl complex as the wild-type enzyme and exhibits a ∼40-fold diminished EF:RO partition ratio. The selective detriment of this nearly conservative substitution to the EF pathway implies that it has unusually stringent stereoelectronic requirements. An active-site, like-charge guanidinium pair, which involves the l-Arg substrate/activator and is unique to EFE among four crystallographically characterized l-Arg-modifying Fe/2OG oxygenases, may serve to selectively stabilize the transition state leading to the unique EF branch.
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111
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Wolford NJ, Radovic A, Neidig ML. C-Term magnetic circular dichroism (MCD) spectroscopy in paramagnetic transition metal and f-element organometallic chemistry. Dalton Trans 2021; 50:416-428. [PMID: 33315022 DOI: 10.1039/d0dt03730c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Magnetic circular dichroism (MCD) spectroscopy is a powerful experiment used to probe the electronic structure and bonding in paramagnetic metal-based complexes. While C-term MCD spectroscopy has been utilized in many areas of chemistry, it has been underutilized in studying paramagnetic organometallic transition metal and f-element complexes. From the analysis of isolated organometallic complexes to the study of in situ generated species, MCD can provide information regarding ligand interactions, oxidation and spin state, and geometry and coordination environment of paramagnetic species. The pratical aspects of this technique, such as air-free sample preparation and cryogenic experimental temperatures, allow for the study of highly unstable species, something that is often difficult with other spectroscopic techniques. This perspective highlights MCD studies of both transition metal and f-element organometallic complexes, including in situ generated reactive intermediates, to demonstrate the utility of this technique in probing electronic structure, bonding and mechanism in paramagnetic organometallic chemistry.
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Affiliation(s)
- Nikki J Wolford
- Department of Chemistry, University of Rochester, Rochester, New York 14627, USA.
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112
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Shen H, Peng H, Cao R, Yang L, Gao Y, Turak A, Thomas T, Guo X, Zhu Y, Wang J, Yang M. Oxygen Coordination on Fe-N-C to Boost Oxygen Reduction Catalysis. J Phys Chem Lett 2021; 12:517-524. [PMID: 33375789 DOI: 10.1021/acs.jpclett.0c02812] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The coordination environments of iron (Fe) in Fe-N-C catalysts determine their intrinsic activities toward oxygen reduction reactions (ORR). The precise atomic-level regulation of the local coordination environments is thus of critical importance yet quite challenging to achieve. Here, atomically dispersed Fe-N-C catalyst with O-Fe-N2C2 moieties is thoroughly studied for ORR catalysis. Advanced synchrotron X-ray characterizations, along with theoretical modeling, explicitly unraveled the penta-coordinated nature of the Fe center in the catalytic domain and the energetically optimized ORR pathways on the well-tailored O-Fe-N2C2 moieties. The combined structure identification from both experiments and theory provides an opportunity to understand the role of the coordination environments in directing the catalytic activity of single-atom or single-site catalysts; not only the center metal atom but also the whole coordinating atoms participate in the catalytic cycle.
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Affiliation(s)
- Hangjia Shen
- Solid State Functional Materials Research Laboratory, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, China
| | - Hongjie Peng
- Department of Chemical Engineering, Stanford University, Stanford, California 94305, United States
| | - Rui Cao
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Liu Yang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yan Gao
- School of Automation Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Ayse Turak
- Department of Engineering Physics, McMaster University, Hamilton L8S4L7, Canada
| | - Tiju Thomas
- Department of Metallurgical and Materials Engineering, Indian Institute of Technology Madras, Adyar, Chennai 600036, Tamil Nadu, India
| | - Xuyun Guo
- Department of Applied Physics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
| | - Ye Zhu
- Department of Applied Physics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong, China
| | - Jiacheng Wang
- Solid State Functional Materials Research Laboratory, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, China
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, China
| | - Minghui Yang
- Solid State Functional Materials Research Laboratory, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, China
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113
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Yadav V, Siegler MA, Goldberg DP. Temperature-Dependent Reactivity of a Non-heme Fe III(OH)(SR) Complex: Relevance to Isopenicillin N Synthase. J Am Chem Soc 2021; 143:46-52. [PMID: 33356198 DOI: 10.1021/jacs.0c09688] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Non-heme iron complexes with cis-FeIII(OH)(SAr/OAr) coordination were isolated and examined for their reactivity with a tertiary carbon radical. The sulfur-ligated complex shows a temperature dependence on •OH versus ArS• transfer, whereas the oxygen-ligated complex does not. These results provide the first working model for C-S bond formation in isopenicillin N synthase and indicate that kinetic control may be a key factor in the selectivity of non-heme iron "rebound" processes.
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Affiliation(s)
- Vishal Yadav
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - David P Goldberg
- Department of Chemistry, The Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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114
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Kumar A, Kurbah SD, Syiemlieh I, Dhanpat SA, Borthakur R, Lal RA. Synthesis, characterization, reactivity, and catalytic studies of heterobimetallic vanadium(V) complexes containing hydrazone ligands. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2020.120068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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115
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Basak T, Frontera A, Chattopadhyay S. Insight into non-covalent interactions in two triamine-based mononuclear iron( iii) Schiff base complexes with special emphasis on the formation of Br⋯π halogen bonding. CrystEngComm 2021. [DOI: 10.1039/d0ce01534b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The nature and characteristics of noncovalent interactions that play important roles in the crystal packing of two iron(iii) complexes have been discussed.
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Affiliation(s)
- Tanmoy Basak
- Department of Chemistry
- Inorganic Section
- Jadavpur University
- Kolkata 700032
- India
| | - Antonio Frontera
- Departamento de Química
- Universitat de les IllesBalears
- 07122 Palma
- Spain
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116
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Ali HS, Henchman RH, de Visser SP. What Determines the Selectivity of Arginine Dihydroxylation by the Nonheme Iron Enzyme OrfP? Chemistry 2020; 27:1795-1809. [PMID: 32965733 DOI: 10.1002/chem.202004019] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/22/2020] [Indexed: 12/13/2022]
Abstract
The nonheme iron enzyme OrfP reacts with l-Arg selectively to form the 3R,4R-dihydroxyarginine product, which in mammals can inhibit the nitric oxide synthase enzymes involved in blood pressure control. To understand the mechanisms of dioxygen activation of l-Arg by OrfP and how it enables two sequential oxidation cycles on the same substrate, we performed a density functional theory study on a large active site cluster model. We show that substrate binding and positioning in the active site guides a highly selective reaction through C3 -H hydrogen atom abstraction. This happens despite the fact that the C3 -H and C4 -H bond strengths of l-Arg are very similar. Electronic differences in the two hydrogen atom abstraction pathways drive the reaction with an initial C3 -H activation to a low-energy 5 σ-pathway, while substrate positioning destabilizes the C4 -H abstraction and sends it over the higher-lying 5 π-pathway. We show that substrate and monohydroxylated products are strongly bound in the substrate binding pocket and hence product release is difficult and consequently its lifetime will be long enough to trigger a second oxygenation cycle.
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Affiliation(s)
- Hafiz Saqib Ali
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Richard H Henchman
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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117
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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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118
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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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119
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Hofmann AJ, Niederegger L, Hess CR. Neighbouring effects on catalytic epoxidation by Fe-cyclam in M 2-PDIxCy complexes. Dalton Trans 2020; 49:17642-17648. [PMID: 33226393 DOI: 10.1039/d0dt03758c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The unsymmetric PDIeCy ligand, featuring pyridinediimine and cylam sites, can be selectively metalated. Complementing the diiron compound, we have synthesized two heterobimetallic isomers, [ZnPDIFeCy(PDIeCy)(OTf)4] (3) and [FePDIZnCy(PDIeCy)(OTf)4] (4), and a dizinc complex, [Zn2(PDIeCy)(OTf)4] (5). Olefin epoxidation by the series of complexes was investigated. The M-PDI site influences the reactivity of the M-cyclam, resulting in increased activity toward enones.
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Affiliation(s)
- Andreas J Hofmann
- Technische Universität München, Department of Chemistry and Catalysis Research Center, 85747 Garching, Germany.
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120
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Andris E, Segers K, Mehara J, Rulíšek L, Roithová J. Closed Shell Iron(IV) Oxo Complex with an Fe–O Triple Bond: Computational Design, Synthesis, and Reactivity. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202009347] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Erik Andris
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Koen Segers
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Jaya Mehara
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences Flemingovo náměstí 2 16610 Praha 6 Czech Republic
| | - Jana Roithová
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
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121
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Andris E, Segers K, Mehara J, Rulíšek L, Roithová J. Closed Shell Iron(IV) Oxo Complex with an Fe-O Triple Bond: Computational Design, Synthesis, and Reactivity. Angew Chem Int Ed Engl 2020; 59:23137-23144. [PMID: 32926539 PMCID: PMC7756500 DOI: 10.1002/anie.202009347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Indexed: 12/11/2022]
Abstract
Iron(IV)-oxo intermediates in nature contain two unpaired electrons in the Fe-O antibonding orbitals, which are thought to contribute to their high reactivity. To challenge this hypothesis, we designed and synthesized closed-shell singlet iron(IV) oxo complex [(quinisox)Fe(O)]+ (1+ ; quinisox-H=(N-(2-(2-isoxazoline-3-yl)phenyl)quinoline-8-carboxamide). We identified the quinisox ligand by DFT computational screening out of over 450 candidates. After the ligand synthesis, we detected 1+ in the gas phase and confirmed its spin state by visible and infrared photodissociation spectroscopy (IRPD). The Fe-O stretching frequency in 1+ is 960.5 cm-1 , consistent with an Fe-O triple bond, which was also confirmed by multireference calculations. The unprecedented bond strength is accompanied by high gas-phase reactivity of 1+ in oxygen atom transfer (OAT) and in proton-coupled electron transfer reactions. This challenges the current view of the spin-state driven reactivity of the Fe-O complexes.
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Affiliation(s)
- Erik Andris
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610Praha 6Czech Republic
| | - Koen Segers
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Jaya Mehara
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of SciencesFlemingovo náměstí 216610Praha 6Czech Republic
| | - Jana Roithová
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
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122
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Ganguly S, Mayans J, Ghosh A. Modulation of Nuclearity in Cu II -Mn II Complexes of a N 2 O 2 Donor Ligand Depending upon Carboxylate Anions: Structures, Magnetic Properties and Catalytic Oxidase Activities. Chem Asian J 2020; 15:4055-4069. [PMID: 32722886 DOI: 10.1002/asia.202000706] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 07/24/2020] [Indexed: 12/12/2022]
Abstract
Three new hetero-metallic copper(II)-manganese(II) complexes, [(CuL)2 Mn3 (C6 H5 CO2 )6 ] (1), [(CuL)2 Mn(CH3 CO2 )2 ] (2), and {[(CuL)2 Mn(C6 H5 CH2 CO2 )2 ] ⋅ 2CH3 CN} (3), have been synthesized using [CuL] as ''metalloligand'' (where H2 L=N,N'-bis(2-hydroxynaphthyl-methylidene)-1,3-propanediamine). Single-crystal structural analyses show an almost linear penta-nuclear structure for complex 1 where a square planar [CuL] unit is connected to each of the two terminal MnII ions of a linear, centrosymmetric [Mn3 (benzoate)6 ] unit through the double phenoxido bridges. Both complexes 2 and 3 possess a linear tri-nuclear structure where two terminal square-pyramidal [CuL] units are bonded to the central MnII ion through double phenoxido oxygen atoms along with a syn-syn bridging acetate (for 2)/phenyl acetate (for 3). All three complexes exhibit catecholase, and phenoxazinone synthase-like activities under aerial conditions. For catecholase like activity, the turnover numbers (kcat ) are 595, 40, and 205 h-1 whereas, for phenoxazinone synthase like activity, the turnover numbers are 25, 4, and 11 h-1 for complexes 1-3, respectively. The mechanism of both catalytic oxidase activities is proposed on the basis of mass spectral evidences. Variable-temperature (2-300 K) dc molar magnetic susceptibility measurements of 1 reveal antiferromagnetic interactions between the Cu-Mn centres (J1 =-29.3 cm-1 ), and also between the Mn-Mn centres of the [Mn3 (benzoate)6 ] unit (J2 =-0.68 cm-1 ). On increasing the magnetic field at 2 K, its ground spin state changes from S=3/2 to S=5/2 at 4 T, attributable to the low value of J2 which makes the excited spin states close in energy with the ground spin state. Complexes 2 and 3 show antiferromagnetic coupling interactions between the Cu-Mn pairs with J values of -9.51, and -5.32 cm-1 , respectively.
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Affiliation(s)
- Sayantan Ganguly
- Department of Chemistry, University College of Science, University of Calcutta, 92, A. P. C. Road, Kolkata, 700 009, India.,Department of Chemistry, Taki Government College, Taki, Hasnabad, West Bengal, 743429, India
| | - Júlia Mayans
- Instituto de Ciencia Molecular (ICMol), Universitat de València, c/ Catedrático José Beltrán 2, 46980 Paterna, València, Spain
| | - Ashutosh Ghosh
- Department of Chemistry, University College of Science, University of Calcutta, 92, A. P. C. Road, Kolkata, 700 009, India.,Rani Rashmoni Green University, Tarakeswar, Hooghly, 712419, West Bengal, India
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123
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Liu L, Feng X, Wang W, Chen Y, Chen Z, Gao H. Free Rather Than Total Iron Content Is Critically Linked to the Fur Physiology in Shewanella oneidensis. Front Microbiol 2020; 11:593246. [PMID: 33329474 PMCID: PMC7732582 DOI: 10.3389/fmicb.2020.593246] [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: 08/10/2020] [Accepted: 09/29/2020] [Indexed: 11/30/2022] Open
Abstract
Ferric uptake regulator (Fur) is a transcriptional regulator playing a central role in iron homeostasis of many bacteria, and Fur inactivation commonly results in pleiotropic phenotypes. In Shewanella oneidensis, a representative of dissimilatory metal-reducing γ-proteobacteria capable of respiring a variety of chemicals as electron acceptors (EAs), Fur loss substantially impairs respiration. However, to date the mechanism underlying the physiological phenomenon remains obscure. This investigation reveals that Fur loss compromises activity of iron proteins requiring biosynthetic processes for their iron cofactors, heme in particular. We then show that S. oneidensis Fur is critical for maintaining heme homeostasis by affecting both its biosynthesis and decomposition of the molecule. Intriguingly, the abundance of iron-containing proteins controlled by H2O2-responding regulator OxyR increases in the fur mutant because the Fur loss activates OxyR. By comparing suppression of membrane-impermeable, membrane-permeable, and intracellular-only iron chelators on heme deficiency and elevated H2O2 resistance, our data suggest that the elevation of the free iron content by the Fur loss is likely to be the predominant factor for the Fur physiology. Overall, these results provide circumstantial evidence that Fur inactivation disturbs bacterial iron homeostasis by altering transcription of its regulon members, through which many physiological processes, such as respiration and oxidative stress response, are transformed.
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Affiliation(s)
| | | | | | | | | | - Haichun Gao
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, China
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124
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Latifi R, Minnick JL, Quesne MG, de Visser SP, Tahsini L. Computational studies of DNA base repair mechanisms by nonheme iron dioxygenases: selective epoxidation and hydroxylation pathways. Dalton Trans 2020; 49:4266-4276. [PMID: 32141456 DOI: 10.1039/d0dt00007h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
DNA base repair mechanisms of alkylated DNA bases is an important reaction in chemical biology and particularly in the human body. It is typically catalyzed by an α-ketoglutarate-dependent nonheme iron dioxygenase named the AlkB repair enzyme. In this work we report a detailed computational study into the structure and reactivity of AlkB repair enzymes with alkylated DNA bases. In particular, we investigate the aliphatic hydroxylation and C[double bond, length as m-dash]C epoxidation mechanisms of alkylated DNA bases by a high-valent iron(iv)-oxo intermediate. Our computational studies use quantum mechanics/molecular mechanics methods on full enzymatic structures as well as cluster models on active site systems. The work shows that the iron(iv)-oxo species is rapidly formed after dioxygen binding to an iron(ii) center and passes a bicyclic ring structure as intermediate. Subsequent cluster models explore the mechanism of substrate hydroxylation and epoxidation of alkylated DNA bases. The work shows low energy barriers for substrate activation and consequently energetically feasible pathways are predicted. Overall, the work shows that a high-valent iron(iv)-oxo species can efficiently dealkylate alkylated DNA bases and return them into their original form.
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Affiliation(s)
- Reza Latifi
- Department of Chemistry, Oklahoma State University, 107 Physical Science Building, Stillwater, Oklahoma 74078, USA.
| | - Jennifer L Minnick
- Department of Chemistry, Oklahoma State University, 107 Physical Science Building, Stillwater, Oklahoma 74078, USA.
| | - Matthew G Quesne
- Cardiff University, School of Chemistry, Main Building, Park Place, Cardiff, CF10 3AT, UK. and Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxon, OX110FA, UK
| | - Sam P de Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science, 131 Princess Street, Manchester M1 7DN, UK.
| | - Laleh Tahsini
- Department of Chemistry, Oklahoma State University, 107 Physical Science Building, Stillwater, Oklahoma 74078, USA.
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125
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Zsombor-Pindera J, Effaty F, Escomel L, Patrick B, Kennepohl P, Ottenwaelder X. Five Nitrogen Oxidation States from Nitro to Amine: Stabilization and Reactivity of a Metastable Arylhydroxylamine Complex. J Am Chem Soc 2020; 142:19023-19028. [PMID: 33124796 DOI: 10.1021/jacs.0c09300] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Redox noninnocent ligands enhance the reactivity of the metal they complex, a strategy used by metalloenzymes and in catalysis. Herein, we report a series of copper complexes with the same ligand framework, but with a pendant nitrogen group that spans five different redox states between nitro and amine. Of particular interest is the synthesis of a unprecedented copper(I)-arylhydroxylamine complex. While hydroxylamines typically disproportionate or decompose in the presence of transition metal ions, the reactivity of this metastable species is arrested by the presence of an intramolecular hydrogen bond. Two-electron oxidation yields a copper(II)-(arylnitrosyl radical) complex that can dissociate to a copper(I) species with uncoordinated arylnitroso. This combination of ligand redox noninnocence and hemilability provides opportunities in catalysis for two-electron chemistry via a one-electron copper(I/II) shuttle, as exemplified with an aerobic alcohol oxidation.
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Affiliation(s)
- Joseph Zsombor-Pindera
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC H4B 1R6, Canada.,Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Farshid Effaty
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Léon Escomel
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC H4B 1R6, Canada
| | - Brian Patrick
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Pierre Kennepohl
- Department of Chemistry, University of British Columbia, Vancouver, BC V6T 1Z1, Canada
| | - Xavier Ottenwaelder
- Department of Chemistry and Biochemistry, Concordia University, Montreal, QC H4B 1R6, Canada
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126
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Carcinogenesis as Side Effects of Iron and Oxygen Utilization: From the Unveiled Truth toward Ultimate Bioengineering. Cancers (Basel) 2020; 12:cancers12113320. [PMID: 33182727 PMCID: PMC7698037 DOI: 10.3390/cancers12113320] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 12/27/2022] Open
Abstract
Simple Summary Cancer is a major cause of human mortality worldwide. No life on earth can live without iron. Persistent oxidative stress resulting from continuous use of iron and oxygen may be a fundamental cause of carcinogenesis. Many animal models demonstrated that excess iron may lead to carcinogenesis. This is supported by a variety of human epidemiological data on cancer risk and prognosis. Cancer is basically a disease of the genome with persistently activated oncogenes and inactivated tumor suppressor genes through which iron addiction with ferroptosis-resistance is established. We predict that fine use of nanomaterials and non-thermal plasma may be able to reverse this situation. Abstract Evolution from the first life on earth to humans took ~3.8 billion years. During the time there have been countless struggles among the species. Mycobacterium tuberculosis was the last major uncontrollable species against the human public health worldwide. After the victory with antibiotics, cancer has become the leading cause of death since 1981 in Japan. Considering that life inevitably depends on ceaseless electron transfers through iron and oxygen, we believe that carcinogenesis is intrinsically unavoidable side effects of using iron and oxygen. Many animal models unequivocally revealed that excess iron is a risk for carcinogenesis. This is supported by a variety of human epidemiological data on cancer risk and prognosis. Cancer is basically a disease of the genome with persistently activated oncogenes and inactivated tumor suppressor genes through which iron addiction with ferroptosis-resistance is maintained. Engineering has made a great advance in the past 50 years. In particular, nanotechnology is distinct in that the size of the engineered molecules is similar to that of our biomolecules. While some nano-molecules are found carcinogenic, there are principles to avoid such carcinogenicity with a smart possibility to use nano-molecules to specifically kill cancer cells. Non-thermal plasma is another modality to fight against cancer.
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127
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Zimmermann TP, Orth N, Finke S, Limpke T, Stammler A, Bögge H, Walleck S, Ivanović-Burmazović I, Glaser T. Catalytic H 2O 2 Activation by a Diiron Complex for Methanol Oxidation. Inorg Chem 2020; 59:15563-15569. [PMID: 33081463 DOI: 10.1021/acs.inorgchem.0c02698] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In nature, C-H bond oxidation of CH4 involves a peroxo intermediate that decays to the high-valent active species of either a "closed" {FeIV(μ-O)2FeIV} core or an "open" {FeIV(O)(μ-O)FeIV(O)} core. To mimic and to obtain more mechanistic insight in this reaction mode, we have investigated the reactivity of the bioinspired diiron complex [(susan){Fe(OH)(μ-O)Fe(OH)}]2+ [susan = 4,7-dimethyl-1,1,10,10-tetrakis(2-pyridylmethyl)-1,4,7,10-tetraazadecane], which catalyzes CH3OH oxidation with H2O2 to HCHO and HCO2H. The kinetics is faster in the presence of a proton. 18O-labeling experiments show that the active species, generated by a decay of the initially formed peroxo intermediate [(susan){FeIII(μ-O)(μ-O2)FeIII}]2+, contains one reactive oxygen atom from the μ-oxo and another from the μ-peroxo bridge of its peroxo precursor. Considering an FeIVFeIV active species, a "closed" {FeIV(μ-O)2FeIV} core explains the observed labeling results, while a scrambling of the terminal and bridging oxo ligands is required to account for an "open" {FeIV(O)(μ-O)FeIV(O)} core.
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Affiliation(s)
| | - Nicole Orth
- Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, D-91058 Erlangen, Germany
| | - Sebastian Finke
- Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Thomas Limpke
- Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Anja Stammler
- Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Hartmut Bögge
- Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Stephan Walleck
- Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
| | - Ivana Ivanović-Burmazović
- Department Chemie und Pharmazie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstraße 1, D-91058 Erlangen, Germany.,Department Chemie, Ludwigs-Maximilians-Universität, Butenandtstraße 5-13, 81377 München, Germany
| | - Thorsten Glaser
- Fakultät für Chemie, Universität Bielefeld, Universitätsstraße 25, D-33615 Bielefeld, Germany
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128
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Kannan N, Patil AR, Sinha A. Direct C-H bond halogenation and pseudohalogenation of hydrocarbons mediated by high-valent 3d metal-oxo species. Dalton Trans 2020; 49:14344-14360. [PMID: 33057538 DOI: 10.1039/d0dt02533j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Late-stage direct functionalization of the C-H bond is synthetically desirable. Metalloenzymes having metal-oxo active sites are well known to selectively catalyze hydroxylation and halogenation reactions with high efficiency. This review highlights the recent developments in the field of direct C-H halogenation and pseudohalogenation reactions catalyzed by the functional models of metalloenzymes.
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Affiliation(s)
- Neppoliyan Kannan
- Department of Chemistry, School of Advanced Science, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India.
| | - Akshay R Patil
- Department of Chemistry, School of Advanced Science, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India.
| | - Arup Sinha
- Department of Chemistry, School of Advanced Science, Vellore Institute of Technology, Vellore-632014, Tamil Nadu, India.
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129
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Ansari M, Senthilnathan D, Rajaraman G. Deciphering the origin of million-fold reactivity observed for the open core diiron [HO-Fe III-O-Fe IV[double bond, length as m-dash]O] 2+ species towards C-H bond activation: role of spin-states, spin-coupling, and spin-cooperation. Chem Sci 2020; 11:10669-10687. [PMID: 33209248 PMCID: PMC7654192 DOI: 10.1039/d0sc02624g] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 06/16/2020] [Indexed: 01/26/2023] Open
Abstract
High-valent metal-oxo species have been characterised as key intermediates in both heme and non-heme enzymes that are found to perform efficient aliphatic hydroxylation, epoxidation, halogenation, and dehydrogenation reactions. Several biomimetic model complexes have been synthesised over the years to mimic both the structure and function of metalloenzymes. The diamond-core [Fe2(μ-O)2] is one of the celebrated models in this context as this has been proposed as the catalytically active species in soluble methane monooxygenase enzymes (sMMO), which perform the challenging chemical conversion of methane to methanol at ease. In this context, a report of open core [HO(L)FeIII-O-FeIV(O)(L)]2+ (1) gains attention as this activates C-H bonds a million-fold faster compared to the diamond-core structure and has the dual catalytic ability to perform hydroxylation as well as desaturation with organic substrates. In this study, we have employed density functional methods to probe the origin of the very high reactivity observed for this complex and also to shed light on how this complex performs efficient hydroxylation and desaturation of alkanes. By modelling fifteen possible spin-states for 1 that could potentially participate in the reaction mechanism, our calculations reveal a doublet ground state for 1 arising from antiferromagnetic coupling between the quartet FeIV centre and the sextet FeIII centre, which regulates the reactivity of this species. The unusual stabilisation of the high-spin ground state for FeIV[double bond, length as m-dash]O is due to the strong overlap of with the orbital, reducing the antibonding interactions via spin-cooperation. The electronic structure features computed for 1 are consistent with experiments offering confidence in the methodology chosen. Further, we have probed various mechanistic pathways for the C-H bond activation as well as -OH rebound/desaturation of alkanes. An extremely small barrier height computed for the first hydrogen atom abstraction by the terminal FeIV[double bond, length as m-dash]O unit was found to be responsible for the million-fold activation observed in the experiments. The barrier height computed for -OH rebound by the FeIII-OH unit is also smaller suggesting a facile hydroxylation of organic substrates by 1. A strong spin-cooperation between the two iron centres also reduces the barrier for second hydrogen atom abstraction, thus making the desaturation pathway competitive. Both the spin-state as well as spin-coupling between the two metal centres play a crucial role in dictating the reactivity for species 1. By exploring various mechanistic pathways, our study unveils the fact that the bridged μ-oxo group is a poor electrophile for both C-H activation as well for -OH rebound. As more and more evidence is gathered in recent years for the open core geometry of sMMO enzymes, the idea of enhancing the reactivity via an open-core motif has far-reaching consequences.
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Affiliation(s)
- Mursaleem Ansari
- Department of Chemistry , Indian Institute of Technology Bombay , Mumbai 400076 , India .
| | - Dhurairajan Senthilnathan
- Center for Computational Chemistry , CRD , PRIST University , Vallam , Thanjavur , Tamilnadu 613403 , India
| | - Gopalan Rajaraman
- Department of Chemistry , Indian Institute of Technology Bombay , Mumbai 400076 , India .
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130
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Dunham NP, Arnold FH. Nature's Machinery, Repurposed: Expanding the Repertoire of Iron-Dependent Oxygenases. ACS Catal 2020; 10:12239-12255. [PMID: 33282461 PMCID: PMC7710332 DOI: 10.1021/acscatal.0c03606] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Iron is an especially important redox-active cofactor in biology because of its ability to mediate reactions with atmospheric O2. Iron-dependent oxygenases exploit this earth-abundant transition metal for the insertion of oxygen atoms into organic compounds. Throughout the astounding diversity of transformations catalyzed by these enzymes, the protein framework directs reactive intermediates toward the precise formation of products, which, in many cases, necessitates the cleavage of strong C-H bonds. In recent years, members of several iron-dependent oxygenase families have been engineered for new-to-nature transformations that offer advantages over conventional synthetic methods. In this Perspective, we first explore what is known about the reactivity of heme-dependent cytochrome P450 oxygenases and nonheme iron-dependent oxygenases bearing the 2-His-1-carboxylate facial triad by reviewing mechanistic studies with an emphasis on how the protein scaffold maximizes the catalytic potential of the iron-heme and iron cofactors. We then review how these cofactors have been repurposed for abiological transformations by engineering the protein frameworks of these enzymes. Finally, we discuss contemporary challenges associated with engineering these platforms and comment on their roles in biocatalysis moving forward.
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Affiliation(s)
- Noah P. Dunham
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
| | - Frances H. Arnold
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 210-41, Pasadena, California 91125, United States
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131
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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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132
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Li G, Gu D, Cao R, Hong S, Liu Y, Liu Y. Highly Catalytically Active High-spin Single-atom Iron Catalyst Supported by Catechol-containing Microporous 2D Polymer. CHEM LETT 2020. [DOI: 10.1246/cl.200416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Guangwen Li
- School of Chemistry, Beihang University, Beijing 100191, P. R. China
| | - Defa Gu
- School of Chemistry, Beihang University, Beijing 100191, P. R. China
| | - Rui Cao
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA
| | - Song Hong
- Center for Instrumental Analysis, Beijing University of Chemical Technology, Chaoyang, Beijing 100029, P. R. China
| | - Yushan Liu
- Trinity School of Durham and Chapel Hill, Durham and Chapel Hill, Durham, NC, 27708, USA
| | - Yuzhou Liu
- School of Chemistry, Beihang University, Beijing 100191, P. R. China
- Beijing Advanced Innovation Center for Biomedical Engineering, Beihang University, Beijing 100191, P. R. China
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133
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Moltved KA, Kepp KP. Dioxygen Binding to all 3d, 4d, and 5d Transition Metals from Coupled-Cluster Theory. Chemphyschem 2020; 21:2173-2186. [PMID: 32757346 DOI: 10.1002/cphc.202000529] [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: 06/17/2020] [Revised: 08/04/2020] [Indexed: 11/11/2022]
Abstract
Understanding how transition metals bind and activate dioxygen (O2 ) is limited by experimental and theoretical uncertainties, making accurate quantum mechanical descriptors of interest. Here we report coupled-cluster CCSD(T) energies with large basis sets and vibrational and relativistic corrections for 160 3d, 4d, and 5d metal-O2 systems. We define four reaction energies (120 in total for the 30 metals) that quantify O-O activation and reveal linear relationships between metal-oxygen and O-O binding energies. The CCSD(T) data can be combined with thermochemical cycles to estimate chemisorption and physisorption energies for each metal from metal oxide embedding energies, in good correlation with atomization enthalpies (R2 =0.75). Spin-geometry variations can break the linearities, of interest to circumventing the Sabatier principle. Pt, Pd, Co, and Fe form a distinct group with the weakest O2 binding. R2 up to 0.84 between surface adsorption energies and our energies for MO2 systems indicate relevance also to real catalytic systems.
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Affiliation(s)
- Klaus A Moltved
- Technical University of Denmark DTU Chemistry, Building 206, 2800, Kgs. Lyngby, Denmark
| | - Kasper P Kepp
- Technical University of Denmark DTU Chemistry, Building 206, 2800, Kgs. Lyngby, Denmark
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134
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Sun D, Chen X, Gao L, Zhao Y, Wang Y. Theoretical Study on the Structural-Function Relationship of Manganese(III)-Iodosylarene Adducts. Front Chem 2020; 8:744. [PMID: 32974286 PMCID: PMC7469263 DOI: 10.3389/fchem.2020.00744] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 07/17/2020] [Indexed: 11/18/2022] Open
Abstract
Metal-iodosylarene complexes have been recently viewed as a second oxidant alongside of the well-known high-valent metal-oxo species. Extensive efforts have been exerted to unveil the structure-function relationship of various metal-iodosylarene complexes. In the present manuscript, density functional theoretical calculations were employed to investigate such relationship of a specific manganese-iodosylbenzene complex [MnIII(TBDAP)(PhIO)(OH)]2+ (1). Our results fit the experimental observations and revealed new mechanistic findings. 1 acts as a stepwise 1e+1e oxidant in sulfoxidation reactions. Surprisingly, C-H bond activation of 9,10-dihydroanthracene (DHA) by 1 proceeds via a novel ionic hydride transfer/proton transfer (HT/PT) mechanism. As a comparison to 1, the electrophilicity of an iodosylbenzene monomer PhIO was investigated. PhIO performs concerted 2e-oxidations both in sulfoxidation and C-H activation. Hydroxylation of DHA by PhIO was found to proceed via a novel ionic and concerted proton-transfer/hydroxyl-rebound mechanism involving 2e-oxidation to form a transient carbonium species.
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Affiliation(s)
- Dongru Sun
- School of Material Science and Chemical Engineering, Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
| | - Xiaolu Chen
- School of Material Science and Chemical Engineering, Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
| | - Lanping Gao
- School of Material Science and Chemical Engineering, Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
| | - Yufen Zhao
- School of Material Science and Chemical Engineering, Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
| | - Yong Wang
- School of Material Science and Chemical Engineering, Institute of Drug Discovery Technology, Ningbo University, Ningbo, China
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135
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Müller L, Hoof S, Keck M, Herwig C, Limberg C. Enhancing Tris(pyrazolyl)borate-Based Models of Cysteine/Cysteamine Dioxygenases through Steric Effects: Increased Reactivities, Full Product Characterization and Hints to Initial Superoxide Formation. Chemistry 2020; 26:11851-11861. [PMID: 32432367 PMCID: PMC7540079 DOI: 10.1002/chem.202001818] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Indexed: 02/03/2023]
Abstract
The design of biomimetic model complexes for the cysteine dioxygenase (CDO) and cysteamine dioxygenase (ADO) is reported, where the 3-His coordination of the iron ion is simulated by three pyrazole donors of a trispyrazolyl borate ligand (Tp) and protected cysteine and cysteamine represent substrate ligands. It is found that the replacement of phenyl groups-attached at the 3-positions of the pyrazole units in a previous model-by mesityl residues has massive consequences, as the latter arrange to a more spacious reaction pocket. Thus, the reaction with O2 proceeds much faster and afterwards the first structural characterization of an iron(II) η2 -O,O-sulfinate product became possible. If one of the three Tp-mesityl groups is placed in the 5-position, an even larger reaction pocket results, which leads to yet faster rates and accumulation of a reaction intermediate at low temperatures, as shown by UV/Vis and Mössbauer spectroscopy. After comparison with the results of investigations on the cobalt analogues this intermediate is tentatively assigned to an iron(III) superoxide species.
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Affiliation(s)
- Lars Müller
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Santina Hoof
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Matthias Keck
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Christian Herwig
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
| | - Christian Limberg
- Institut für ChemieHumboldt-Universität zu BerlinBrook-Taylor-Straße 212489BerlinGermany
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136
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Abstract
Although the gastrointestinal tract is regarded as mainly anoxic, low O2 tension is present in the gut and tends to increase following antibiotic-induced disruption of the host microbiota. Two decreasing O2 gradients are observed, a longitudinal one from the small to the large intestine and a second one from the intestinal epithelium toward the colon lumen. Thus, O2 concentration fluctuations within the gastrointestinal tract are a challenge for anaerobic bacteria such as C. difficile. This enteropathogen has developed efficient strategies to detoxify O2. In this work, we identified reverse rubrerythrins and flavodiiron proteins as key actors for O2 tolerance in C. difficile. These enzymes are responsible for the reduction of O2 protecting C. difficile vegetative cells from associated damages. Original and complex detoxification pathways involving O2-reductases are crucial in the ability of C. difficile to tolerate O2 and survive to O2 concentrations encountered in the gastrointestinal tract. Clostridioides difficile is a major cause of diarrhea associated with antibiotherapy. After germination of C. difficile spores in the small intestine, vegetative cells are exposed to low oxygen (O2) tensions. While considered strictly anaerobic, C. difficile is able to grow in nonstrict anaerobic conditions (1 to 3% O2) and tolerates brief air exposure indicating that this bacterium harbors an arsenal of proteins involved in O2 detoxification and/or protection. Tolerance of C. difficile to low O2 tensions requires the presence of the alternative sigma factor, σB, involved in the general stress response. Among the genes positively controlled by σB, four encode proteins likely involved in O2 detoxification: two flavodiiron proteins (FdpA and FdpF) and two reverse rubrerythrins (revRbr1 and revRbr2). As previously observed for FdpF, we showed that both purified revRbr1 and revRbr2 harbor NADH-linked O2- and H2O2-reductase activities in vitro, while purified FdpA mainly acts as an O2-reductase. The growth of a fdpA mutant is affected at 0.4% O2, while inactivation of both revRbrs leads to a growth defect above 0.1% O2. O2-reductase activities of these different proteins are additive since the quadruple mutant displays a stronger phenotype when exposed to low O2 tensions compared to the triple mutants. Our results demonstrate a key role for revRbrs, FdpF, and FdpA proteins in the ability of C. difficile to grow in the presence of physiological O2 tensions such as those encountered in the colon.
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137
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Xi ZH, Sun Y, Wang X, Zhao XL, Han J, Chen XD. Rare earth metal complexes based on a tripodal ligand and their application as highly selective “turn-on” fluorescent probe for Fe3+ ion. INORG CHEM COMMUN 2020. [DOI: 10.1016/j.inoche.2020.108046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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138
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Shteinman AA. Bioinspired Oxidation of Methane: From Academic Models of Methane Monooxygenases to Direct Conversion of Methane to Methanol. KINETICS AND CATALYSIS 2020. [DOI: 10.1134/s0023158420030180] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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139
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Ferousi C, Majer SH, DiMucci IM, Lancaster KM. Biological and Bioinspired Inorganic N-N Bond-Forming Reactions. Chem Rev 2020; 120:5252-5307. [PMID: 32108471 PMCID: PMC7339862 DOI: 10.1021/acs.chemrev.9b00629] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The metallobiochemistry underlying the formation of the inorganic N-N-bond-containing molecules nitrous oxide (N2O), dinitrogen (N2), and hydrazine (N2H4) is essential to the lifestyles of diverse organisms. Similar reactions hold promise as means to use N-based fuels as alternative carbon-free energy sources. This review discusses research efforts to understand the mechanisms underlying biological N-N bond formation in primary metabolism and how the associated reactions are tied to energy transduction and organismal survival. These efforts comprise studies of both natural and engineered metalloenzymes as well as synthetic model complexes.
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Affiliation(s)
- Christina Ferousi
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Sean H Majer
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Ida M DiMucci
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
| | - Kyle M Lancaster
- Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, New York 14853, United States
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140
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Oswald VF, Lee JL, Biswas S, Weitz AC, Mittra K, Fan R, Li J, Zhao J, Hu MY, Alp EE, Bominaar EL, Guo Y, Green MT, Hendrich MP, Borovik AS. Effects of Noncovalent Interactions on High-Spin Fe(IV)-Oxido Complexes. J Am Chem Soc 2020; 142:11804-11817. [PMID: 32489096 DOI: 10.1021/jacs.0c03085] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
High-valent nonheme FeIV-oxido species are key intermediates in biological oxidation, and their properties are proposed to be influenced by the unique microenvironments present in protein active sites. Microenvironments are regulated by noncovalent interactions, such as hydrogen bonds (H-bonds) and electrostatic interactions; however, there is little quantitative information about how these interactions affect crucial properties of high valent metal-oxido complexes. To address this knowledge gap, we introduced a series of FeIV-oxido complexes that have the same S = 2 spin ground state as those found in nature and then systematically probed the effects of noncovalent interactions on their electronic, structural, and vibrational properties. The key design feature that provides access to these complexes is the new tripodal ligand [poat]3-, which contains phosphinic amido groups. An important structural aspect of [FeIVpoat(O)]- is the inclusion of an auxiliary site capable of binding a Lewis acid (LAII); we used this unique feature to further modulate the electrostatic environment around the Fe-oxido unit. Experimentally, studies confirmed that H-bonds and LAII s can interact directly with the oxido ligand in FeIV-oxido complexes, which weakens the Fe═O bond and has an impact on the electronic structure. We found that relatively large vibrational changes in the Fe-oxido unit correlate with small structural changes that could be difficult to measure, especially within a protein active site. Our work demonstrates the important role of noncovalent interactions on the properties of metal complexes, and that these interactions need to be considered when developing effective oxidants.
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Affiliation(s)
- Victoria F Oswald
- Department of Chemistry, 1102 Natural Sciences II, University of California at Irvine, Irvine, California 92697, United States
| | - Justin L Lee
- Department of Chemistry, 1102 Natural Sciences II, University of California at Irvine, Irvine, California 92697, United States
| | - Saborni Biswas
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Andrew C Weitz
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Kaustuv Mittra
- Department of Molecular Biosciences and Biochemistry, University of California at Irvine, Irvine, California 92697, United States
| | - Ruixi Fan
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jikun Li
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Jiyong Zhao
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Michael Y Hu
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Esen E Alp
- Advanced Photon Source, Argonne National Laboratory, Lemont, Illinois 60439, United States
| | - Emile L Bominaar
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Yisong Guo
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Michael T Green
- Department of Chemistry, 1102 Natural Sciences II, University of California at Irvine, Irvine, California 92697, United States.,Department of Molecular Biosciences and Biochemistry, University of California at Irvine, Irvine, California 92697, United States
| | - Michael P Hendrich
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - A S Borovik
- Department of Chemistry, 1102 Natural Sciences II, University of California at Irvine, Irvine, California 92697, United States
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141
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Van Stappen C, Decamps L, Cutsail GE, Bjornsson R, Henthorn JT, Birrell JA, DeBeer S. The Spectroscopy of Nitrogenases. Chem Rev 2020; 120:5005-5081. [PMID: 32237739 PMCID: PMC7318057 DOI: 10.1021/acs.chemrev.9b00650] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Indexed: 01/08/2023]
Abstract
Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.
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Affiliation(s)
- Casey Van Stappen
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Laure Decamps
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - George E. Cutsail
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Ragnar Bjornsson
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Justin T. Henthorn
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - James A. Birrell
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
| | - Serena DeBeer
- Max Planck Institute for
Chemical Energy Conversion, Stiftstrasse 34-36, 45470 Mülheim an der Ruhr, Germany
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142
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Structural basis for divergent C-H hydroxylation selectivity in two Rieske oxygenases. Nat Commun 2020; 11:2991. [PMID: 32532989 PMCID: PMC7293229 DOI: 10.1038/s41467-020-16729-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 05/15/2020] [Indexed: 12/05/2022] Open
Abstract
Biocatalysts that perform C–H hydroxylation exhibit exceptional substrate specificity and site-selectivity, often through the use of high valent oxidants to activate these inert bonds. Rieske oxygenases are examples of enzymes with the ability to perform precise mono- or dioxygenation reactions on a variety of substrates. Understanding the structural features of Rieske oxygenases responsible for control over selectivity is essential to enable the development of this class of enzymes for biocatalytic applications. Decades of research has illuminated the critical features common to Rieske oxygenases, however, structural information for enzymes that functionalize diverse scaffolds is limited. Here, we report the structures of two Rieske monooxygenases involved in the biosynthesis of paralytic shellfish toxins (PSTs), SxtT and GxtA, adding to the short list of structurally characterized Rieske oxygenases. Based on these structures, substrate-bound structures, and mutagenesis experiments, we implicate specific residues in substrate positioning and the divergent reaction selectivity observed in these two enzymes. Rieske oxygenases are iron-dependent enzymes that catalyse C–H mono- and dihydroxylation reactions. Here, the authors characterise two cyanobacterial Rieske oxygenases, SxtT and GxtA that are involved in the biosynthesis of paralytic shellfish toxins and determine their substrate free and saxitoxin analog-bound crystal structures and by using mutagenesis experiments identify residues, which are important for substrate positioning and reaction selectivity.
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143
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Bím D, Chalupský J, Culka M, Solomon EI, Rulíšek L, Srnec M. Proton-Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ 9-Desaturase. J Am Chem Soc 2020; 142:10412-10423. [PMID: 32406236 DOI: 10.1021/jacs.0c01786] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A full understanding of the catalytic action of non-heme iron (NHFe) and non-heme diiron (NHFe2) enzymes is still beyond the grasp of contemporary computational and experimental techniques. Many of these enzymes exhibit fascinating chemo-, regio-, and stereoselectivity, in spite of employing highly reactive intermediates which are necessary for activations of most stable chemical bonds. Herein, we study in detail one intriguing representative of the NHFe2 family of enzymes: soluble Δ9 desaturase (Δ9D), which desaturates rather than performing the thermodynamically favorable hydroxylation of substrate. Its catalytic mechanism has been explored in great detail by using QM(DFT)/MM and multireference wave function methods. Starting from the spectroscopically observed 1,2-μ-peroxo diferric P intermediate, the proton-electron uptake by P is the favored mechanism for catalytic activation, since it allows a significant reduction of the barrier of the initial (and rate-determining) H-atom abstraction from the stearoyl substrate as compared to the "proton-only activated" pathway. Also, we ruled out that a Q-like intermediate (high-valent diamond-core bis-μ-oxo-[FeIV]2 unit) is involved in the reaction mechanism. Our mechanistic picture is consistent with the experimental data available for Δ9D and satisfies fairly stringent conditions required by Nature: the chemo-, stereo-, and regioselectivity of the desaturation of stearic acid. Finally, the mechanisms evaluated are placed into a broader context of NHFe2 chemistry, provided by an amino acid sequence analysis through the families of the NHFe2 enzymes. Our study thus represents an important contribution toward understanding the catalytic action of the NHFe2 enzymes and may inspire further work in NHFe(2) biomimetic chemistry.
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Affiliation(s)
- Daniel Bím
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, Prague 8 182 23, Czech Republic.,Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Jakub Chalupský
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Edward I Solomon
- Department of Chemistry, Stanford University, 333 Campus Drive, Stanford, California 94305-5080, United States
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Flemingovo nám. 2, Prague 6 166 10, Czech Republic
| | - Martin Srnec
- J. Heyrovský Institute of Physical Chemistry, The Czech Academy of Sciences, Dolejškova 3, Prague 8 182 23, Czech Republic
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144
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Chakraborty T, Mondal R, Ghanta R, Chakraborty A, Chattopadhyay T. Triton X‐100 functionalized Cu(II) dihydrazone based complex immobilized on Fe
3
O
4
@dopa: A highly efficient catalyst for oxidation of alcohols, alkanes, and sulfides and epoxidation of alkenes. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.5695] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tonmoy Chakraborty
- Department of Chemistry University of Calcutta 92, A.P.C.Road Kolkata 700009 India
| | - Rimpa Mondal
- Department of Chemistry Diamond Harbour Women's University Diamond Harbour Road, Sarisha, South 24 Parganas (S) West Bengal 743368 India
| | - Rinku Ghanta
- Department of Chemistry Diamond Harbour Women's University Diamond Harbour Road, Sarisha, South 24 Parganas (S) West Bengal 743368 India
| | - Aratrika Chakraborty
- Department of Chemistry University of Calcutta 92, A.P.C.Road Kolkata 700009 India
| | - Tanmay Chattopadhyay
- Department of Chemistry Diamond Harbour Women's University Diamond Harbour Road, Sarisha, South 24 Parganas (S) West Bengal 743368 India
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145
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Waheed S, Ramanan R, Chaturvedi SS, Lehnert N, Schofield CJ, Christov CZ, Karabencheva-Christova TG. Role of Structural Dynamics in Selectivity and Mechanism of Non-heme Fe(II) and 2-Oxoglutarate-Dependent Oxygenases Involved in DNA Repair. ACS CENTRAL SCIENCE 2020; 6:795-814. [PMID: 32490196 PMCID: PMC7256942 DOI: 10.1021/acscentsci.0c00312] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Indexed: 05/08/2023]
Abstract
AlkB and its human homologue AlkBH2 are Fe(II)- and 2-oxoglutarate (2OG)-dependent oxygenases that repair alkylated DNA bases occurring as a consequence of reactions with mutagenic agents. We used molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) methods to investigate how structural dynamics influences the selectivity and mechanisms of the AlkB- and AlkBH2-catalyzed demethylation of 3-methylcytosine (m3C) in single (ssDNA) and double (dsDNA) stranded DNA. Dynamics studies reveal the importance of the flexibility in both the protein and DNA components in determining the preferences of AlkB for ssDNA and of AlkBH2 for dsDNA. Correlated motions, including of a hydrophobic β-hairpin, are involved in substrate binding in AlkBH2-dsDNA. The calculations reveal that 2OG rearrangement prior to binding of dioxygen to the active site Fe is preferred over a ferryl rearrangement to form a catalytically productive Fe(IV)=O intermediate. Hydrogen atom transfer proceeds via a σ-channel in AlkBH2-dsDNA and AlkB-dsDNA; in AlkB-ssDNA, there is a competition between σ- and π-channels, implying that the nature of the complexed DNA has potential to alter molecular orbital interactions during the substrate oxidation. Our results reveal the importance of the overall protein-DNA complex in determining selectivity and how the nature of the substrate impacts the mechanism.
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Affiliation(s)
- Sodiq
O. Waheed
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Rajeev Ramanan
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Shobhit S. Chaturvedi
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Nicolai Lehnert
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Christopher J. Schofield
- The
Chemistry Research Laboratory, The Department of Chemistry, Mansfield
Road, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Christo Z. Christov
- Department
of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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146
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Miller KR, Paretsky JD, Follmer AH, Heinisch T, Mittra K, Gul S, Kim IS, Fuller FD, Batyuk A, Sutherlin KD, Brewster AS, Bhowmick A, Sauter NK, Kern J, Yano J, Green MT, Ward TR, Borovik AS. Artificial Iron Proteins: Modeling the Active Sites in Non-Heme Dioxygenases. Inorg Chem 2020; 59:6000-6009. [PMID: 32309932 PMCID: PMC7219546 DOI: 10.1021/acs.inorgchem.9b03791] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An important class of non-heme dioxygenases contains a conserved Fe binding site that consists of a 2-His-1-carboxylate facial triad. Results from structural biology show that, in the resting state, these proteins are six-coordinate with aqua ligands occupying the remaining three coordination sites. We have utilized biotin-streptavidin (Sav) technology to design new artificial Fe proteins (ArMs) that have many of the same structural features found within active sites of these non-heme dioxygenases. An Sav variant was isolated that contains the S112E mutation, which installed a carboxylate side chain in the appropriate position to bind to a synthetic FeII complex confined within Sav. Structural studies using X-ray diffraction (XRD) methods revealed a facial triad binding site that is composed of two N donors from the biotinylated ligand and the monodentate coordination of the carboxylate from S112E. Two aqua ligands complete the primary coordination sphere of the FeII center with both involved in hydrogen bond networks within Sav. The corresponding FeIII protein was also prepared and structurally characterized to show a six-coordinate complex with two exogenous acetato ligands. The FeIII protein was further shown to bind an exogenous azido ligand through replacement of one acetato ligand. Spectroscopic studies of the ArMs in solution support the results found by XRD.
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Affiliation(s)
- Kelsey R. Miller
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
| | - Jonathan D. Paretsky
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
| | - Alec H. Follmer
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
| | - Tillmann Heinisch
- Department of Chemistry, University of Basel, PO Box 3350, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - Kaustuv Mittra
- Department of Molecular Biosciences and Biochemistry, University of California, Irvine, CA 92697
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - In-Sik Kim
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Franklin D. Fuller
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025 USA
| | - Alexander Batyuk
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California 94025 USA
| | - Kyle D. Sutherlin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Aaron S. Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Asmit Bhowmick
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Nicholas K. Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Michael T. Green
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
- Department of Molecular Biosciences and Biochemistry, University of California, Irvine, CA 92697
| | - Thomas R. Ward
- Department of Chemistry, University of Basel, PO Box 3350, Mattenstrasse 24a, BPR 1096, CH-4002 Basel, Switzerland
| | - A. S. Borovik
- Department of Chemistry, 1102 Natural Science II, University of California, Irvine, CA 9269
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147
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Synthesis, Structures, Electrochemistry, and Catalytic Activity towards Cyclohexanol Oxidation of Mono-, Di-, and Polynuclear Iron(III) Complexes with 3-Amino-2-Pyrazinecarboxylate. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10082692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The synthesis and characterization of a set of iron(III) complexes, viz. the mononuclear [Fe(L)3] (1) and [NHEt3][Fe(L)2(Cl)2] (2), the dinuclear methoxido-bridged [Fe(L)2(μ-OMe)]2.DMF.1.5MeOH (3), and the heteronuclear Fe(III)/Na(I) two-dimensional coordination polymer [Fe(N3)(μ-L)2(μ-O)1/2(Na)(μ-H2O)1/2]n (4), are reported. Reactions of 3-amino-2-pyrazinecarboxylic acid (HL) with iron(III) chloride under different reaction conditions were studied, and the obtained compounds were characterized by elemental analysis, Fourier Transform Infrared (FT-IR) spectroscopy, and X-ray single-crystal diffraction. Compound 1 is a neutral mononuclear complex, whereas 2 is mono-anionic with its charge being neutralized by triethylammonium cation. Compounds 3 and 4 display a di-methoxido-bridged dinuclear complex and a two-dimensional heterometallic Fe(III)/Na(I) polynuclear coordination polymer, respectively. Compounds 3 and 4 are the first examples of methoxido- and oxido-bridged iron(III) complexes, respectively, with 3-amino-2-pyrazinecarboxylate ligands. The electrochemical study of these compounds reveals a facile single-electron reversible Fe(III)-to-Fe(II) reduction at a positive potential of 0.08V vs. saturated calomel electrode (SCE), which is in line with their ability to act as efficient oxidants and heterogeneous catalysts for the solvent-free microwave-assisted peroxidative oxidation (with tert-butyl hydroperoxide) of cyclohexanol to cyclohexanone (almost quantitative yields after 1 h). Moreover, the catalysts are easily recovered and reused for five consecutive cycles, maintaining a high activity and selectivity.
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148
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Tao Y, Pei Z, Bellonzi N, Mao Y, Zou Z, Liang W, Yang Z, Shao Y. Constructing Spin-Adiabatic States for the Modeling of Spin-Crossing Reactions. I. A Shared-Orbital Implementation. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY 2020; 120:e26123. [PMID: 32773885 PMCID: PMC7409987 DOI: 10.1002/qua.26123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 11/19/2019] [Indexed: 06/11/2023]
Abstract
In the modeling of spin-crossing reactions, it has become popular to directly explore the spin-adiabatic surfaces. Specifically, through constructing spin-adiabatic states from a two-state Hamiltonian (with spin-orbit coupling matrix elements) at each geometry, one can readily employ advanced geometry optimization algorithms to acquire a "transition state" structure, where the spin crossing occurs. In this work, we report the implementation of a fully-variational spin-adiabatic approach based on Kohn-Sham density functional theory spin states (sharing the same set of molecular orbitals) and the Breit-Pauli one-electron spin-orbit operator. For three model spin-crossing reactions [predissociation of N2O, singlet-triplet conversion in CH2, and CO addition to Fe(CO)4], the spin-crossing points were obtained. Our results also indicated the Breit-Pauli one-electron spin-orbit coupling can vary significantly along the reaction pathway on the spin-adiabatic energy surface. On the other hand, due to the restriction that low-spin and high-spin states share the same set of molecular orbitals, the acquired spin-adiabatic energy surface shows a cusp (i.e. a first-order discontinuity) at the crossing point, which prevents the use of standard geometry optimization algorithms to pinpoint the crossing point. An extension with this restriction removed is being developed to achieve the smoothness of spin-adiabatic surfaces.
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Affiliation(s)
- Yunwen Tao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Zheng Pei
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Nicole Bellonzi
- Department of Chemistry, University of Pennsylvania, Philadelpha, PA 19104
| | - Yuezhi Mao
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Zhu Zou
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Wanzhen Liang
- State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P. R. China
| | - Zhibo Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019
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149
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Ricciarelli D, Belpassi L, Harvey JN, Belanzoni P. Spin-Forbidden Reactivity of Transition Metal Oxo Species: Exploring the Potential Energy Surfaces. Chemistry 2020; 26:3080-3089. [PMID: 31846105 DOI: 10.1002/chem.201904314] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Indexed: 11/06/2022]
Abstract
Spin-forbidden reactions are frequently encountered when transition metal oxo species are involved, particularly in oxygen transfer reactivity. The computational study of such reactions is challenging, because reactants and products are located on different spin potential energy surfaces (PESs). One possible approach to describe these reactions is the so-called minimum energy crossing point (MECP) between the diabatic reactants and products PESs. Alternatively, inclusion of spin-orbit coupling (SOC) effects allows to locate a saddle point on a single adiabatic PES (TS SOC). The TS SOC approach is rarely applied because of its high computational cost. Recently evidence for a TS SOC impact on significantly lowering the activation barrier in dioxygen addition to a carbene-gold(I)-hydride complex reaction (Chem. Sci. 2016, 7, 7034-7039) or even on predicting a qualitatively different reaction mechanism in mercury methylation by cobalt corrinoid (Angew. Chem. Int. Ed. 2016, 55, 11503-11506) has been put forward. Using MECP and TS SOC approaches a systematic analysis is provided here of three prototypical transition metal oxo spin-forbidden processes to investigate their implications on reactivity. Cycloaddition of ethylene to chromyl chloride (CrO2 Cl2 +C2 H4 ), iron oxide cation insertion into the hydrogen molecule (FeO+ +H2 ) and H-abstraction from toluene by a MnV -oxo-porphyrin cation (MnOP(H2 O)+ +C6 H5 CH3 ) are case studies. For all these processes the MECP and TS SOC results are compared, which show that the spin-forbidden reactivity of transition metal oxo species can be safely described by a MECP approach, at least for the first-row transition metals investigated here, where the spin-orbit coupling is relatively weak. However, for the Mn-oxo reactivity, the MECP and TS SOC have been found to be crucial for a correct description of the reaction mechanism. In particular, the TS SOC approach allows to straightforwardly explore detailed features of the adiabatic potential energy surface which in principle could affect the overall reaction rate in cases where the involved diabatic PESs are tricky.
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Affiliation(s)
- Damiano Ricciarelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy
| | - Leonardo Belpassi
- CNR Institute of Chemical Science and Technologies "Giulio Natta" (CNR-SCITEC), via Elce di Sotto 8, 06123, Perugia, Italy.,Consortium for Computational Molecular and Materials Sciences (CMS)2, via Elce di Sotto 8, 06123, Perugia, Italy
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001, Leuven, Belgium
| | - Paola Belanzoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy.,CNR Institute of Chemical Science and Technologies "Giulio Natta" (CNR-SCITEC), via Elce di Sotto 8, 06123, Perugia, Italy.,Consortium for Computational Molecular and Materials Sciences (CMS)2, via Elce di Sotto 8, 06123, Perugia, Italy
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150
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Evaluation of a concerted vs. sequential oxygen activation mechanism in α-ketoglutarate-dependent nonheme ferrous enzymes. Proc Natl Acad Sci U S A 2020; 117:5152-5159. [PMID: 32094179 DOI: 10.1073/pnas.1922484117] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Determining the requirements for efficient oxygen (O2) activation is key to understanding how enzymes maintain efficacy and mitigate unproductive, often detrimental reactivity. For the α-ketoglutarate (αKG)-dependent nonheme iron enzymes, both a concerted mechanism (both cofactor and substrate binding prior to reaction with O2) and a sequential mechanism (cofactor binding and reaction with O2 precede substrate binding) have been proposed. Deacetoxycephalosporin C synthase (DAOCS) is an αKG-dependent nonheme iron enzyme for which both of these mechanisms have been invoked to generate an intermediate that catalyzes oxidative ring expansion of penicillin substrates in cephalosporin biosynthesis. Spectroscopy shows that, in contrast to other αKG-dependent enzymes (which are six coordinate when only αKG is bound to the FeII), αKG binding to FeII-DAOCS results in ∼45% five-coordinate sites that selectively react with O2 relative to the remaining six-coordinate sites. However, this reaction produces an FeIII species that does not catalyze productive ring expansion. Alternatively, simultaneous αKG and substrate binding to FeII-DAOCS produces five-coordinate sites that rapidly react with O2 to form an FeIV=O intermediate that then reacts with substrate to produce cephalosporin product. These results demonstrate that the concerted mechanism is operative in DAOCS and by extension, other nonheme iron enzymes.
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