1
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Thomas M, Jaber Sathik Rifayee SB, Chaturvedi SS, Gorantla KR, White W, Wildey J, Schofield CJ, Christov CZ. The Unique Role of the Second Coordination Sphere to Unlock and Control Catalysis in Nonheme Fe(II)/2-Oxoglutarate Histone Demethylase KDM2A. Inorg Chem 2024; 63:10737-10755. [PMID: 38781256 PMCID: PMC11168414 DOI: 10.1021/acs.inorgchem.4c01365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/26/2024] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Nonheme Fe(II) and 2-oxoglutarate (2OG)-dependent histone lysine demethylases 2A (KDM2A) catalyze the demethylation of the mono- or dimethylated lysine 36 residue in the histone H3 peptide (H3K36me1/me2), which plays a crucial role in epigenetic regulation and can be involved in many cancers. Although the overall catalytic mechanism of KDMs has been studied, how KDM2 catalysis takes place in contrast to other KDMs remains unknown. Understanding such differences is vital for enzyme redesign and can help in enzyme-selective drug design. Herein, we employed molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) to explore the complete catalytic mechanism of KDM2A, including dioxygen diffusion and binding, dioxygen activation, and substrate oxidation. Our study demonstrates that the catalysis of KDM2A is controlled by the conformational change of the second coordination sphere (SCS), specifically by a change in the orientation of Y222, which unlocks the 2OG rearrangement from off-line to in-line mode. The study demonstrates that the variant Y222A makes the 2OG rearrangement more favorable. Furthermore, the study reveals that it is the size of H3K36me3 that prevents the 2OG rearrangement, thus rendering the enzyme inactivity with trimethylated lysine. Calculations show that the SCS and long-range interacting residues that stabilize the HAT transition state in KDM2A differ from those in KDM4A, KDM7B, and KDM6A, thus providing the basics for the enzyme-selective redesign and modulation of KDM2A without influencing other KDMs.
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Affiliation(s)
- Midhun
George Thomas
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
| | | | - Shobhit S. Chaturvedi
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
| | - Koteswara Rao Gorantla
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
| | - Walter White
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
| | - Jon Wildey
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
| | - Christopher J. Schofield
- Chemistry
Research Laboratory, Department of Chemistry and the Ineos Oxford
Institute for Antimicrobial Research, University
of Oxford, 12, Mansfield Road, Oxford OX1 5JJ, U.K.
| | - Christo Z. Christov
- Department
of Chemistry, and Department of Chemical Engineering, Michigan
Technological University, Houghton, Michigan 49931, United States
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2
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Khamaru K, Pal U, Shee S, Lo R, Seal K, Ghosh P, Maiti NC, Banerji B. Metal-Free Activation of Molecular Oxygen by Quaternary Ammonium-Based Ionic Liquid: A Detail Mechanistic Study. J Am Chem Soc 2024; 146:6912-6925. [PMID: 38421821 DOI: 10.1021/jacs.3c14366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Most oxidation processes in common organic synthesis and chemical biology require transition metal catalysts or metalloenzymes. Herein, we report a detailed mechanistic study of a metal-free oxygen (O2) activation protocol on benzylamine/alcohols using simple quaternary alkylammonium-based ionic liquids to produce products such as amide, aldehyde, imine, and in some cases, even aromatized products. NMR and various control experiments established the product formation and reaction mechanism, which involved the conversion of molecular oxygen into a hydroperoxyl radical via a proton-coupled electron transfer process. Detection of hydrogen peroxide in the reaction medium using colorimetric analysis supported the proposed mechanism of oxygen activation. Furthermore, first-principles calculations using density functional theory (DFT) revealed that reaction coordinates and transition state spin densities have a unique spin conversion of triplet oxygen leading to formation of singlet products via a minimum energy crossing point. In addition to DFT, domain-based local pair natural orbital coupled cluster, (DLPNO-CCSD(T)), and complete active space self-consistent field, CASSCF(20,14) methods complemented the above findings. Partial density of states analysis showed stabilization of π* orbital of oxygen in the presence of ionic liquid, making it susceptible to hydrogen abstraction in a mild, metal-free condition. Inductively coupled plasma atomic emission spectroscopic (ICP-AES) analysis of reactant and ionic liquids clearly showed the absence of any significant transition metal contamination. The current results described the origin of O2 activation within the context of molecular orbital (MO) theory and opened up a new avenue for the use of ionic liquids as inexpensive, multifunctional and high-performance alternative to metal-based catalysts for O2 activation.
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Affiliation(s)
| | - Uttam Pal
- CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Subhankar Shee
- CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Kaushik Seal
- CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Prasanta Ghosh
- Department of Chemistry, Ramakrishna Mission Residential College (Autonomous), Narendrapur, Kolkata 700103, India
| | - Nakul Chandra Maiti
- CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Kolkata 700032, India
| | - Biswadip Banerji
- CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
- Academy of Scientific and Innovative Research (AcSIR), Kolkata 700032, India
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3
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Monika, Ansari A. Electronic structures and energetic of metal(II)-superoxo species: a DFT exploration. Struct Chem 2022. [DOI: 10.1007/s11224-022-02030-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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4
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Zhao R, Zhang BB, Liu Z, Cheng GJ, Wang ZX. DFT Mechanistic Insights into Aldehyde Deformylations with Biomimetic Metal-Dioxygen Complexes: Distinct Mechanisms and Reaction Rules. JACS AU 2022; 2:745-761. [PMID: 35373207 PMCID: PMC8970012 DOI: 10.1021/jacsau.2c00014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Indexed: 05/12/2023]
Abstract
Aldehyde deformylations occurring in organisms are catalyzed by metalloenzymes through metal-dioxygen active cores, attracting great interest to study small-molecule metal-dioxygen complexes for understanding relevant biological processes and developing biomimetic catalysts for aerobic transformations. As the known deformylation mechanisms, including nucleophilic attack, aldehyde α-H-atom abstraction, and aldehyde hydrogen atom abstraction, undergo outer-sphere pathways, we herein report a distinct inner-sphere mechanism based on density functional theory (DFT) mechanistic studies of aldehyde deformylations with a copper (II)-superoxo complex. The inner-sphere mechanism proceeds via a sequence mainly including aldehyde end-on coordination, homolytic aldehyde C-C bond cleavage, and dioxygen O-O bond cleavage, among which the C-C bond cleavage is the rate-determining step with a barrier substantially lower than those of outer-sphere pathways. The aldehyde C-C bond cleavage, enabled through the activation of the dioxygen ligand radical in a second-order nucleophilic substitution (SN2)-like fashion, leads to an alkyl radical and facilitates the subsequent dioxygen O-O bond cleavage. Furthermore, we deduced the rules for the reactions of metal-dioxygen complexes with aldehydes and nitriles via the inner-sphere mechanism. Expectedly, our proposed inner-sphere mechanisms and the reaction rules offer another perspective to understand relevant biological processes involving metal-dioxygen cores and to discover metal-dioxygen catalysts for aerobic transformations.
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Affiliation(s)
- Ruihua Zhao
- School
of Chemical Sciences, University of Chinese
Academy of Sciences, Beijing 100039, China
- Warshel
Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
| | - Bei-Bei Zhang
- School
of Chemical Sciences, University of Chinese
Academy of Sciences, Beijing 100039, China
| | - Zheyuan Liu
- College
of Materials Science and Engineering, Fuzhou
University, Fuzhou 350108, China
| | - Gui-Juan Cheng
- Warshel
Institute for Computational Biology, School of Life and Health Sciences, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China
| | - Zhi-Xiang Wang
- School
of Chemical Sciences, University of Chinese
Academy of Sciences, Beijing 100039, China
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5
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Affiliation(s)
- Milica Feldt
- Leibniz Institute for Catalysis: Leibniz-Institut fur Katalyse eV Theory & Catalysis Albert-Einstein-Str 29A 18059 Rostock GERMANY
| | - Quan Manh Phung
- Nagoya University: Nagoya Daigaku Department of Chemistry JAPAN
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6
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Nath R, Manna RN, Paul A. Decoding Regioselective Reaction Mechanism of the Gentisic Acid Catalyzed by Gentisate 1,2-Dioxygenase Enzyme. Catal Sci Technol 2022. [DOI: 10.1039/d2cy00510g] [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
Gentisate 1,2-dioxygenase (GDO), a ring-fission non-heme dioxygenase enzyme, displays a unique regioselective reaction of gentisic acid (GTQ) in the presence of molecular oxygen. GTQ is an important intermediate in the...
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7
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Zhang S, Li X, Wang Y, Yan L, Wei J, Liu Y. Computational Study of the C5-Hydroxylation Mechanism Catalyzed by the Diiron Monooxygenase PtmU3 as Part of the Platensimycin Biosynthesis. Inorg Chem 2021; 60:17783-17796. [PMID: 34762413 DOI: 10.1021/acs.inorgchem.1c02407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
PtmU3 is a newly identified nonheme diiron monooxygenase, which installs a C-5 β-hydroxyl group into the C-19 CoA-ester intermediate involved in the biosynthesis of unique diterpene-derived scaffolds of platensimycin and platencin. PtmU3 possesses a noncanonical diiron active site architecture of a saturated six-coordinate iron center and lacks the μ-oxo bridge. Although the hydroxylation process is a simple reaction for nonheme mononuclear iron-dependent enzymes, how PtmU3 employs the diiron center to catalyze the H-abstraction and OH-rebound is still unknown. In particular, the electronic characteristic of diiron is also unclear. To understand the catalytic mechanism of PtmU3, we constructed two reactant models in which both the Fe1II-Fe2III-superoxo and Fe1II-Fe2IV═O are considered to trigger the H-abstraction and performed a series of quantum mechanics/molecular mechanics calculations. Our calculation results reveal that PtmU3 is a special monooxygenase, that is, both atoms of the dioxygen molecule can be incorporated into two molecules of the substrate by the successive reactions. In the first-round reaction, PtmU3 uses the Fe1II-Fe2III-superoxo to install a hydroxyl group into the substrate, generating the high-reactive Fe1II-Fe2IV═O complex. In the second-round reaction, the Fe1II-Fe2IV═O species is responsible for the hydroxylation of another molecule of the substrate. In the diiron center, Fe2 adopts the high spin state (S = 5/2) during the catalysis, whereas for Fe1, in addition to its structural role, it may also play an assistant role for Fe1 catalysis. In the two successive OH-installing steps, the H-abstraction is always the rate-liming step. E241 and D308 not only act as bridging ligands to connect two Fe ions but also take part in the electron reorganization. Owing to the high reactivity of Fe1II-Fe2IV═O compared to Fe1II-Fe2III-superoxo, besides the C5-hydroxylation, the C3- or C18-hydroxylation was also calculated to be feasible.
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Affiliation(s)
- Shiqing Zhang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Xinyi Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Yijing Wang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Lijuan Yan
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Jingjing Wei
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan 250100, Shandong, China
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8
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Yeh CCG, Pierides C, Jameson GNL, de Visser SP. Structure and Functional Differences of Cysteine and 3-Mercaptopropionate Dioxygenases: A Computational Study. Chemistry 2021; 27:13793-13806. [PMID: 34310770 DOI: 10.1002/chem.202101878] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Indexed: 11/09/2022]
Abstract
Thiol dioxygenases are important enzymes for human health; they are involved in the detoxification and catabolism of toxic thiol-containing natural products such as cysteine. As such, these enzymes have relevance to the development of Alzheimer's and Parkinson's diseases in the brain. Recent crystal structure coordinates of cysteine and 3-mercaptopropionate dioxygenase (CDO and MDO) showed major differences in the second-coordination spheres of the two enzymes. To understand the difference in activity between these two analogous enzymes, we created large, active-site cluster models. We show that CDO and MDO have different iron(III)-superoxo-bound structures due to differences in ligand coordination. Furthermore, our studies show that the differences in the second-coordination sphere and particularly the position of a positively charged Arg residue results in changes in substrate positioning, mobility and enzymatic turnover. Furthermore, the substrate scope of MDO is explored with cysteinate and 2-mercaptosuccinic acid and their reactivity is predicted.
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Affiliation(s)
- C-C George Yeh
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Christos Pierides
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | - Guy N L Jameson
- School of Chemistry, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, 30 Flemington Road, Parkville, Vic, 3010, Australia
| | - Sam P de Visser
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.,Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
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9
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Wang J, Wang X, Ouyang Q, Liu W, Shan J, Tan H, Li X, Chen G. N-Nitrosation Mechanism Catalyzed by Non-heme Iron-Containing Enzyme SznF Involving Intramolecular Oxidative Rearrangement. Inorg Chem 2021; 60:7719-7731. [PMID: 34004115 DOI: 10.1021/acs.inorgchem.1c00057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The non-heme iron-dependent enzyme SznF catalyzes a critical N-nitrosation step during the N-nitrosourea pharmacophore biosynthesis in streptozotocin. The intramolecular oxidative rearrangement process is known to proceed at the FeII-containing active site in the cupin domain of SznF, but its mechanism has not been elucidated to date. In this study, based on the density functional theory calculations, a unique mechanism was proposed for the N-nitrosation reaction catalyzed by SznF in which a four-electron oxidation process is accomplished through a series of complicated electron transferring between the iron center and substrate to bypass the high-valent FeIV═O species. In the catalytic reaction pathway, the O2 binds to the iron center and attacks on the substrate to form the peroxo bridge intermediate by obtaining two electrons from the substrate exclusively. Then, instead of cleaving the peroxo bridge, the Cε-Nω bond of the substrate is homolytically cleaved first to form a carbocation intermediate, which polarizes the peroxo bridge and promotes its heterolysis. After O-O bond cleavage, the following reaction steps proceed effortlessly so that the N-nitrosation is accomplished without NO exchange among reaction species.
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Affiliation(s)
- Junkai Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xixi Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Qingwen Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Wei Liu
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jiankai Shan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hongwei Tan
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xichen Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Guangju Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
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10
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Cheng C, Hayashi S. Ab Initio Evaluation of the Redox Potential of Cytochrome c. J Chem Theory Comput 2021; 17:1194-1207. [PMID: 33459006 DOI: 10.1021/acs.jctc.0c00889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Various biochemical activities of metabolism and biosynthesis are fulfilled by redox processes with explicit electron exchange, which furnish redox enzymes with high chemical reactivity. However, theoretical investigation of a redox process, which simultaneously involves a complex electronic change at a redox metal center and conformational reorganization of the surrounding protein environment coupled to the electronic change, requires computationally conflicting approaches, highly accurate quantum chemical calculations, and long-time molecular dynamics (MD) simulations, limiting the physicochemical understanding of biological redox processes. Here, we theoretically examined a redox process of cytochrome c by means of a hybrid molecular simulation technique, which enables one to consistently treat the redox center at the ab initio quantum chemistry level of theory and the protein reorganization with long-time MD simulations on the microsecond timescale. The calculations successfully evaluated a large absolute redox potential, 4.34 eV, with errors of only 0.03 to 0.34 eV to the experimental ones without any problem-specific empirical parameters. Through the long-time MD sampling, large and nonlinear reorganization of the protein environment was unveiled and the molecular determinants for the redox potential were identified. The present ab initio approach significantly expands the applicability of theoretical investigation to biological redox systems with more electronically complicated redox centers such as polynuclear transition metal complexes.
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Affiliation(s)
- Cheng Cheng
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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11
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Chaturvedi SS, Ramanan R, Hu J, Hausinger RP, Christov CZ. Atomic and Electronic Structure Determinants Distinguish between Ethylene Formation and l-Arginine Hydroxylation Reaction Mechanisms in the Ethylene-Forming Enzyme. ACS Catal 2021. [DOI: 10.1021/acscatal.0c03349] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Shobhit S. Chaturvedi
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Rajeev Ramanan
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
| | | | | | - Christo Z. Christov
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931, United States
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12
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Tetteh S. Halide effect on the electron distribution in oxovanadium complexes bearing side-on (η2) dioxygen ligands: A combined crystallographic and theoretical study. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Weak O 2 binding and strong H 2O 2 binding at the non-heme diiron center of trypanosome alternative oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148356. [PMID: 33385341 DOI: 10.1016/j.bbabio.2020.148356] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/10/2020] [Accepted: 12/12/2020] [Indexed: 12/20/2022]
Abstract
Alternative oxidase (AOX) catalyzes the four-electron reduction of dioxygen to water as an additional terminal oxidase, and the catalytic reaction is critical for the parasite to survive in its bloodstream form. Recently, the X-ray crystal structure of trypanosome alternative oxidase (TAO) complexed with ferulenol was reported and the molecular structure of the non-heme diiron center was determined. The binding of O2 was a unique side-on type compared to other iron proteins. In order to characterize the O2 binding state of TAO, the O2 binding states were searched at a quantum mechanics/molecular mechanics (QM/MM) theoretical level in the present study. We found that the most stable O2 binding state is the end-on type, and the binding states of the side-on type are higher in energy. Based on the binding energies and electronic structure analyses, O2 binds very weakly to the TAO iron center (ΔE =6.7 kcal mol-1) in the electronic state of Fe(II)…OO, not in the suggested charge transferred state such as the superoxide state (Fe(III)OO· -) as seen in hemerythrin. Coordination of other ligands such as water, Cl-, CN-, CO, N3- and H2O2 was also examined, and H2O2 was found to bind most strongly to the Fe(II) site by ΔE = 14.0 kcal mol-1. This was confirmed experimentally through the measurement of ubiquinol oxidase activity of TAO and Cryptosporidium parvum AOX which was found to be inhibited by H2O2 in a dose-dependent and reversible manner.
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14
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Ramanan R, Chaturvedi SS, Lehnert N, Schofield CJ, Karabencheva-Christova TG, Christov CZ. Catalysis by the JmjC histone demethylase KDM4A integrates substrate dynamics, correlated motions and molecular orbital control. Chem Sci 2020; 11:9950-9961. [PMID: 34094257 PMCID: PMC8162366 DOI: 10.1039/d0sc03713c] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The Nε-methyl lysine status of histones is important in the regulation of eukaryotic transcription. The Fe(ii) and 2-oxoglutarate (2OG) -dependent JmjC domain enzymes are the largest family of histone Nε-methyl lysine demethylases (KDMs). The human KDM4 subfamily of JmjC KDMs is linked with multiple cancers and some of its members are medicinal chemistry targets. We describe the use of combined molecular dynamics (MD) and Quantum Mechanical/Molecular Mechanical (QM/MM) methods to study the mechanism of KDM4A, which catalyzes demethylation of both tri- and di-methylated forms of histone H3 at K9 and K36. The results show that the oxygen activation at the active site of KDM4A is optimized towards the generation of the reactive Fe(iv)-oxo intermediate. Factors including the substrate binding mode, correlated motions of the protein and histone substrates, and molecular orbital control synergistically contribute to the reactivity of the Fe(iv)-oxo intermediate. In silico substitutions were performed to investigate the roles of residues (Lys241, Tyr177, and Asn290) in substrate orientation. The Lys241Ala substitution abolishes activity due to altered substrate orientation consistent with reported experimental studies. Calculations with a macrocyclic peptide substrate analogue reveal that induced conformational changes/correlated motions in KDM4A are sequence-specific in a manner that influences substrate binding affinity. Second sphere residues, such as Ser288 and Thr289, may contribute to KDM4A catalysis by correlated motions with active site residues. Residues that stabilize key intermediates, and which are predicted to be involved in correlated motions with other residues in the second sphere and beyond, are shown to be different in KDM4A compared to those in another JmjC KDM (PHF8), which acts on H3K9 di- and mono-methylated forms, suggesting that allosteric type inhibition is of interest from the perspective of developing selective JmjC KDM inhibitors. The second sphere residues and regions of the protein in histone demethylase enzymes that makes correlated motion with the active site contribute to efficient catalysis.![]()
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Affiliation(s)
- Rajeev Ramanan
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
| | - Shobhit S Chaturvedi
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
| | - Nicolai Lehnert
- Department of Chemistry, University of Michigan Ann Arbor MI 48019 USA
| | | | | | - Christo Z Christov
- Department of Chemistry, Michigan Technological University Houghton Michigan 49931 USA
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15
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Theoretical Study on Electronic Structural Properties of Catalytically Reactive Metalloporphyrin Intermediates. Catalysts 2020. [DOI: 10.3390/catal10020224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Metalloporphyrins have attracted great attention in the potential application of biomimetic catalysis. Especially, they were widely investigated as green catalysts in the chemical oxidation of various hydrocarbons through the catalytic activation of molecular oxygen. The structural properties of active central metal ions were reported to play a decisive role in catalytic activity. However, those delicate structural changes are difficult to be experimentally captured or elucidated in detail. Herein, we explored the electronic structural properties of metalloporphyrins (metal porphyrin (PMII, PMIIICl)) and their corresponding catalytically active intermediates (metal(III)-peroxo(PMIII-O2), metal(III)-hydroperoxo(PMIII-OH), and metal(IV)-oxo(PMIV=O), (M=Fe, Mn, and Co)) through the density functional theory method. The ground states of these intermediates were determined based on the assessment of relative energy and the corresponding geometric structures of ground states also further confirmed the stability of energy. Furthermore, our analyses of Mulliken charges and frontier molecular orbitals revealed the potential catalytic behavior of reactive metalloporphyrin intermediates.
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16
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Zhao R, Guo J, Zhang C, Lu Y, Dagnaw WM, Wang ZX. DFT Mechanistic Insight into the Dioxygenase-like Reactivity of a Co III-peroxo Complex: O–O Bond Cleavage via a [1,3]-Sigmatropic Rearrangement-like Mechanism. Inorg Chem 2020; 59:2051-2061. [DOI: 10.1021/acs.inorgchem.9b03470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ruihua Zhao
- School of Chemical Sciences, University of Chinese Academy of Sciences, Jia #19, Yuquan Road, Beijing 100039, China
| | - Jiandong Guo
- School of Chemical Sciences, University of Chinese Academy of Sciences, Jia #19, Yuquan Road, Beijing 100039, China
| | - Chaoshen Zhang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Jia #19, Yuquan Road, Beijing 100039, China
| | - Yu Lu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Jia #19, Yuquan Road, Beijing 100039, China
| | - Wasihun Menberu Dagnaw
- School of Chemical Sciences, University of Chinese Academy of Sciences, Jia #19, Yuquan Road, Beijing 100039, China
| | - Zhi-Xiang Wang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Jia #19, Yuquan Road, Beijing 100039, China
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17
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Fan G, Shang Z, Li R, Shafiei-Haghighi S, Peng Q, Findlater M, Xu X. Mechanism of the Iron(0)-Catalyzed Hydrosilylation of Aldehydes: A Combined DFT and Experimental Investigation. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00388] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guilan Fan
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Zhenfeng Shang
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Ruifang Li
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Sara Shafiei-Haghighi
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Qian Peng
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Michael Findlater
- Department of Chemistry & Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
| | - Xiufang Xu
- Key Laboratory of Advanced Energy Materials Chemistry (Ministry of Education), State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China
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18
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Marino T, Fortino MG, Russo N, Toscano M, Alberto ME. Computational Mechanistic Insights on the NO Oxidation Reaction Catalyzed by Non-Heme Biomimetic Cr-N-Tetramethylated Cyclam Complexes. Int J Mol Sci 2019; 20:ijms20163955. [PMID: 31416223 PMCID: PMC6721035 DOI: 10.3390/ijms20163955] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 07/31/2019] [Accepted: 08/08/2019] [Indexed: 12/16/2022] Open
Abstract
The conversion reaction of NO to NO3− ion catalyzed by the end-on [Cr(III)(n-TMC)(O2)(Cl)]+ superoxo and side-on [Cr(IV)(n-TMC)(O2)(Cl)]+ peroxo non-heme complexes (n = 12, 13, 14 and 15), which are biomimetic systems of nitric oxide dioxygenases (NODs), has been explored using a computational protocol in the framework of density functional theory. Results show that the potential energy profiles for the studied reactions lie above the reagent energies, regardless of the used catalyst. Both the O-O bond breaking in the biomimetics and the NO3− ion formation require low energy barriers suggesting an efficient catalytic power of the studied systems. The rate-determining step depends on ligand size.
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Affiliation(s)
- Tiziana Marino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Rende, Italy.
| | - Maria Grazia Fortino
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Rende, Italy
| | - Nino Russo
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Rende, Italy.
| | - Marirosa Toscano
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Rende, Italy
| | - Marta Erminia Alberto
- Dipartimento di Chimica e Tecnologie Chimiche, Università della Calabria, 87036 Rende, Italy
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19
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A computational DFT study of methane C H and ammine N H activations by group 9 N-pyrrolyl complexes. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.112503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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20
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Vorontsov AV. Advancing Fenton and photo-Fenton water treatment through the catalyst design. JOURNAL OF HAZARDOUS MATERIALS 2019; 372:103-112. [PMID: 29709242 DOI: 10.1016/j.jhazmat.2018.04.033] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2017] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 05/29/2023]
Abstract
The review is devoted to modern Fenton, photo-Fenton, as well as Fenton-like and photo-Fenton-like reactions with participation of iron species in liquid phase and as heterogeneous catalysts. Mechanisms of these reactions were considered that include hydroxyl radical and oxoferryl species as the reactive intermediates. The barriers in the way of application of these reactions to wastewater treatment were discussed. The following fundamental problems need further research efforts: inclusion of more mechanism steps and quantum calculations of all rate constants lacking in the literature, checking the outer sphere electron transfer contribution, determination of the causes for the key changes in the homogeneous Fenton reaction mechanism with a change in the reagents concentration. The key advances for Fenton reactions implementation for the water treatment are related to tremendous hydrodynamical effects on the catalytic activity, design of ligands for high rate and completeness of mineralization in short time, and design of highly active heterogeneous catalysts. While both homogeneous and heterogeneous Fenton and photo-Fenton systems are open for further improvements, heterogeneous photo-Fenton systems are most promising for practical applications because of the inherent higher catalyst stability. Modern methods of quantum chemistry are expected to play a continuously increasing role in development of such catalysts.
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21
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Manna RN, Malakar T, Jana B, Paul A. Unraveling the Crucial Role of Single Active Water Molecule in the Oxidative Cleavage of Aliphatic C–C Bond of 2,4′-Dihydroxyacetophenone Catalyzed by 2,4′-Dihydroxyacetophenone Dioxygenase Enzyme: A Quantum Mechanics/Molecular Mechanics Investigation. ACS Catal 2018. [DOI: 10.1021/acscatal.8b03201] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Rabindra Nath Manna
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Tanmay Malakar
- Raman Center for Atomic, Molecular, and Optical Science, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Ankan Paul
- Raman Center for Atomic, Molecular, and Optical Science, Indian Association for the Cultivation of Science, 2A & 2B Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
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22
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Tian G, Su H, Liu Y. Mechanism of Sulfoxidation and C–S Bond Formation Involved in the Biosynthesis of Ergothioneine Catalyzed by Ergothioneine Synthase (EgtB). ACS Catal 2018. [DOI: 10.1021/acscatal.8b01473] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ge Tian
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, People’s Republic of China
| | - Hao Su
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, People’s Republic of China
| | - Yongjun Liu
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, People’s Republic of China
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23
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Phung QM, Pierloot K. The dioxygen adducts of iron and manganese porphyrins: electronic structure and binding energy. Phys Chem Chem Phys 2018; 20:17009-17019. [DOI: 10.1039/c8cp03078b] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The electronic structures of adducts of O2 and metal porphyrins were thoroughly investigated by highly accurate DMRG-CASPT2.
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24
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Zhao C, Chen H. Mechanism of Organophosphonate Catabolism by Diiron Oxygenase PhnZ: A Third Iron-Mediated O–O Activation Scenario in Nature. ACS Catal 2017. [DOI: 10.1021/acscatal.7b00578] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chongyang Zhao
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, CAS Research/Education Center for Excellence in
Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Hui Chen
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, CAS Research/Education Center for Excellence in
Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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25
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Jiang Y, Zhang X, Mao Q, Tan H, Li X, Chen G, Jia Z. A theoretical study on oxidative cleavage of olefins to carbonyls catalysed by Fe(iii)-PyBisulidine. Dalton Trans 2017; 46:3825-3832. [DOI: 10.1039/c7dt00229g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The oxidative cleavage of olefins to carbonyls catalyzed by the Fe(iii)-PyBisulidine catalyst was investigated by DFT calculations.
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Affiliation(s)
- Yafei Jiang
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Xiaotong Zhang
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Qiuyun Mao
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Hongwei Tan
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Xichen Li
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Guangju Chen
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Zongchao Jia
- Department of Biomedical and Molecular Sciences
- Queen's University
- Kingston
- Canada K7N 3L6
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26
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Zhang S, Wang X, Liu Y. Cleavage mechanism of the aliphatic C–C bond catalyzed by 2,4′-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP: a QM/MM study. Catal Sci Technol 2017. [DOI: 10.1039/c6cy02553f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Calculations suggest that the reactant complex may firstly undergo a triplet–quintet crossing to initiate the reaction and then the subsequent chemistry occurs on the multiple-states surfaces. The key C–C bond cleavage is accompanied by an insertion reaction of oxygen radical.
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Affiliation(s)
- Shujun Zhang
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Xiya Wang
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan
- China
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27
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Attia AAA, Silaghi-Dumitrescu R. A mononuclear non-heme-iron dioxygen-carrying protein? J Mol Graph Model 2016; 69:103-10. [PMID: 27607306 DOI: 10.1016/j.jmgm.2016.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 08/31/2016] [Accepted: 09/01/2016] [Indexed: 10/21/2022]
Abstract
The ability of mononuclear non-heme iron complexes to function as molecular oxygen transporters is investigated by density functional theory. The factors governing the efficiency of the reversible binding of dioxygen at the active site of the dinuclear non-heme iron enzyme hemerythrin, including antiferromagnetic coupling and the conversion of dioxygen to hydroperoxo by a proton coupled 2-electron transfer mechanism, are revisited and considered as possible tools in mononuclear non-heme complexes. Several mononuclear non-heme model complexes, including active sites of enzymes already known to interact with dioxgenic ligands, are constructed and the molecular oxygen transportation capabilities of these complexes are examined computationally. The high-spin nature of the ground state of these complexes implies an intrinsic kinetic lability of the oxy structures, as also evident from potential energy surface calculations towards iron-dioxygen cleavage. Proton affinities as calibrated with reference compounds showed that these complexes are highly unlikely to undergo protonation to form hydroperoxo-like adducts. Mixed superoxo descriptions of the dissociated dioxygenic ligands in all complexes add to the overall conclusion that these model structures are significantly disadvantaged in any attempt to be employed for molecular oxygen transportation.
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Affiliation(s)
- Amr A A Attia
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania.
| | - Radu Silaghi-Dumitrescu
- Department of Chemistry, Faculty of Chemistry and Chemical Engineering, Babeş-Bolyai University, Cluj-Napoca, Romania.
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28
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Minaev B, Baryshnikova A, Sun WH. Spin-dependent effects in ethylene polymerization with bis(imino)pyridine iron(II) complexes. J Organomet Chem 2016. [DOI: 10.1016/j.jorganchem.2016.03.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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29
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Mono- and binuclear non-heme iron chemistry from a theoretical perspective. J Biol Inorg Chem 2016; 21:619-44. [DOI: 10.1007/s00775-016-1357-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 04/29/2016] [Indexed: 10/21/2022]
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30
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Qi Y, Lu J, Lai W. Insights into the Reaction Mechanism of Aromatic Ring Cleavage by Homogentisate Dioxygenase: A Quantum Mechanical/Molecular Mechanical Study. J Phys Chem B 2016; 120:4579-90. [PMID: 27119315 DOI: 10.1021/acs.jpcb.6b03006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
To elucidate the reaction mechanism of the ring cleavage of homogentisate by homogentisate dioxygenase, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out by using two systems in different protonation states of the substrate C2 hydroxyl group. When the substrate C2 hydroxyl group is ionized (the ionized pathway), the superoxo attack on the substrate is the rate-limiting step in the catalytic cycle, with a barrier of 15.9 kcal/mol. Glu396 was found to play an important role in stabilizing the bridge species and its O-O cleavage product by donating a proton via a hydrogen-bonded water molecule. When the substrate C2 hydroxyl group is not ionized (the nonionized pathway), the O-O bond cleavage of the bridge species is the rate-limiting step, with a barrier of 15.3 kcal/mol. The QM/MM-optimized geometries for the dioxygen and alkylperoxo complexes using the nonionized model (for the C2 hydroxyl group) are in agreement with the experimental crystal structures, suggesting that the C2 hydroxyl group is more likely to be nonionized.
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Affiliation(s)
- Yue Qi
- Department of Chemistry, Renmin University of China , Beijing, 100872, China
| | - Jiarui Lu
- Department of Chemistry, Renmin University of China , Beijing, 100872, China
| | - Wenzhen Lai
- Department of Chemistry, Renmin University of China , Beijing, 100872, China
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31
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Stout HD, Kleespies ST, Chiang CW, Lee WZ, Que L, Münck E, Bominaar EL. Spectroscopic and Theoretical Study of Spin-Dependent Electron Transfer in an Iron(III) Superoxo Complex. Inorg Chem 2016; 55:5215-26. [PMID: 27159412 DOI: 10.1021/acs.inorgchem.6b00134] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It was shown previously (J. Am. Chem. Soc. 2014, 136, 10846) that bubbling of O2 into a solution of Fe(II)(BDPP) (H2BDPP = 2,6-bis[[(S)-2-(diphenylhydroxymethyl)-1-pyrrolidinyl]methyl]pyridine) in tetrahydrofuran at -80 °C generates a high-spin (SFe = (5)/2) iron(III) superoxo adduct, 1. Mössbauer studies revealed that 1 is an exchange-coupled system, [Formula: see text], where SR = (1)/2 is the spin of the superoxo radical, of which the spectra were not well enough resolved to determine whether the coupling was ferromagnetic (S = 3 ground state) or antiferromagnetic (S = 2). The glass-forming 2-methyltetrahydrofuran solvent yields highly resolved Mössbauer spectra from which the following data have been extracted: (i) the ground state of 1 has S = 3 (J < 0); (ii) |J| > 15 cm(-1); (iii) the zero-field-splitting parameters are D = -1.1 cm(-1) and E/D = 0.02; (iv) the major component of the electric-field-gradient tensor is tilted ≈7° relative to the easy axis of magnetization determined by the MS = ±3 and ±2 doublets. The excited-state MS = ±2 doublet yields a narrow parallel-mode electron paramagnetic resonance signal at g = 8.03, which was used to probe the magnetic hyperfine splitting of (17)O-enriched O2. A theoretical model that considers spin-dependent electron transfer for the cases where the doubly occupied π* orbital of the superoxo ligand is either "in" or "out" of the plane defined by the bent Fe-OO moiety correctly predicts that 1 has an S = 3 ground state, in contrast to the density functional theory calculations for 1, which give a ground state with both the wrong spin and orbital configuration. This failure has been traced to a basis set superposition error in the interactions between the superoxo moiety and the adjacent five-membered rings of the BDPP ligand and signals a fundamental problem in the quantum chemistry of O2 activation.
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Affiliation(s)
- Heather D Stout
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Scott T Kleespies
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Chien-Wei Chiang
- Department of Chemistry, National Taiwan Normal University , 88, Section 4, Ting-Chow Road, Taipei 11677, Taiwan (R.O.C.)
| | - Way-Zen Lee
- Department of Chemistry, National Taiwan Normal University , 88, Section 4, Ting-Chow Road, Taipei 11677, Taiwan (R.O.C.)
| | - Lawrence Que
- Department of Chemistry and Center for Metals in Biocatalysis, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Eckard Münck
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
| | - Emile L Bominaar
- Department of Chemistry, Carnegie Mellon University , Pittsburgh, Pennsylvania 15213, United States
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32
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Sun Y, Tang H, Chen K, Hu L, Yao J, Shaik S, Chen H. Two-State Reactivity in Low-Valent Iron-Mediated C–H Activation and the Implications for Other First-Row Transition Metals. J Am Chem Soc 2016; 138:3715-30. [DOI: 10.1021/jacs.5b12150] [Citation(s) in RCA: 108] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Yihua Sun
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Hao Tang
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Kejuan Chen
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Lianrui Hu
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Jiannian Yao
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Sason Shaik
- Institute
of Chemistry and the Lise Meitner-Minerva Center for Computational
Quantum Chemistry, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
| | - Hui Chen
- Beijing
National Laboratory for Molecular Sciences (BNLMS), Key Laboratory
of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
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33
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Zhang J, Wang Y, Luo N, Chen Z, Wu K, Yin G. Redox inactive metal ion triggered N-dealkylation by an iron catalyst with dioxygen activation: a lesson from lipoxygenases. Dalton Trans 2016; 44:9847-59. [PMID: 25939391 DOI: 10.1039/c5dt00804b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Utilization of dioxygen as the terminal oxidant at ambient temperature is always a challenge in redox chemistry, because it is hard to oxidize a stable redox metal ion like iron(III) to its high oxidation state to initialize the catalytic cycle. Inspired by the dioxygenation and co-oxidase activity of lipoxygenases, herein, we introduce an alternative protocol to activate the sluggish iron(III) species with non-redox metal ions, which can promote its oxidizing power to facilitate substrate oxidation with dioxygen, thus initializing the catalytic cycle. In oxidations of N,N-dimethylaniline and its analogues, adding Zn(OTf)2 to the [Fe(TPA)Cl2]Cl catalyst can trigger the amine oxidation with dioxygen, whereas [Fe(TPA)Cl2]Cl alone is very sluggish. In stoichiometric oxidations, it has also been confirmed that the presence of Zn(OTf)2 can apparently improve the electron transfer capability of the [Fe(TPA)Cl2]Cl complex. Experiments using different types of substrates as trapping reagents disclosed that the iron(IV) species does not occur in the catalytic cycle, suggesting that oxidation of amines is initialized by electron transfer rather than hydrogen abstraction. Combined experiments from UV-Vis, high resolution mass spectrometry, electrochemistry, EPR and oxidation kinetics support that the improved electron transfer ability of iron(III) species originates from its interaction with added Lewis acids like Zn(2+) through a plausible chloride or OTf(-) bridge, which has promoted the redox potential of iron(III) species. The amine oxidation mechanism was also discussed based on the available data, which resembles the co-oxidase activity of lipoxygenases in oxidative dealkylation of xenobiotic metabolisms where an external electron donor is not essential for dioxygen activation.
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Affiliation(s)
- Jisheng Zhang
- School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Key Laboratory for Large-Format Battery Materials and System, Ministry of Education, Luoyu Road 1037, Wuhan 430074, PR China.
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34
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Taabazuing CY, Fermann J, Garman S, Knapp MJ. Substrate Promotes Productive Gas Binding in the α-Ketoglutarate-Dependent Oxygenase FIH. Biochemistry 2016; 55:277-86. [PMID: 26727884 PMCID: PMC4793777 DOI: 10.1021/acs.biochem.5b01003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Fe(2+)/α-ketoglutarate (αKG)-dependent oxygenases use molecular oxygen to conduct a wide variety of reactions with important biological implications, such as DNA base excision repair, histone demethylation, and the cellular hypoxia response. These enzymes follow a sequential mechanism in which O2 binds and reacts after the primary substrate binds, making those structural factors that promote productive O2 binding central to their chemistry. A large challenge in this field is to identify strategies that engender productive turnover. Factor inhibiting HIF (FIH) is a Fe(2+)/αKG-dependent oxygenase that forms part of the O2 sensing machinery in human cells by hydroxylating the C-terminal transactivation domain (CTAD) found within the HIF-1α protein. The structure of FIH was determined with the O2 analogue NO bound to Fe, offering the first direct insight into the gas binding geometry in this enzyme. Through a combination of density functional theory calculations, {FeNO}(7) electron paramagnetic resonance spectroscopy, and ultraviolet-visible absorption spectroscopy, we demonstrate that CTAD binding stimulates O2 reactivity by altering the orientation of the bound gas molecule. Although unliganded FIH binds NO with moderate affinity, the bound gas can adopt either of two orientations with similar stability; upon CTAD binding, NO adopts a single preferred orientation that is appropriate for supporting oxidative decarboxylation. Combined with other studies of related enzymes, our data suggest that substrate-induced reorientation of bound O2 is the mechanism utilized by the αKG oxygenases to tightly couple O2 activation to substrate hydroxylation.
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Affiliation(s)
| | - Justin Fermann
- Department of Chemistry, University of Massachusetts, Amherst
| | - Scott Garman
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst
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35
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Anneser MR, Haslinger S, Pöthig A, Cokoja M, D'Elia V, Högerl MP, Basset JM, Kühn FE. Binding of molecular oxygen by an artificial heme analogue: investigation on the formation of an Fe–tetracarbene superoxo complex. Dalton Trans 2016; 45:6449-55. [DOI: 10.1039/c6dt00538a] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reactivity of a heme-like organometallic Fe–NHC complex with O2 is studied. The formation of a superoxo Fe(iii) intermediate is observed. The reactivity of the intermediate in acetone and acetonitrile is described and the products are identified.
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Affiliation(s)
- Markus R. Anneser
- Chair of Inorganic Chemistry/Molecular Catalysis
- Catalysis Research Center
- Ernst-Otto-Fischer-Strasse 1 and Faculty of Chemistry
- D-85747 Garching bei München
- Germany
| | - Stefan Haslinger
- Chair of Inorganic Chemistry/Molecular Catalysis
- Catalysis Research Center
- Ernst-Otto-Fischer-Strasse 1 and Faculty of Chemistry
- D-85747 Garching bei München
- Germany
| | - Alexander Pöthig
- Chair of Inorganic Chemistry/Molecular Catalysis
- Catalysis Research Center
- Ernst-Otto-Fischer-Strasse 1 and Faculty of Chemistry
- D-85747 Garching bei München
- Germany
| | - Mirza Cokoja
- Chair of Inorganic Chemistry/Molecular Catalysis
- Catalysis Research Center
- Ernst-Otto-Fischer-Strasse 1 and Faculty of Chemistry
- D-85747 Garching bei München
- Germany
| | - Valerio D'Elia
- KAUST Catalysis Center
- King Abdullah University of Science and Technology
- Thuwal
- Kingdom of Saudi Arabia
- Department of Materials Science and Engineering
| | - Manuel P. Högerl
- KAUST Catalysis Center
- King Abdullah University of Science and Technology
- Thuwal
- Kingdom of Saudi Arabia
| | - Jean-Marie Basset
- KAUST Catalysis Center
- King Abdullah University of Science and Technology
- Thuwal
- Kingdom of Saudi Arabia
| | - Fritz E. Kühn
- Chair of Inorganic Chemistry/Molecular Catalysis
- Catalysis Research Center
- Ernst-Otto-Fischer-Strasse 1 and Faculty of Chemistry
- D-85747 Garching bei München
- Germany
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36
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Huang XC, Wang HF, Lang JP. Theoretical view on a linear end-on manganese–dioxygen complex bearing a calix[4]arene ligand. RSC Adv 2016. [DOI: 10.1039/c6ra11199h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Mn–O–O angle of mononuclear manganese(iii)-superoxo complexes supported by zwitterionic calix[4]arene ligands can be modulated via solvent polarity perturbations and/or ligand size adjustment as indicated by DFT calculations.
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Affiliation(s)
- Xiang-Cui Huang
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- People's Republic of China
| | - Hui-Fang Wang
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- People's Republic of China
| | - Jian-Ping Lang
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- People's Republic of China
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37
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Sun Y, Chen H. DFT Methods to Study the Reaction Mechanism of Iridium-Catalyzed Hydrogenation of Olefins: Which Functional Should be Chosen? Chemphyschem 2015; 17:119-27. [DOI: 10.1002/cphc.201500817] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Yihua Sun
- Beijing National Laboratory for Molecular Sciences (BNLMS); CAS Key Laboratory of Photochemistry; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
| | - Hui Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS); CAS Key Laboratory of Photochemistry; Institute of Chemistry; Chinese Academy of Sciences; Beijing 100190 China
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38
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Goo YR, Maity AC, Cho KB, Lee YM, Seo MS, Park YJ, Cho J, Nam W. Tuning the Reactivity of Chromium(III)-Superoxo Species by Coordinating Axial Ligands. Inorg Chem 2015; 54:10513-20. [PMID: 26486819 DOI: 10.1021/acs.inorgchem.5b02068] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metal-superoxo species have attracted much attention recently as key intermediates in enzymatic and biomimetic oxidation reactions. The effect(s) of axial ligands on the chemical properties of metal-superoxo complexes has never been explored previously. In this study, we synthesized and characterized chromium(III)-superoxo complexes bearing TMC derivatives with pendant pyridine and imidazole donors, such as [Cr(III)(O2)(TMC-Py)](2+) (1, TMC-Py = 4,8,11-trimethyl-1-(2-pyridylmethyl)-1,4,8,11-tetraazacyclotetradecane) and [Cr(III)(O2)(TMC-Im)](2+) (2, TMC-Im = 4,8,11-trimethyl-1-(2-methylimidazolmethyl)-1,4,8,11-tetraazacyclotetradecane). The reactivity of chromium(III)-superoxo complexes binding different axial ligands, such as 1, 2, and [Cr(III)(O2)(TMC)(Cl)](+) (3, TMC = 1,4,8,11-tetramethyl-1,4,8,11-tetraazacyclotetradecane), was then investigated in C-H bond activation and oxygen atom transfer reactions. Kinetic studies revealed that the reactivity of the Cr(III)-superoxo complexes depends on the axial ligands, showing the reactivity order of 1 > 2 > 3 in those electrophilic oxidation reactions. It was also shown that there is a good correlation between the reactivity of the chromium(III)-superoxo complexes and their redox potentials, in which the redox potentials of the chromium(III)-superoxo complexes are in the order 1 > 2 > 3. DFT calculations reproduced the reactivity order between 1 and 3 in both C-H bond activation and oxygen atom transfer reactions, and the latter reaction is described using orbital interactions. The calculations are also in agreement with the experimentally obtained redox potentials. The present results provide the first example showing that the reactivity of metal-superoxo species can be tuned by the electron-donating ability of axial ligands bound trans to the metal-superoxo moiety.
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Affiliation(s)
- Yi Re Goo
- Department of Chemistry and Nano Science, Ewha Womans University , Seoul 03760, Korea
| | - Annada C Maity
- Department of Chemistry and Nano Science, Ewha Womans University , Seoul 03760, Korea
| | - Kyung-Bin Cho
- Department of Chemistry and Nano Science, Ewha Womans University , Seoul 03760, Korea
| | - Yong-Min Lee
- Department of Chemistry and Nano Science, Ewha Womans University , Seoul 03760, Korea
| | - Mi Sook Seo
- Department of Chemistry and Nano Science, Ewha Womans University , Seoul 03760, Korea
| | - Young Jun Park
- Department of Chemistry and Nano Science, Ewha Womans University , Seoul 03760, Korea
| | - Jaeheung Cho
- Department of Emerging Materials Science, DGIST , Daegu 42988, Korea
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University , Seoul 03760, Korea
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39
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Hu L, Chen H. Assessment of DFT Methods for Computing Activation Energies of Mo/W-Mediated Reactions. J Chem Theory Comput 2015; 11:4601-14. [DOI: 10.1021/acs.jctc.5b00373] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Lianrui Hu
- Beijing National Laboratory
for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Hui Chen
- Beijing National Laboratory
for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry,
Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
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40
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Wang B, Zhou X, Wang D, Yin JJ, Chen H, Gao X, Zhang J, Ibrahim K, Chai Z, Feng W, Zhao Y. Structure and catalytic activities of ferrous centers confined on the interface between carbon nanotubes and humic acid. NANOSCALE 2015; 7:2651-2658. [PMID: 25580558 DOI: 10.1039/c4nr06665k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Preparation of heterogeneous catalysts with active ferrous centers is of great significance for industrial and environmental catalytic processes. Nanostructured carbon materials (NCM), which possess free-flowing π electrons, can coordinate with transition metals, provide a confinement environment for catalysis, and act as potential supports or ligands to construct analogous complexes. However, designing such catalysts using NCM is still seldom studied to date. Herein, we synthesized a sandwich structured ternary complex via the coordination of Fe-loaded humic acid (HA) with C=C bonds in the aromatic rings of carbon nanotubes (CNTs), in which the O/N-Fe-C interface configuration provides the confinement environment for the ferrous sites. The experimental and theoretical results revealed octahedrally/tetrahedrally coordinated geometry at Fe centers, and the strong hybridization between CNT C π* and Fe 3d orbitals induces discretization of the atomic charges on aromatic rings of CNTs, which facilitates O2 adsorption and electron transfer from carbon to O2, which enhances O2 activation. The O2 activation by the novel HA/Fe-CNT complex can be applied in the oxidative degradation of phenol red (PR) and bisphenol A (BPA) in aqueous media.
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Affiliation(s)
- Bing Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Key Laboratory of Nuclear Radiation and Nuclear Energy Technology, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
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41
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Di Fiore A, Vergara A, Caterino M, Alterio V, Monti SM, Ombouma J, Dumy P, Vullo D, Supuran CT, Winum JY, De Simone G. Hydroxylamine-O-sulfonamide is a versatile lead compound for the development of carbonic anhydrase inhibitors. Chem Commun (Camb) 2015; 51:11519-22. [DOI: 10.1039/c5cc03711e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydroxylamine-O-sulfonamide has been investigated as CA inhibitor by means of kinetic and structural studies clarifying its mechanism of action.
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Affiliation(s)
- Anna Di Fiore
- Istituto di Biostrutture e Bioimmagini-CNR
- 80134 Napoli
- Italy
| | - Alessandro Vergara
- Istituto di Biostrutture e Bioimmagini-CNR
- 80134 Napoli
- Italy
- Department of Chemical Sciences
- Napoli
| | | | | | | | - Joanna Ombouma
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS
- ENSCM
- Université de Montpellier
- Bâtiment de Recherche Max Mousseron
- Ecole Nationale Supérieure de Chimie de Montpellier
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS
- ENSCM
- Université de Montpellier
- Bâtiment de Recherche Max Mousseron
- Ecole Nationale Supérieure de Chimie de Montpellier
| | - Daniela Vullo
- Università degli Studi di Firenze
- Polo Scientifico
- Laboratorio di Chimica Bioinorganica
- Florence
- Italy
| | - Claudiu T. Supuran
- Università degli Studi di Firenze
- Polo Scientifico
- Laboratorio di Chimica Bioinorganica
- Florence
- Italy
| | - Jean-Yves Winum
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS
- ENSCM
- Université de Montpellier
- Bâtiment de Recherche Max Mousseron
- Ecole Nationale Supérieure de Chimie de Montpellier
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42
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Abstract
In order to address how diverse metalloprotein active sites, in particular those containing iron and copper, guide O₂binding and activation processes to perform diverse functions, studies of synthetic models of the active sites have been performed. These studies have led to deep, fundamental chemical insights into how O₂coordinates to mono- and multinuclear Fe and Cu centers and is reduced to superoxo, peroxo, hydroperoxo, and, after O-O bond scission, oxo species relevant to proposed intermediates in catalysis. Recent advances in understanding the various factors that influence the course of O₂activation by Fe and Cu complexes are surveyed, with an emphasis on evaluating the structure, bonding, and reactivity of intermediates involved. The discussion is guided by an overarching mechanistic paradigm, with differences in detail due to the involvement of disparate metal ions, nuclearities, geometries, and supporting ligands providing a rich tapestry of reaction pathways by which O₂is activated at Fe and Cu sites.
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43
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Hong S, Sutherlin KD, Park J, Kwon E, Siegler MA, Solomon EI, Nam W. Crystallographic and spectroscopic characterization and reactivities of a mononuclear non-haem iron(III)-superoxo complex. Nat Commun 2014; 5:5440. [PMID: 25510711 DOI: 10.1038/ncomms6440] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/30/2014] [Indexed: 01/09/2023] Open
Abstract
Mononuclear non-haem iron(III)-superoxo species (Fe(III)-O2(-·)) have been implicated as key intermediates in the catalytic cycles of dioxygen activation by non-haem iron enzymes. Although non-haem iron(III)-superoxo species have been trapped and characterized spectroscopically in enzymatic and biomimetic reactions, no structural information has yet been obtained. Here we report the isolation, spectroscopic characterization and crystal structure of a mononuclear side-on (η(2)) iron(III)-superoxo complex with a tetraamido macrocyclic ligand. The non-haem iron(III)-superoxo species undergoes both electrophilic and nucleophilic oxidation reactions, as well as O2-transfer between metal complexes. In the O2-transfer reaction, the iron(III)-superoxo complex transfers the bound O2 unit to a manganese(III) analogue, resulting in the formation of a manganese(IV)-peroxo complex, which is characterized structurally and spectroscopically as a mononuclear side-on (η(2)) manganese(IV)-peroxo complex. The difference in the redox distribution between the metal ions and O2 in iron(III)-superoxo and manganese(IV)-peroxo complexes is rationalized using density functional theory calculations.
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Affiliation(s)
- Seungwoo Hong
- Department of Chemistry and Nano Science, Ewha Womans University, 11-1 Daehyun-dong, Seodaemun-ku, Seoul 120-750, Korea
| | - Kyle D Sutherlin
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Jiyoung Park
- Department of Chemistry and Nano Science, Ewha Womans University, 11-1 Daehyun-dong, Seodaemun-ku, Seoul 120-750, Korea
| | - Eunji Kwon
- Department of Chemistry and Nano Science, Ewha Womans University, 11-1 Daehyun-dong, Seodaemun-ku, Seoul 120-750, Korea
| | - Maxime A Siegler
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Edward I Solomon
- 1] Department of Chemistry, Stanford University, Stanford, California 94305, USA [2] Stanford Synchrotron Radiation Laboratory, Stanford Linear Accelerator Center, Menlo Park, California 94025, USA
| | - Wonwoo Nam
- Department of Chemistry and Nano Science, Ewha Womans University, 11-1 Daehyun-dong, Seodaemun-ku, Seoul 120-750, Korea
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44
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Ansari A, Jayapal P, Rajaraman G. CH Bond Activation by Metal-Superoxo Species: Magnetic Coupling Correlated to High Reactivity in Metal-Superoxo species. Angew Chem Int Ed Engl 2014; 54:564-8. [DOI: 10.1002/anie.201409844] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Indexed: 11/12/2022]
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45
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Ansari A, Jayapal P, Rajaraman G. CH Bond Activation by Metal-Superoxo Species: What Drives High Reactivity? Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409844] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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46
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Prince BM, Cundari TR, Tymczak CJ. DFT study of the reaction of a two-coordinate iron(II) dialkyl complex with molecular oxygen. J Phys Chem A 2014; 118:11056-61. [PMID: 25355170 DOI: 10.1021/jp5082438] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
DFT studies are reported of a monomeric iron dialkyl for which oxygen atom insertion into metal-methyl bonds occurs with O2: FeMe2 + O2 → Fe(OMe)2. Computation of the reaction coordinate implicates the intermediacy of Fe(III)-peroxo, Fe(VI)-dioxo, and Fe(IV)-oxo intermediates, connected by O2 oxidative addition and two methyl migration steps. Analysis of the reaction of O2 with d(6)-Fe(Me)2 indicates that oxy-insertion for this iron complex occurs with lower free energy barriers than competing homolytic/radical pathways, exploiting "spin-flip" processes via minimum energy crossing points (MECPs).
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Affiliation(s)
- Bruce M Prince
- Center for Research on Complex Networks (CRCN), Department of Physics, Texas Southern University , Houston, Texas 77004, United States
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47
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Hirao H, Thellamurege N, Zhang X. Applications of density functional theory to iron-containing molecules of bioinorganic interest. Front Chem 2014; 2:14. [PMID: 24809043 PMCID: PMC4010748 DOI: 10.3389/fchem.2014.00014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/10/2014] [Indexed: 12/29/2022] Open
Abstract
The past decades have seen an explosive growth in the application of density functional theory (DFT) methods to molecular systems that are of interest in a variety of scientific fields. Owing to its balanced accuracy and efficiency, DFT plays particularly useful roles in the theoretical investigation of large molecules. Even for biological molecules such as proteins, DFT finds application in the form of, e.g., hybrid quantum mechanics and molecular mechanics (QM/MM), in which DFT may be used as a QM method to describe a higher prioritized region in the system, while a MM force field may be used to describe remaining atoms. Iron-containing molecules are particularly important targets of DFT calculations. From the viewpoint of chemistry, this is mainly because iron is abundant on earth, iron plays powerful (and often enigmatic) roles in enzyme catalysis, and iron thus has the great potential for biomimetic catalysis of chemically difficult transformations. In this paper, we present a brief overview of several recent applications of DFT to iron-containing non-heme synthetic complexes, heme-type cytochrome P450 enzymes, and non-heme iron enzymes, all of which are of particular interest in the field of bioinorganic chemistry. Emphasis will be placed on our own work.
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Affiliation(s)
- Hajime Hirao
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological UniversitySingapore, Singapore
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48
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Sun Y, Chen H. Performance of Density Functionals for Activation Energies of Re-Catalyzed Organic Reactions. J Chem Theory Comput 2014; 10:579-88. [DOI: 10.1021/ct4010855] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yihua Sun
- Beijing National
Laboratory
for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry,
Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Hui Chen
- Beijing National
Laboratory
for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry,
Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
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49
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Comba P, Lee YM, Nam W, Waleska A. Catalytic oxidation of alkanes by iron bispidine complexes and dioxygen: oxygen activation versus autoxidation. Chem Commun (Camb) 2014; 50:412-4. [DOI: 10.1039/c3cc47013j] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Cho KB, Kang H, Woo J, Park YJ, Seo MS, Cho J, Nam W. Mechanistic Insights into the C–H Bond Activation of Hydrocarbons by Chromium(IV) Oxo and Chromium(III) Superoxo Complexes. Inorg Chem 2013; 53:645-52. [DOI: 10.1021/ic402831f] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Kyung-Bin Cho
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Hyeona Kang
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Jaeyoung Woo
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Young Jun Park
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Mi Sook Seo
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
| | - Jaeheung Cho
- Department
of Emerging Materials Science, DGIST, Daegu 711-873, Korea
| | - Wonwoo Nam
- Department
of Chemistry and Nano Science, Center for Biomimetic Systems, Ewha Womans University, Seoul 120-750, Korea
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