1
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Kingsbury CJ, Senge MO. Quantifying near-symmetric molecular distortion using symmetry-coordinate structural decomposition. Chem Sci 2024:d4sc01670j. [PMID: 39129773 PMCID: PMC11310747 DOI: 10.1039/d4sc01670j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 08/01/2024] [Indexed: 08/13/2024] Open
Abstract
We imagine molecules to be perfect, but rigidified units can be designed to bend from their ideal shape, discarding their symmetric elements as they progress through vibrations and larger, more permanent distortions. The shape of molecules is either simulated or measured by crystallography and strongly affects chemical properties but, beyond an image or tabulation of atom-to-atom distances, little is often discussed of the accessed conformation. We have simplified the process of shape quantification across multiple molecular types with a new web-accessible program - SCSD - through which a molecular subunit possessing near-symmetry can be dissected into symmetry coordinates with ease. This parameterization allows a common set of numbers for comparing and understanding molecular shape, and is a simple method for database analysis; this program is available at https://www.kingsbury.id.au/scsd.
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Affiliation(s)
- Christopher J Kingsbury
- School of Chemistry, Chair of Organic Chemistry, Trinity College Dublin, The University of Dublin, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin D02R590 Ireland
| | - Mathias O Senge
- School of Chemistry, Chair of Organic Chemistry, Trinity College Dublin, The University of Dublin, Trinity Biomedical Sciences Institute 152-160 Pearse Street Dublin D02R590 Ireland
- Institute for Advanced Study (TUM-IAS), Technical University of Munich Lichtenberg-Str. 2a 85748 Garching Germany
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2
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Kumar A, Kim D, Kumar S, Mahammed A, Churchill DG, Gross Z. Milestones in corrole chemistry: historical ligand syntheses and post-functionalization. Chem Soc Rev 2023; 52:573-600. [PMID: 36537842 DOI: 10.1039/d1cs01137e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Corroles are synthetic porphyrin analogs that contain one meso carbon atom lesser and bear a trianionic N4 metal-chelating core. They require in-depth preparative chemistry, demonstrate unique coordination chemistry and have impressive and diverse physical properties, and these are commonly compared to their respective porphyrins. The corrole's macrocyclic system is inherently electron rich and chelates metal ions in a more compact, less symmetric tetranitrogen cavity compared to that of porphyrins. Herein, we cover the highlights of the corrole research through the decades by first reviewing, in a chronological sense, multi-step syntheses; some routes have since been discontinued. This is followed by describing post-functionalization of already formed corroles via reactions performed on either the macrocycle's periphery or the inner nitrogen atoms or on the existing substituents. We do also mention milestones in literature reviewing, publication of encyclopedias, and the creation of professional organizations and conferences (ICPP) which make up the corrole/porphyrin research landscape. Also highlighted are still existing challenges and future perspectives.
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Affiliation(s)
- Anil Kumar
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa 32000, Israel. .,Department of Applied Chemistry, Delhi Technological University, Delhi 110042, India
| | - Donghyeon Kim
- Department of Chemistry, Molecular Logic Gate Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
| | - Sachin Kumar
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa 32000, Israel.
| | - Atif Mahammed
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa 32000, Israel.
| | - David G Churchill
- Department of Chemistry, Molecular Logic Gate Laboratory, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea. .,Center for Catalytic Hydrocarbon Functionalizations, Institute for Basic Science (IBS), Daejeon 34141, Republic of Korea
| | - Zeev Gross
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa 32000, Israel.
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3
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Mizrahi A, Bhowmik S, Manna AK, Sinha W, Kumar A, Saphier M, Mahammed A, Patra M, Fridman N, Zilbermann I, Kronik L, Gross Z. Electronic Coupling and Electrocatalysis in Redox Active Fused Iron Corroles. Inorg Chem 2022; 61:20725-20733. [PMID: 36512733 PMCID: PMC9799712 DOI: 10.1021/acs.inorgchem.2c01389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Indexed: 12/15/2022]
Abstract
Conjugated arrays composed of corrole macrocycles are increasingly more common, but their chemistry still lags behind that of their porphyrin counterparts. Here, we report on the insertion of iron(III) into a β,β-fused corrole dimer and on the electronic effects that this redox active metal center has on the already rich coordination chemistry of [H3tpfc] COT, where COT = cyclo-octatetraene and tpfc = tris(pentafluorophenyl)corrole. Synthetic manipulations were performed for the isolation and full characterization of both the 5-coordinate [FeIIItpfc(py)]2COT and 6-coordinate [FeIIItpfc(py)2]2COT, with one and two axial pyridine ligands per metal, respectively. X-Ray crystallography reveals a dome-shaped structure for [FeIIItpfc(py)]2COT and a perfectly planar geometry which (surprisingly at first) is also characterized by shorter Fe-N (corrole) and Fe-N (pyridine) distances. Computational investigations clarify that the structural phenomena are due to a change in the iron(III) spin state from intermediate (S = 3/2) to low (S = 1/2), and that both the 5- and 6-coordinated complexes are enthalpically favored. Yet, in contrast to iron(III) porphyrins, the formation enthalpy for the coordination of the first pyridine to Fe(III) corrole is more negative than that of the second pyridine coordination. Possible interactions between the two corrole subunits and the chelated iron ions were examined by UV-Vis spectroscopy, electrochemical techniques, and density functional theory (DFT). The large differences in the electronic spectra of the dimer relative to the monomer are concluded to be due to a reduced electronic gap, owing to the extensive electron delocalization through the fusing bridge. A cathodic sweep for the dimer discloses two redox processes, separated by 230 mV. The DFT self-consistent charge density for the neutral and cationic states (1- and 2-electron oxidized) reveals that the holes are localized on the macrocycle. A different picture emerges from the reduction process, where both the electrochemistry and the calculated charge density point toward two consecutive electron transfers with similar energetics, indicative of very weak electron communication between the two redox active iron(III) sites. The binuclear complex was determined to be a much better catalyst for the electrochemical hydrogen evolution reaction (HER) than the analogous mononuclear corrole.
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Affiliation(s)
- Amir Mizrahi
- Chemistry
Department, Nuclear Research Centre Negev, Beer-Sheva84190, Israel
- Schulich
Faculty of Chemistry, Technion Institute
of Technology, Haifa3200003, Israel
| | - Susovan Bhowmik
- Schulich
Faculty of Chemistry, Technion Institute
of Technology, Haifa3200003, Israel
- Bankura
Sammilani College (W.B), Bankura722102, India
| | - Arun K. Manna
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot76100, Israel
| | - Woormileela Sinha
- Schulich
Faculty of Chemistry, Technion Institute
of Technology, Haifa3200003, Israel
- Department
of Chemistry, BITS PilaniK K Birla Goa Campus, NH17B, Zuarinagar, Goa403726, India
| | - Amit Kumar
- Schulich
Faculty of Chemistry, Technion Institute
of Technology, Haifa3200003, Israel
| | - Magal Saphier
- Chemistry
Department, Nuclear Research Centre Negev, Beer-Sheva84190, Israel
| | - Atif Mahammed
- Schulich
Faculty of Chemistry, Technion Institute
of Technology, Haifa3200003, Israel
| | | | - Natalia Fridman
- Schulich
Faculty of Chemistry, Technion Institute
of Technology, Haifa3200003, Israel
| | - Israel Zilbermann
- Chemistry
Department, Nuclear Research Centre Negev, Beer-Sheva84190, Israel
- Chemistry
Department, Ben-Gurion University of the
Negev, Beer-Sheva84105, Israel
| | - Leeor Kronik
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot76100, Israel
| | - Zeev Gross
- Schulich
Faculty of Chemistry, Technion Institute
of Technology, Haifa3200003, Israel
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4
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Lacerda PSS, Bartolomeu M, Gomes ATPC, Duarte AS, Almeida A, Faustino MAF, Neves MGPMS, Barata JFB. Can Corrole Dimers Be Good Photosensitizers to Kill Bacteria? Microorganisms 2022; 10:microorganisms10061167. [PMID: 35744685 PMCID: PMC9230841 DOI: 10.3390/microorganisms10061167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 06/01/2022] [Accepted: 06/03/2022] [Indexed: 01/27/2023] Open
Abstract
Corroles possess key photophysical and photochemical properties to be exploited as therapeutic agents in antimicrobial photodynamic therapy (aPDT). Herein, we present for the first time the antimicrobial efficiency of three corrole dimers and of the corresponding precursor against the Gram(+) bacterium Staphylococcus aureus. Additionally, to explore future clinical applications, the cytotoxicity of the most promising derivatives towards Vero cells was evaluated. The aPDT assays performed under white light irradiation (50 mW/cm2; light dose 450 J/cm2) and at a corrole concentration of 15 µM showed that some dimers were able to reduce 99.9999% of S. aureus strain (decrease of 5 log10 CFU/mL) and their photodynamic efficiency was dependent on position, type of linkage, and aggregation behavior. Under the same light conditions, the corrole precursor 1 demonstrated notable photodynamic efficiency, achieving total photoinactivation (>8.0 log10 CFU/mL reduction) after the same period of irradiation (light dose 450 J/cm2). No cytotoxicity was observed when Vero cells were exposed to corrole 1 and dimer 3 for 24 h according to ISO guidelines (ISO 10993-5) for in vitro cytotoxicity of medical devices. The results show that corrole dimers, dependent on their structures, can be considered good photosensitizers to kill Staphylococcus aureus.
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Affiliation(s)
- Paula S. S. Lacerda
- CESAM, University of Aveiro, 3810-193 Aveiro, Portugal; (P.S.S.L.); (M.B.); (A.A.)
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (M.A.F.F.); (M.G.P.M.S.N.)
| | - Maria Bartolomeu
- CESAM, University of Aveiro, 3810-193 Aveiro, Portugal; (P.S.S.L.); (M.B.); (A.A.)
- Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Ana T. P. C. Gomes
- Universidade Católica Portuguesa, Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), 3504-505 Viseu, Portugal; (A.T.P.C.G.); (A.S.D.)
| | - Ana S. Duarte
- Universidade Católica Portuguesa, Faculty of Dental Medicine (FMD), Center for Interdisciplinary Research in Health (CIIS), 3504-505 Viseu, Portugal; (A.T.P.C.G.); (A.S.D.)
| | - Adelaide Almeida
- CESAM, University of Aveiro, 3810-193 Aveiro, Portugal; (P.S.S.L.); (M.B.); (A.A.)
- Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Maria A. F. Faustino
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (M.A.F.F.); (M.G.P.M.S.N.)
| | - Maria G. P. M. S. Neves
- LAQV-REQUIMTE and Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; (M.A.F.F.); (M.G.P.M.S.N.)
| | - Joana F. B. Barata
- CESAM, University of Aveiro, 3810-193 Aveiro, Portugal; (P.S.S.L.); (M.B.); (A.A.)
- Correspondence:
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5
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Kroeger AA, Karton A. Graphene-induced planarization of cyclooctatetraene derivatives. J Comput Chem 2022; 43:96-105. [PMID: 34677827 DOI: 10.1002/jcc.26774] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 09/10/2021] [Accepted: 10/08/2021] [Indexed: 11/09/2022]
Abstract
Stable equilibrium compounds containing a planar antiaromatic cyclooctatetraene (COT) ring are promising candidates for organic electronic devices such as organic semiconductor transistors. The planarization of COT by incorporation into rigid planar π-systems, as well as by oxidation or reduction has attracted considerable attention in recent years. Using dispersion-corrected density functional theory calculations, we explore an alternative approach of planarizing COT derivatives by adsorption onto graphene. We show that strong π-π stacking interactions between graphene and COT derivatives induce a planar structure with an antiaromatic central COT ring. In addition to being reversible, this strategy provides a novel approach for planarizing COT without the need for incorporation into a rigid structure, atomic substitution, oxidation, or reduction.
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Affiliation(s)
- Asja A Kroeger
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
| | - Amir Karton
- School of Molecular Sciences, The University of Western Australia, Perth, Australia
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6
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Borissov A, Maurya YK, Moshniaha L, Wong WS, Żyła-Karwowska M, Stępień M. Recent Advances in Heterocyclic Nanographenes and Other Polycyclic Heteroaromatic Compounds. Chem Rev 2022; 122:565-788. [PMID: 34850633 PMCID: PMC8759089 DOI: 10.1021/acs.chemrev.1c00449] [Citation(s) in RCA: 231] [Impact Index Per Article: 115.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Indexed: 12/21/2022]
Abstract
This review surveys recent progress in the chemistry of polycyclic heteroaromatic molecules with a focus on structural diversity and synthetic methodology. The article covers literature published during the period of 2016-2020, providing an update to our first review of this topic (Chem. Rev. 2017, 117 (4), 3479-3716).
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Affiliation(s)
| | | | | | | | | | - Marcin Stępień
- Wydział Chemii, Uniwersytet
Wrocławski, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
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7
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Ooi S, Ueta K, Tanaka T, Osuka A. Singly, Doubly, and Triply Linked Corrole Oligomers: Synthesis, Structures, and Linking Position Dependent Properties. Chempluschem 2019; 84:578-588. [DOI: 10.1002/cplu.201800570] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Revised: 12/01/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Shota Ooi
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa Oiwake-cho Sakyo-ku Japan
| | - Kento Ueta
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa Oiwake-cho Sakyo-ku Japan
| | - Takayuki Tanaka
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa Oiwake-cho Sakyo-ku Japan
| | - Atsuhiro Osuka
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa Oiwake-cho Sakyo-ku Japan
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8
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Ooi S, Shimizu D, Furukawa K, Tanaka T, Osuka A. Stable Face-to-Face Singlet Diradicaloids: Triply Linked Corrole Dimer Gallium(III) Complexes with Two μ
-Hydroxo-Bridges. Angew Chem Int Ed Engl 2018; 57:14916-14920. [DOI: 10.1002/anie.201810200] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Shota Ooi
- Department of Chemistry; Graduate School of Science; Kyoto University; Sakyo-ku Kyoto 606-8502 Japan
| | - Daiki Shimizu
- Department of Chemistry; Graduate School of Science; Kyoto University; Sakyo-ku Kyoto 606-8502 Japan
| | - Ko Furukawa
- Center for Coordination of Research Facilities; Niigata University; Nishi-ku Niigata 950-2181 Japan
| | - Takayuki Tanaka
- Department of Chemistry; Graduate School of Science; Kyoto University; Sakyo-ku Kyoto 606-8502 Japan
| | - Atsuhiro Osuka
- Department of Chemistry; Graduate School of Science; Kyoto University; Sakyo-ku Kyoto 606-8502 Japan
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9
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Ooi S, Shimizu D, Furukawa K, Tanaka T, Osuka A. Stable Face-to-Face Singlet Diradicaloids: Triply Linked Corrole Dimer Gallium(III) Complexes with Two μ
-Hydroxo-Bridges. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Shota Ooi
- Department of Chemistry; Graduate School of Science; Kyoto University; Sakyo-ku Kyoto 606-8502 Japan
| | - Daiki Shimizu
- Department of Chemistry; Graduate School of Science; Kyoto University; Sakyo-ku Kyoto 606-8502 Japan
| | - Ko Furukawa
- Center for Coordination of Research Facilities; Niigata University; Nishi-ku Niigata 950-2181 Japan
| | - Takayuki Tanaka
- Department of Chemistry; Graduate School of Science; Kyoto University; Sakyo-ku Kyoto 606-8502 Japan
| | - Atsuhiro Osuka
- Department of Chemistry; Graduate School of Science; Kyoto University; Sakyo-ku Kyoto 606-8502 Japan
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10
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Affiliation(s)
- Takayuki Tanaka
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa Oiwake-cho Sakyo-ku, 606-8502 Kyoto Japan
| | - Atsuhiro Osuka
- Department of Chemistry; Graduate School of Science; Kyoto University; Kitashirakawa Oiwake-cho Sakyo-ku, 606-8502 Kyoto Japan
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11
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Nagai T, Takiguchi A, Ueda M, Oda K, Hiroto S, Shinokubo H. X-Shaped Cyclobutane-Linked Tetraporphyrins through a Thermal [2+2] Cycloaddition of Etheno-Fused Diporphyrins. J Am Chem Soc 2018; 140:8392-8395. [PMID: 29925230 DOI: 10.1021/jacs.8b04673] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A nickel-mediated tandem double cyclization of ethynylene-linked dibromodiporphyrins afforded highly reactive etheno-fused diporphyrins, which undergo a thermal [2+2] cycloaddition at the fused C-C double bond to afford the cyclobutane moiety in X-shaped cyclobutane-linked tetraporphyrins. During the reaction of a Zn(II) complex precursor, the initial double cyclization product was converted into the diketodiporphyrin, which exhibits red chemiluminescence under ambient conditions.
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Affiliation(s)
- Tomohiro Nagai
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering , Nagoya University , Nagoya 464-8603 , Japan
| | - Asahi Takiguchi
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering , Nagoya University , Nagoya 464-8603 , Japan
| | - Masayuki Ueda
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering , Nagoya University , Nagoya 464-8603 , Japan
| | - Kazuma Oda
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering , Nagoya University , Nagoya 464-8603 , Japan
| | - Satoru Hiroto
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering , Nagoya University , Nagoya 464-8603 , Japan
| | - Hiroshi Shinokubo
- Department of Molecular and Macromolecular Chemistry, Graduate School of Engineering , Nagoya University , Nagoya 464-8603 , Japan
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12
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Ke XS, Hong Y, Lynch VM, Kim D, Sessler JL. Metal-Stabilized Quinoidal Dibenzo[g, p]chrysene-Fused Bis-dicarbacorrole System. J Am Chem Soc 2018; 140:7579-7586. [DOI: 10.1021/jacs.8b02718] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Xian-Sheng Ke
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712-1224, United States
| | - Yongseok Hong
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Vincent M. Lynch
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712-1224, United States
| | - Dongho Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Jonathan L. Sessler
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712-1224, United States
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13
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Shimizu D, Osuka A. Porphyrinoids as a platform of stable radicals. Chem Sci 2018; 9:1408-1423. [PMID: 29675188 PMCID: PMC5892410 DOI: 10.1039/c7sc05210c] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 01/05/2018] [Indexed: 12/15/2022] Open
Abstract
The non-innocent ligand nature of porphyrins was observed for compound I in enzymatic cycles of cytochrome P450. Such porphyrin radicals were first regarded as reactive intermediates in catabolism, but recent studies have revealed that porphyrinoids, including porphyrins, ring-contracted porphyrins, and ring-expanded porphyrins, display excellent radical-stabilizing abilities to the extent that radicals can be handled like usual closed-shell organic molecules. This review surveys four types of stable porphyrinoid radical and covers their synthetic methods and properties such as excellent redox properties, NIR absorption, and magnetic properties. The radical-stabilizing abilities of porphyrinoids stem from their unique macrocyclic conjugated systems with high electronic and structural flexibilities.
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Affiliation(s)
- Daiki Shimizu
- Department of Chemistry , Graduate School of Science , Kyoto University , Kyoto 606-8502 , Japan .
| | - Atsuhiro Osuka
- Department of Chemistry , Graduate School of Science , Kyoto University , Kyoto 606-8502 , Japan .
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