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Yao Q, Yuan K, Li M, Zhao Y, Liu Y, Zhao X. Synergistic regulation of chloride anion recognition using a triple-functional sites receptor with two different cationic effectors. J Comput Chem 2024; 45:1630-1641. [PMID: 38539259 DOI: 10.1002/jcc.27357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/02/2024] [Accepted: 03/16/2024] [Indexed: 06/04/2024]
Abstract
The synergistic regulation of the multi-functional sites on one receptor molecule with different cationic effectors for anion recognition is scarce to be well understood from the experiment and theory. In this work, a new anion receptor with three functional zones including ether hole, biurea and double bipyridine groups (EUPR) is designed expecting to enhance the chloride anion recognition together with a rational synthesis path being proposed based on four simple and mature organic reaction steps. The conformational structures of the designed receptor EUPR and the binding behaviors for three kinds of ions (Cl-, Na+, and Ag+) are deeply investigated by using density functional theoretical calculations. It is found that Cl- binding via the hydrogen bond interaction can be significantly enhanced and synergistically regulated by the two kinds of cations and the corresponding conformational changes of receptor EUPR. Especially, the conformational pre-organization of receptor caused by the encapsulation of sodium ion into ether hole is benefit to the binding for Cl- in both thermodynamics and kinetics. Na+ binding, in turn, can ever be enhanced by chloride anion, whereas it seems that Ag+ binding cannot always be enhanced by chloride anion, reflecting an electrical complementary matching and mutual enhancement effect for different counter ions. Moreover, solvent effect calculations indicate that EUPR may be an ideal candidate structure for Cl- recognition by strategy of counter ion enhancement in water. Additionally, a visual study of intermolecular noncovalent interaction (NCI) and molecular electrostatic potential (ESP) are used for the analysis on the nature of interactions between receptor and bound ions.
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Affiliation(s)
- Qingqing Yao
- College of Chemical Engineering and Technology, Key Laboratory for New Molecule Materials Design and Function of Gansu Universities, Gansu Key Laboratory of Advanced Optoelectronic Functional Materials, Tianshui Normal University, Tianshui, China
| | - Kun Yuan
- College of Chemical Engineering and Technology, Key Laboratory for New Molecule Materials Design and Function of Gansu Universities, Gansu Key Laboratory of Advanced Optoelectronic Functional Materials, Tianshui Normal University, Tianshui, China
| | - Mengyang Li
- School of Physics, Xidian University, Xi'an, China
| | - Yaoxiao Zhao
- School of Materials Science and Chemical Engineering, Xi'an Technological University, Xi'an, China
| | - Yanzhi Liu
- College of Chemical Engineering and Technology, Key Laboratory for New Molecule Materials Design and Function of Gansu Universities, Gansu Key Laboratory of Advanced Optoelectronic Functional Materials, Tianshui Normal University, Tianshui, China
| | - Xiang Zhao
- School of Chemistry, Xi'an Jiaotong University, Xi'an, China
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2
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Modrušan M, Glazer L, Otmačić L, Crnolatac I, Cindro N, Vidović N, Piantanida I, Speranza G, Horvat G, Tomišić V. Anion-Binding Properties of Short Linear Homopeptides. Int J Mol Sci 2024; 25:5235. [PMID: 38791275 PMCID: PMC11121566 DOI: 10.3390/ijms25105235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/05/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
A comprehensive thermodynamic and structural study of the complexation affinities of tetra (L1), penta (L2), and hexaphenylalanine (L3) linear peptides towards several inorganic anions in acetonitrile (MeCN) and N,N-dimethylformamide (DMF) was carried out. The influence of the chain length on the complexation thermodynamics and structural changes upon anion binding are particularly addressed here. The complexation processes were characterized by means of spectrofluorimetric, 1H NMR, microcalorimetric, and circular dichroism spectroscopy titrations. The results indicate that all three peptides formed complexes of 1:1 stoichiometry with chloride, bromide, hydrogen sulfate, dihydrogen phosphate (DHP), and nitrate anions in acetonitrile and DMF. In the case of hydrogen sulfate and DHP, anion complexes of higher stoichiometries were observed as well, namely those with 1:2 and 2:1 (peptide:anion) complexes. Anion-induced peptide backbone structural changes were studied by molecular dynamic simulations. The anions interacted with backbone amide protons and one of the N-terminal amine protons through hydrogen bonding. Due to the anion binding, the main chain of the studied peptides changed its conformation from elongated to quasi-cyclic in all 1:1 complexes. The accomplishment of such a conformation is especially important for cyclopeptide synthesis in the head-to-tail macrocyclization step, since it is most suitable for ring closure. In addition, the studied peptides can act as versatile ionophores, facilitating transmembrane anion transport.
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Affiliation(s)
- Matija Modrušan
- Department of Chemistry, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia; (M.M.); (L.G.); (L.O.); (N.C.); (V.T.)
| | - Lucija Glazer
- Department of Chemistry, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia; (M.M.); (L.G.); (L.O.); (N.C.); (V.T.)
| | - Lucija Otmačić
- Department of Chemistry, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia; (M.M.); (L.G.); (L.O.); (N.C.); (V.T.)
| | - Ivo Crnolatac
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.C.); (I.P.)
| | - Nikola Cindro
- Department of Chemistry, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia; (M.M.); (L.G.); (L.O.); (N.C.); (V.T.)
| | - Nikolina Vidović
- Faculty of Biotechnology and Drug Development, University of Rijeka, Radmile Matejčić 2, 51000 Rijeka, Croatia;
| | - Ivo Piantanida
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.C.); (I.P.)
| | - Giovanna Speranza
- Department of Chemistry, University of Milan, Via Golgi 19, 20122 Milan, Italy;
| | - Gordan Horvat
- Department of Chemistry, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia; (M.M.); (L.G.); (L.O.); (N.C.); (V.T.)
| | - Vladislav Tomišić
- Department of Chemistry, Faculty of Science, Horvatovac 102a, 10000 Zagreb, Croatia; (M.M.); (L.G.); (L.O.); (N.C.); (V.T.)
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Budimir ZL, Patel RS, Eggly A, Evans CN, Rondon-Cordero HM, Adams JJ, Das C, Parkinson EI. Biocatalytic cyclization of small macrolactams by a penicillin-binding protein-type thioesterase. Nat Chem Biol 2024; 20:120-128. [PMID: 38062262 PMCID: PMC10999230 DOI: 10.1038/s41589-023-01495-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
Macrocyclic peptides represent promising scaffolds for chemical tools and potential therapeutics. Synthetic methods for peptide macrocyclization are often hampered by C-terminal epimerization and oligomerization, leading to difficult scalability. While chemical strategies to circumvent this issue exist, they often require specific amino acids to be present in the peptide sequence. Herein, we report the characterization of Ulm16, a peptide cyclase belonging to the penicillin-binding protein-type class of thioesterases that catalyze head-to-tail macrolactamization of nonribosmal peptides. Ulm16 efficiently cyclizes various nonnative peptides ranging from 4 to 6 amino acids with catalytic efficiencies of up to 3 × 106 M-1 s-1. Unlike many previously described homologs, Ulm16 tolerates a variety of C- and N-terminal amino acids. The crystal structure of Ulm16, along with modeling of its substrates and site-directed mutagenesis, allows for rationalization of this wide substrate scope. Overall, Ulm16 represents a promising tool for the biocatalytic production of macrocyclic peptides.
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Affiliation(s)
| | - Rishi S Patel
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Alyssa Eggly
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Claudia N Evans
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | | | - Jessica J Adams
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Chittaranjan Das
- Department of Chemistry, Purdue University, West Lafayette, IN, USA
| | - Elizabeth I Parkinson
- Department of Chemistry, Purdue University, West Lafayette, IN, USA.
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN, USA.
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4
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Petters I, Modrušan M, Vidović N, Crnolatac I, Cindro N, Piantanida I, Speranza G, Horvat G, Tomišić V. Anion-Sensing Properties of Cyclopentaphenylalanine. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123918. [PMID: 35745042 PMCID: PMC9228215 DOI: 10.3390/molecules27123918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/16/2022]
Abstract
Cyclic pentaphenylalanine was studied as an efficient anion sensor for halides, thiocyanate and oxoanions in acetonitrile and methanol. Stability constants of the corresponding complexes were determined by means of fluorimetric, spectrophotometric, 1H NMR, and microcalorimetric titrations. A detailed structural overview of receptor–anion complexes was obtained by classical molecular dynamics (MD) simulations. The results of 1H NMR and MD studies indicated that the bound anions were coordinated by the amide groups of cyclopeptide, as expected. Circular dichroism (CD) titrations were also carried out in acetonitrile. To the best of our knowledge, this is the first example of the detection of anion binding by cyclopeptide using CD spectroscopy. The CD spectra were calculated from the structures obtained by MD simulations and were qualitatively in agreement with the experimental data. The stoichiometry of almost all complexes was 1:1 (receptor:anion), except for dihydrogen phosphate where the binding of dihydrogen phosphate dimer was observed in acetonitrile. The affinity of the cyclopeptide receptor was correlated with the structure of anion coordination sphere, as well as with the solvation properties of the examined solvents.
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Affiliation(s)
- Ivan Petters
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (I.P.); (M.M.); (N.C.)
| | - Matija Modrušan
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (I.P.); (M.M.); (N.C.)
| | - Nikolina Vidović
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi, 19, 20133 Milan, Italy; (N.V.); (G.S.)
- Institute of Agriculture and Tourism, Department of Agriculture and Nutrition, Karla Huguesa 8, 52440 Poreč, Croatia
| | - Ivo Crnolatac
- Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (I.C.); (I.P.)
| | - Nikola Cindro
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (I.P.); (M.M.); (N.C.)
| | - Ivo Piantanida
- Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (I.C.); (I.P.)
| | - Giovanna Speranza
- Dipartimento di Chimica, Università degli Studi di Milano, Via C. Golgi, 19, 20133 Milan, Italy; (N.V.); (G.S.)
| | - Gordan Horvat
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (I.P.); (M.M.); (N.C.)
- Correspondence: (G.H.); (V.T.)
| | - Vladislav Tomišić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia; (I.P.); (M.M.); (N.C.)
- Correspondence: (G.H.); (V.T.)
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Barišić D, Lešić F, Tireli Vlašić M, Užarević K, Bregović N, Tomišić V. Anion binding by receptors containing NH donating groups – What do anions prefer? Tetrahedron 2022. [DOI: 10.1016/j.tet.2022.132875] [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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6
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Niedbała P, Ceborska M, Mehmet M, Ignacak W, Jurczak J, Dąbrowa K. Anion Recognition by a Pincer-Type Host Constructed from Two Polyamide Macrocyclic Frameworks Jointed by a Photo-Addressable Azobenzene Switch. MATERIALS (BASEL, SWITZERLAND) 2022; 15:692. [PMID: 35057408 PMCID: PMC8777895 DOI: 10.3390/ma15020692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 01/04/2022] [Accepted: 01/10/2022] [Indexed: 12/10/2022]
Abstract
A sterically crowded light-responsive host 1 was synthetized with a 93% yield by applying a post-functionalization protocol utilizing the double amidation of 4,4'-azodibenzoyl dichloride with a readily available 26-membered macrocyclic amine. X-ray structures of two hydrates of trans-1 demonstrate a very different alignment of the azobenzene linkage, which is involved in T-shape or parallel-displaced π⋯π stacking interactions with the pyridine-2,6-dicarboxamide moieties from the macrocyclic backbone. Despite the rigidity of the macrocyclic framework, which generates a large steric hindrance around the azobenzene chromophore, the host 1 retains the ability to undergo a reversible cis⟷trans isomerization upon irradiation with UVA (368 nm) and blue (410 nm) light. Moreover, thermal cis→trans back-isomerization (ΔG0 = 106.5 kJ∙mol-1, t½ = 141 h) is markedly slowed down as compared to the non-macrocyclic analog. 1H NMR titration experiments in DMSO-d6/0.5% water solution reveal that trans-1 exhibits a strong preference for dihydrogenphosphate (H2PO4-) over other anions (Cl-, MeCO2-, and PhCO2-), whereas the photogenerated metastable cis-1 shows lower affinity for the H2PO4- anion.
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Affiliation(s)
- Patryk Niedbała
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland; (P.N.); (M.M.); (W.I.)
| | - Magdalena Ceborska
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland;
| | - Mart Mehmet
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland; (P.N.); (M.M.); (W.I.)
| | - Wiktor Ignacak
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland; (P.N.); (M.M.); (W.I.)
| | - Janusz Jurczak
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland; (P.N.); (M.M.); (W.I.)
| | - Kajetan Dąbrowa
- Institute of Organic Chemistry, Polish Academy of Sciences, 01-224 Warsaw, Poland; (P.N.); (M.M.); (W.I.)
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7
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Horvat G, Tarana S, Vidović N, Cindro N, Speranza G, Tomišić V. Thermodynamic and MD studies of anion complexation by cyclopentaleucine in acetonitrile and dimethyl sulfoxide. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Feng H, Wang F, Cao L, Van der Eycken EV, Yin X. Switchable Mono‐ and Dipropargylation of Amino Alcohols: A Unique Property of the Iodide Anion in Controlling Ring‐Opening Alkynylation. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100634] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Huangdi Feng
- Department College of Chemistry and Chemical Engineering Shanghai University of Engineering Science Shanghai 201620 China
| | - Fang Wang
- Department College of Chemistry and Chemical Engineering Shanghai University of Engineering Science Shanghai 201620 China
| | - Leilei Cao
- Department College of Chemistry and Chemical Engineering Shanghai University of Engineering Science Shanghai 201620 China
| | - Erik V. Van der Eycken
- Department of Chemistry KU Leuven Celestijnenlaan 200F, Leuven 3001 Belgium
- Peoples' Friendship University of Russia RUDN University) 6 Miklukho-Maklaya Street Moscow 117198 Russia
| | - Xiaoying Yin
- Department College of Chemistry and Chemical Engineering Shanghai University of Engineering Science Shanghai 201620 China
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9
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Barišić D, Cindro N, Vidović N, Bregović N, Tomišić V. Protonation and anion-binding properties of aromatic sulfonylurea derivatives. RSC Adv 2021; 11:23992-24000. [PMID: 35479025 PMCID: PMC9039416 DOI: 10.1039/d1ra04738h] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022] Open
Abstract
In this work the anion-binding properties of three aromatic sulfonylurea derivatives in acetonitrile and dimethyl sulfoxide were explored by means of NMR titrations. It was found that the studied receptors effectively bind anions of low basicity (Cl-, Br-, I-, NO3 - and HSO4 -). The stoichiometry of the complexes with receptors containing one binding site was 1 : 1 exclusively, whereas in the case of the receptor containing two sulfonylurea groups 1 : 2 (receptor : anion) complexes were also detected in some cases. The presence of strongly basic anions (acetate and dihydrogen phosphate) led to the deprotonation of the sulfonylurea moiety. This completely hindered its anion-binding properties in DMSO and only proton transfer occurred upon the addition of basic anions to the studied receptors. In MeCN, a complex system of equilibria including both ligand deprotonation and anion binding was established. Since ionisation of receptors was proven to be a decisive factor defining the behaviour of the sulfonylurea receptors, their pK a values were determined using several deprotonation agents in both solvents. The results were interpreted in the context of receptor structures and solvent properties and applied for the identification of the interactions with basic anions.
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Affiliation(s)
- D Barišić
- Department of Chemistry, Faculty of Science, University of Zagreb Horvatovac 102/A 10000 Zagreb Croatia .,Division of Physical Chemistry, Ruđer Bošković Institute Bijenička cesta 54 10000 Zagreb Croatia
| | - N Cindro
- Department of Chemistry, Faculty of Science, University of Zagreb Horvatovac 102/A 10000 Zagreb Croatia
| | - N Vidović
- Department of Chemistry, Faculty of Science, University of Zagreb Horvatovac 102/A 10000 Zagreb Croatia .,Institute of Agriculture and Tourism K. Huguesa 8 52440 Poreč Croatia
| | - N Bregović
- Department of Chemistry, Faculty of Science, University of Zagreb Horvatovac 102/A 10000 Zagreb Croatia
| | - V Tomišić
- Department of Chemistry, Faculty of Science, University of Zagreb Horvatovac 102/A 10000 Zagreb Croatia
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Hu RB, Lam YP, Ng WH, Wong CY, Yeung YY. Zwitterion-Induced Organic–Metal Hybrid Catalysis in Aerobic Oxidation. ACS Catal 2021. [DOI: 10.1021/acscatal.0c05684] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rong-Bin Hu
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Ying-Pong Lam
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Wing-Hin Ng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Chun-Yuen Wong
- Department of Chemistry, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong
| | - Ying-Yeung Yeung
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
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Dąbrowa K, Lindner M, Tyszka-Gumkowska A, Jurczak J. Imino-thiolate-templated synthesis of a chloride-selective neutral macrocyclic host with a specific “turn-off–on” fluorescence response for hypochlorite (ClO −). Org Chem Front 2021. [DOI: 10.1039/d1qo00504a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A precise replacement of one oxygen atom with sulfur allowed a novel thioimidate anion-templated macrocyclization to form a crowded host 2 with the ability to act as a highly selective and sensitive fluorescence probe for hypochlorite (ClO−).
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Affiliation(s)
- Kajetan Dąbrowa
- Institute of Organic Chemistry Polish Academy of Sciences, 01-224 Warsaw, Poland
| | - Marcin Lindner
- Institute of Organic Chemistry Polish Academy of Sciences, 01-224 Warsaw, Poland
| | | | - Janusz Jurczak
- Institute of Organic Chemistry Polish Academy of Sciences, 01-224 Warsaw, Poland
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12
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Running rings around chloride. Nat Rev Chem 2020; 4:228. [PMID: 37127986 DOI: 10.1038/s41570-020-0185-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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