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Heinz-Kunert SL, Pandya A, Dang VT, Oktawiec J, Nguyen AI. Pore Restructuring of Peptide Frameworks by Mutations at Distal Packing Residues. Biomacromolecules 2024; 25:2016-2023. [PMID: 38362872 DOI: 10.1021/acs.biomac.3c01418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Porous framework materials are highly useful for catalysis, adsorption, and separations. Though they are usually made from inorganic and organic building blocks, recently, folded peptides have been utilized for constructing frameworks, opening up an enormous structure-space for exploration. These peptides assemble in a metal-free fashion using π-stacking, H-bonding, dispersion forces, and the hydrophobic effect. Manipulation of pore-defining H-bonding residues is known to generate new topologies, but the impact of mutations in the hydrophobic packing region facing away from the pores is less obvious. To explore their effects, we synthesized variants of peptide frameworks with mutations in the hydrophobic packing positions and found by single-crystal X-ray crystallography (SC-XRD) that they induce significant changes to the framework pore structure. These structural changes are driven by a need to maximize van der Waals interactions of the nonpolar groups, which are achieved by various mechanisms including helix twisting, chain flipping, chain offsetting, and desymmetrization. Even subtle changes to the van der Waals interface, such as the introduction of a methyl group or isomeric replacement, result in significant pore restructuring. This study shows that the dispersion interactions upholding a peptide material are a rich area for structural engineering.
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Affiliation(s)
- Sherrie L Heinz-Kunert
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Ashma Pandya
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Viet Thuc Dang
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
| | - Julia Oktawiec
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Andy I Nguyen
- Department of Chemistry, University of Illinois Chicago, Chicago, Illinois 60607, United States
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2
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Exploring the signaling space of a GPCR using bivalent ligands with a rigid oligoproline backbone. Proc Natl Acad Sci U S A 2021; 118:2108776118. [PMID: 34810259 PMCID: PMC8640787 DOI: 10.1073/pnas.2108776118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2021] [Indexed: 01/14/2023] Open
Abstract
G protein–coupled receptors (GPCRs) are major players in cellular signal transmission. In this work, we have used rigid oligoproline backbones derivatized with two ligands at defined distances to induce GPCR dimer formation as a way to alter its signaling profile. We show that bivalent ligands at distances of 20 and 30 Å induce dimers of the GRPR receptor with different signaling responses. In addition, a nondimer–inducing bivalent ligand (with 10-Å distance between agonists) also induces different signaling patterns, most likely due to allosteric effects. These findings identify bivalent ligands with a stiff oligoproline backbone as tools to explore the natural signaling space of GPCRs. G protein–coupled receptors (GPCRs) are one of the most important drug–target classes in pharmaceutical industry. Their diversity in signaling, which can be modulated with drugs, permits the design of more effective and better-tolerated therapeutics. In this work, we have used rigid oligoproline backbones to generate bivalent ligands for the gastrin-releasing peptide receptor (GRPR) with a fixed distance between their recognition motifs. This allows the stabilization of GPCR dimers irrespective of their physiological occurrence and relevance, thus expanding the space for medicinal chemistry. Specifically, we observed that compounds presenting agonists or antagonists at 20- and 30-Å distance induce GRPR dimerization. Furthermore, we found that 1) compounds with two agonists at 20- and 30-Å distance that induce dimer formation show bias toward Gq efficacy, 2) dimers with 20- and 30-Å distance have different potencies toward β-arrestin-1 and β-arrestin-2, and 3) the divalent agonistic ligand with 10-Å distance specifically reduces Gq potency without affecting β-arrestin recruitment, pointing toward an allosteric effect. In summary, we show that rigid oligoproline backbones represent a tool to develop ligands with biased GPCR signaling.
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3
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Pollastrini M, Lipparini F, Pasquinelli L, Balzano F, Barretta GU, Pescitelli G, Angelici G. A Proline Mimetic for the Design of New Stable Secondary Structures: Solvent-Dependent Amide Bond Isomerization of ( S)-Indoline-2-carboxylic Acid Derivatives. J Org Chem 2021; 86:7946-7954. [PMID: 34080867 PMCID: PMC8456495 DOI: 10.1021/acs.joc.1c00184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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A thorough experimental and computational study on the conformational properties of
(S)-indoline-2-carboxylic acid derivatives has been conducted. Methyl
(S)-1-acetylindoline-2-carboxylate, both a mimetic of proline and
phenylalanine, shows a remarkable tendency toward the cis amide isomer
when dissolved in polar solvents. This behavior is opposite to the general preference of
proline for the trans isomer, making indoline-2-carboxylic acid a good
candidate for the design of different secondary structures and new materials.
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Affiliation(s)
- Matteo Pollastrini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Luca Pasquinelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Federica Balzano
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Gloria Uccello Barretta
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Gaetano Angelici
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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4
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Caporale A, Adorinni S, Lamba D, Saviano M. Peptide-Protein Interactions: From Drug Design to Supramolecular Biomaterials. Molecules 2021; 26:1219. [PMID: 33668767 PMCID: PMC7956380 DOI: 10.3390/molecules26051219] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/15/2021] [Accepted: 02/17/2021] [Indexed: 02/06/2023] Open
Abstract
The self-recognition and self-assembly of biomolecules are spontaneous processes that occur in Nature and allow the formation of ordered structures, at the nanoscale or even at the macroscale, under thermodynamic and kinetic equilibrium as a consequence of specific and local interactions. In particular, peptides and peptidomimetics play an elected role, as they may allow a rational approach to elucidate biological mechanisms to develop new drugs, biomaterials, catalysts, or semiconductors. The forces that rule self-recognition and self-assembly processes are weak interactions, such as hydrogen bonding, electrostatic attractions, and van der Waals forces, and they underlie the formation of the secondary structure (e.g., α-helix, β-sheet, polyproline II helix), which plays a key role in all biological processes. Here, we present recent and significant examples whereby design was successfully applied to attain the desired structural motifs toward function. These studies are important to understand the main interactions ruling the biological processes and the onset of many pathologies. The types of secondary structure adopted by peptides during self-assembly have a fundamental importance not only on the type of nano- or macro-structure formed but also on the properties of biomaterials, such as the types of interaction, encapsulation, non-covalent interaction, or covalent interaction, which are ultimately useful for applications in drug delivery.
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Affiliation(s)
- Andrea Caporale
- IC-CNR, c/o Area Science Park, S.S. 14 Km 163.5 Basovizza, 34149 Trieste, Italy;
| | - Simone Adorinni
- Dipartimento di Scienze Chimiche e Farmaceutiche di Università di Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy;
| | - Doriano Lamba
- IC-CNR, c/o Area Science Park, S.S. 14 Km 163.5 Basovizza, 34149 Trieste, Italy;
- Istituto Nazionale Biostrutture e Biosistemi, Consorzio Interuniversitario, Viale delle Medaglie d’Oro 305, I-00136 Roma, Italy
| | - Michele Saviano
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche (IC-CNR), Via Giovanni Amendola 122/O, 70126 Bari, Italy
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5
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Diels-Alder Cycloaddition to the Bay Region of Perylene and Its Derivatives as an Attractive Strategy for PAH Core Expansion: Theoretical and Practical Aspects. Molecules 2020; 25:molecules25225373. [PMID: 33213037 PMCID: PMC7698498 DOI: 10.3390/molecules25225373] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/31/2020] [Accepted: 11/05/2020] [Indexed: 11/16/2022] Open
Abstract
PAHs (polycyclic aromatics hydrocarbons), the compound group that contains perylene and its derivatives, including functionalized ones, have attracted a great deal of interest in many fields of science and modern technology. This review presents all of the research devoted to modifications of PAHs that are realized via the Diels–Alder (DA) cycloaddition of various dienophiles to the bay regions of PAHs, leading to the π-extension of the starting molecule. This type of annulative π-extension (APEX) strategy has emerged as a powerful and efficient synthetic method for the construction of polycyclic aromatic hydrocarbons and their functionalized derivatives, nanographenes, and π-extended fused heteroarenes. Then, [4 + 2] cycloadditions of ethylenic dienophiles, -N=N-, i.e., diazo-dienophiles and acetylenic dienophiles, are presented. This subject is discussed from the organic synthesis point of view but supported by theoretical calculations. The possible applications of DA cycloaddition to PAH bay regions in various science and technology areas, and the prospects for the development of this synthetic method, are also discussed.
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6
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Kirinda VC, Schrage BR, Ziegler CJ, Hartley CS. ortho
‐Phenylene‐Based Macrocyclic Hydrocarbons Assembled Using Olefin Metathesis. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Viraj C. Kirinda
- Department of Chemistry & Biochemistry Miami University 45056 Oxford OH USA
| | | | | | - C. Scott Hartley
- Department of Chemistry & Biochemistry Miami University 45056 Oxford OH USA
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7
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García‐Calvo J, Robson JA, Torroba T, Wilton‐Ely JDET. Synthesis and Application of Ruthenium(II) Alkenyl Complexes with Perylene Fluorophores for the Detection of Toxic Vapours and Gases. Chemistry 2019; 25:14214-14222. [DOI: 10.1002/chem.201903303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Indexed: 12/18/2022]
Affiliation(s)
- José García‐Calvo
- Department of ChemistryFaculty of ScienceUniversity of Burgos 09001 Burgos Spain
| | - Jonathan A. Robson
- Department of ChemistryImperial College London, Molecular Sciences Research Hub, White City Campus London W12 0BZ UK
| | - Tomás Torroba
- Department of ChemistryFaculty of ScienceUniversity of Burgos 09001 Burgos Spain
| | - James D. E. T. Wilton‐Ely
- Department of ChemistryImperial College London, Molecular Sciences Research Hub, White City Campus London W12 0BZ UK
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8
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Ochs NAK, Lewandowska U, Zajaczkowski W, Corra S, Reger S, Herdlitschka A, Schmid S, Pisula W, Müllen K, Bäuerle P, Wennemers H. Oligoprolines guide the self-assembly of quaterthiophenes. Chem Sci 2019; 10:5391-5396. [PMID: 31191896 PMCID: PMC6540903 DOI: 10.1039/c8sc05742g] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 04/25/2019] [Indexed: 12/14/2022] Open
Abstract
Control over the molecular organization of π-conjugated oligothiophenes into different types of supramolecular assemblies is key to their use in organic electronics but difficult to achieve as these chromophores have a pronounced tendency to aggregate. Herein we show that oligoprolines, which do not self-assemble on their own, control the self-assembly of quaterthiophenes. Spectroscopic, microscopic, and diffraction studies with quaterthiophene-oligoproline conjugates revealed the formation of mono- or double-layered sheets or, alternatively, helically twisted ribbons - depending on the length of the oligoproline. The dimensions of the nanoscopic objects, which extend into the micrometer regime, correlate with the molecular dimensions of the quaterthiophene-oligoproline building blocks.
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Affiliation(s)
- Nellie A K Ochs
- Laboratory of Organic Chemistry , ETH Zürich , Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland .
| | - Urszula Lewandowska
- Laboratory of Organic Chemistry , ETH Zürich , Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland .
| | - Wojciech Zajaczkowski
- Max Planck Institute for Polymer Research , Ackermannweg 10 , 55128 Mainz , Germany .
| | - Stefano Corra
- Laboratory of Organic Chemistry , ETH Zürich , Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland .
| | - Stephan Reger
- Institute of Organic Chemistry II and Advanced Materials , University of Ulm , Germany .
| | - Andreas Herdlitschka
- Laboratory of Organic Chemistry , ETH Zürich , Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland .
| | - Sylvia Schmid
- Institute of Organic Chemistry II and Advanced Materials , University of Ulm , Germany .
| | - Wojciech Pisula
- Max Planck Institute for Polymer Research , Ackermannweg 10 , 55128 Mainz , Germany .
- Department of Molecular Physics , Faculty of Chemistry , Lodz University of Technology , Zeromskiego 116 , 90-924 Lodz , Poland
| | - Klaus Müllen
- Max Planck Institute for Polymer Research , Ackermannweg 10 , 55128 Mainz , Germany .
| | - Peter Bäuerle
- Institute of Organic Chemistry II and Advanced Materials , University of Ulm , Germany .
| | - Helma Wennemers
- Laboratory of Organic Chemistry , ETH Zürich , Vladimir-Prelog-Weg 3 , 8093 Zürich , Switzerland .
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9
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Guo Z, Zhang X, Wang Y, Li Z. Supramolecular Self-Assembly of Perylene Bisimide Derivatives Assisted by Various Groups. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:342-358. [PMID: 30577691 DOI: 10.1021/acs.langmuir.8b02964] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Anthra[2,1,9-def:6,5,10-d'e'f']diisoquinoline-1,3,8,10(2H,9H)-tetraone, namely, perylene bisimides (PBIs), belong to n-type organic semiconductors and possess potential applications in optoelectronic devices. The properties/performance of fabricated nanostructures/devices could be greatly influenced by both molecular structures of PBI building blocks and corresponding arrangement in assembled nanostructures. Many efforts have been made to modify the PBI core and then investigate the nanostructures and properties. However, it is still a great challenge to comprehensively understand the influence of molecular structures on the intermolecular interactions, the self-assembled structures, and the resulting performance. In the present contribution, we mainly summarize recent research aspects on supramolecular assembly behaviors of PBI derivatives assisted by various functional groups. First, a short introduction is given about basic molecular structure, properties, and self-assembly of PBI derivatives. Then, we mainly discuss the modulation of self-assembly of PBIs via introducing various functional groups (flexible or nonflexible chains, and biomolecules especially amino-acid-based groups). After that, the assembly of PBI derivatives from out-of-equilibrium states is described. Finally, a perspective is provided on the design of novel PBI derivatives and the fabrication of unique nanostructures with superior properties.
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Affiliation(s)
- Zongxia Guo
- Key Laboratory of Biobased Polymer Materials, Shandong Provincial Education Department , College of Polymer Science and Engineering Qingdao University of Science and Technology , Qingdao 266042 , P. R. China
| | - Xiao Zhang
- Key Laboratory of Biobased Polymer Materials, Shandong Provincial Education Department , College of Polymer Science and Engineering Qingdao University of Science and Technology , Qingdao 266042 , P. R. China
| | - Yujiao Wang
- Key Laboratory of Biobased Polymer Materials, Shandong Provincial Education Department , College of Polymer Science and Engineering Qingdao University of Science and Technology , Qingdao 266042 , P. R. China
| | - Zhibo Li
- Key Laboratory of Biobased Polymer Materials, Shandong Provincial Education Department , College of Polymer Science and Engineering Qingdao University of Science and Technology , Qingdao 266042 , P. R. China
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10
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Dobitz S, Aronoff MR, Wennemers H. Oligoprolines as Molecular Entities for Controlling Distance in Biological and Material Sciences. Acc Chem Res 2017; 50:2420-2428. [PMID: 28885830 DOI: 10.1021/acs.accounts.7b00340] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nature utilizes large biomolecules to fulfill tasks that require spatially well-defined arrangements at the molecular level such as electron transfer, ligand-receptor interactions, or catalysis. The creation of synthetic molecules that enable precise control over spacing and functionalization provides opportunities across diverse disciplines. Key requirements of functionalizable oligomeric scaffolds include the specific control of their molecular properties where the correct balance of flexibility and rigidity must be maintained in addition to the prerequisite of defined length. These molecules must ideally be equally applicable in aqueous and organic environments, they must be easy to synthesize in a controlled stepwise fashion, and they must be easily modified with a palette of chemical appendages having diverse functionalities. Oligoproline, a peptidic polymer comprised of repeating units of the amino acid proline, is an ideal platform to meet such challenges. Oligoproline derives its characteristic rigidity and well-defined secondary structure from the innate features of proline. It is the only naturally occurring amino acid that has its side-chain cyclized to its α-amino group, generating often-populated trans and cis conformers around the tertiary amide bonds formed in proline oligomers. Oligoprolines are widely applied to define distance on the molecular level as they are capable of serving as both a "molecular ruler" with a defined length and as a "molecular scaffold" with precisely located and predictably oriented substitutions along the polymeric backbone. Our investigations focus on the use of oligoproline as a molecular scaffold. Toward this end, we have investigated the role of solvent upon helical structure of oligoproline, and the effect that substituents on the pyrrolidine ring and the oligomer termini have on the stability of the helix. We have also further explored the molecular characteristics of oligoproline through spectroscopic and crystallographic methods. All of these structural insights laid the basis for implementation of oligoproline in materials science and chemical biology. Within this Account, we highlight the value of oligoprolines for applications in distinctly different research areas. Toward materials chemistry, we have utilized oligoprolines for the size-controlled generation of noble metal nanoparticles, and to probe the role of spatial preorganization of π-systems for molecular self-assembly. Within the biological realm, we have applied oligoprolines to probe the role of distance on G-protein coupled receptor-mediated ligand uptake by cancerous cells and to investigate the effects of charge preorganization on the efficacy of cationic cell-penetrating peptides.
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Affiliation(s)
- Stefanie Dobitz
- ETH Zürich, Laboratory of Organic Chemistry, D-CHAB, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Matthew R. Aronoff
- ETH Zürich, Laboratory of Organic Chemistry, D-CHAB, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Helma Wennemers
- ETH Zürich, Laboratory of Organic Chemistry, D-CHAB, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
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11
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Robel FN, Takafuji M, Ihara H. Non-chiral Polymer-induced Chirality Enhancement in Lipidic Nanotube-based Hydrogel System. CHEM LETT 2017. [DOI: 10.1246/cl.170586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Fataha Nur Robel
- Department of Applied Chemistry and Biochemistry, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Sonapur, Noakhali-3814, Bangladesh
| | - Makoto Takafuji
- Department of Applied Chemistry and Biochemistry, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555
- Kumamoto Institute for Photo-Electro Organics (PHOENICS), 3-11-38 Higashimachi, Higashi-ku, Kumamoto 862-0901
| | - Hirotaka Ihara
- Department of New Frontier Science, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto 860-8555
- Kumamoto Institute for Photo-Electro Organics (PHOENICS), 3-11-38 Higashimachi, Higashi-ku, Kumamoto 862-0901
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12
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García‐Calvo J, Ibeas S, Antón‐García E, Torroba T, González‐Aguilar G, Antunes W, González‐Lavado E, Fanarraga ML. Potassium-Ion-Selective Fluorescent Sensors To Detect Cereulide, the Emetic Toxin of B. cereus, in Food Samples and HeLa Cells. ChemistryOpen 2017; 6:562-570. [PMID: 28794952 PMCID: PMC5542764 DOI: 10.1002/open.201700057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Indexed: 12/26/2022] Open
Abstract
We report the development of new chemical probes for cereulide, a toxic metabolite produced by specific strains of Bacillus cereus, through displacement of potassium cations from a preformed specific complex and a subsequent change in the fluorescence emission. For this purpose, we designed fluorescent probes for potassium cations that were suitable for displacement assays with cereulide from organic extracts. The fluorescence detection of natural cereulide in rice samples was achieved by using synthetic cereulide as a reference and a potassium fluorescent reporter, and this was found to be useful as a portable and fast method for the in situ detection of cereulide in food extracts. To study the fate of cereulide in live cells, we designed a procedure that was suitable for live-cell microscopy imaging of HeLa cells by comparing the cellular location of the potassium fluorogenic probe, which stained intracellular endolysosomes, in the absence and presence of cereulide; we concluded that in the presence of cereulide, the fluorescence of the probe was decreased because of complexation of the potassium ions by cereulide.
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Affiliation(s)
- José García‐Calvo
- Department of Chemistry, Faculty of ScienceUniversity of Burgos09001BurgosSpain
| | - Saturnino Ibeas
- Department of Chemistry, Faculty of ScienceUniversity of Burgos09001BurgosSpain
| | | | - Tomás Torroba
- Department of Chemistry, Faculty of ScienceUniversity of Burgos09001BurgosSpain
| | | | - Wilson Antunes
- Laboratório de Bromatologia e de Defesa Biológica (LBDB) do ExércitoAv. Dr. Alfredo Bensaúde1849-012LisboaPortugal
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13
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Kinney ZJ, Hartley CS. Twisted Macrocycles with Folded ortho-Phenylene Subunits. J Am Chem Soc 2017; 139:4821-4827. [DOI: 10.1021/jacs.7b00149] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zacharias J. Kinney
- Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
| | - C. Scott Hartley
- Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
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14
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Miletić T, Fermi A, Orfanos I, Avramopoulos A, De Leo F, Demitri N, Bergamini G, Ceroni P, Papadopoulos MG, Couris S, Bonifazi D. Tailoring Colors by O Annulation of Polycyclic Aromatic Hydrocarbons. Chemistry 2017; 23:2363-2378. [PMID: 27897357 PMCID: PMC5324668 DOI: 10.1002/chem.201604866] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Indexed: 01/24/2023]
Abstract
The synthesis of O-doped polyaromatic hydro- carbons in which two polycyclic aromatic hydrocarbon sub units are bridged through one or two O atoms has been achieved. This includes high-yield ring-closure key steps that, depending on the reaction conditions, result in the formation of furanyl or pyranopyranyl linkages through intramolecular C-O bond formation. Comprehensive photophysical measurements in solution showed that these compounds have exceptionally high emission yields and tunable absorption properties throughout the UV/Vis spectral region. Electrochemical investigations showed that in all cases O annulation increases the electron-donor capabilities by raising the HOMO energy level, whereas the LUMO energy level is less affected. Moreover, third-order nonlinear optical (NLO) measurements on solutions or thin films containing the dyes showed very good values of the second hyperpolarizability. Importantly, poly(methyl methacrylate) films containing the pyranopyranyl derivatives exhibited weak linear absorption and NLO absorption compared to the nonlinearity and NLO refraction, respectively, and thus revealed them to be exceptional organic materials for photonic devices.
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Affiliation(s)
- Tanja Miletić
- Department of Chemical and Pharmaceutical SciencesINSTM UdR TriesteUniversity of TriestePiazzale Europa 134127TriesteItaly
- School of ChemistryCardiff University, Park PlaceCF10 3ATCardiffUK
| | - Andrea Fermi
- School of ChemistryCardiff University, Park PlaceCF10 3ATCardiffUK
- Department of ChemistryUniversity of Namur (UNamur)61 Rue de BruxellesNamur5000Belgium
| | - Ioannis Orfanos
- Department of PhysicsUniversity of Patras26504PatrasGreece
- Institute of Chemical Engineering Sciences (ICE-HT)Foundation for Research and Technology-Hellas (FORTH), P.O. Box 1414Patras26504Greece
| | - Aggelos Avramopoulos
- Institute of Biology, Medicinal Chemistry and BiotechnologyNational Hellenic Research Foundation48 Vas. Constantinou AvenueAthens11635Greece
| | - Federica De Leo
- Department of ChemistryUniversity of Namur (UNamur)61 Rue de BruxellesNamur5000Belgium
| | - Nicola Demitri
- Elettra-Sincrotrone TriesteS.S. 14 Km 163.5 in Area Science Park34149Basovizza-TriesteItaly
| | - Giacomo Bergamini
- Department of Chemistry “Giacomo Ciamician”University of BolognaVia Selmi 240126BolognaItaly
| | - Paola Ceroni
- Department of Chemistry “Giacomo Ciamician”University of BolognaVia Selmi 240126BolognaItaly
| | - Manthos G. Papadopoulos
- Institute of Biology, Medicinal Chemistry and BiotechnologyNational Hellenic Research Foundation48 Vas. Constantinou AvenueAthens11635Greece
| | - Stelios Couris
- Department of PhysicsUniversity of Patras26504PatrasGreece
- Institute of Chemical Engineering Sciences (ICE-HT)Foundation for Research and Technology-Hellas (FORTH), P.O. Box 1414Patras26504Greece
| | - Davide Bonifazi
- Department of Chemical and Pharmaceutical SciencesINSTM UdR TriesteUniversity of TriestePiazzale Europa 134127TriesteItaly
- School of ChemistryCardiff University, Park PlaceCF10 3ATCardiffUK
- Department of ChemistryUniversity of Namur (UNamur)61 Rue de BruxellesNamur5000Belgium
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15
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Lin YJ, Chu LK, Horng JC. Effects of the Terminal Aromatic Residues on Polyproline Conformation: Thermodynamic and Kinetic Studies. J Phys Chem B 2015; 119:15796-806. [PMID: 26641495 DOI: 10.1021/acs.jpcb.5b08717] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In a peptide or protein, the sequence of aromatic residue-proline or proline-aromatic residue shows a high propensity in forming cis prolyl bonds due to aromatic-proline interactions. In this work, we designed and prepared the polyproline peptides with aromatic amino acids (F, Y, W) incorporated into their N-terminal or C-terminal end to investigate the effects of a terminal aromatic residue on polyproline conformation and the transition kinetics of polyproline I (PPI) to polyproline II (PPII) helices. Circular dichroism measurements reveal that the N-terminal aromatic-proline interaction imposes a more pronounced consequence on the forming propensity of PPI conformation than does the C-terminal aromatic-proline interaction in n-propanol. The propensity of forming PPI is correlated with the strength of aromatic-proline interactions in the order of Tyr-Pro > Trp-Pro > Phe-Pro. In aqueous solution, kinetic studies indicate that aromatic-substitution effects are nondirectional and indistinct on the PPI → PPII conversion rates, suggesting that aromatic-proline interactions may not be an important factor in this process. In addition, the temperature-dependent kinetics shows that the hydrophobicity of aromatic side chain may play a critical role affecting the activation enthalpy and entropy of the conversion of PPI to PPII, providing new insights into the folding of polyproline helices.
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Affiliation(s)
- Yu-Ju Lin
- Department of Chemistry, National Tsing Hua University , Hsinchu, Taiwan 30013, R.O.C
| | - Li-Kang Chu
- Department of Chemistry, National Tsing Hua University , Hsinchu, Taiwan 30013, R.O.C.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University , Hsinchu, Taiwan 30013, R.O.C
| | - Jia-Cherng Horng
- Department of Chemistry, National Tsing Hua University , Hsinchu, Taiwan 30013, R.O.C.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University , Hsinchu, Taiwan 30013, R.O.C
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16
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Rocard L, Berezin A, De Leo F, Bonifazi D. Templated Chromophore Assembly by Dynamic Covalent Bonds. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507186] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Lou Rocard
- Namur Research College (NARC) and Department of Chemistry University of Namur (UNamur), Rue de Bruxelles 61, Namur 5000 (Belgium)
| | - Andrey Berezin
- Namur Research College (NARC) and Department of Chemistry University of Namur (UNamur), Rue de Bruxelles 61, Namur 5000 (Belgium)
| | - Federica De Leo
- Namur Research College (NARC) and Department of Chemistry University of Namur (UNamur), Rue de Bruxelles 61, Namur 5000 (Belgium)
| | - Davide Bonifazi
- Namur Research College (NARC) and Department of Chemistry University of Namur (UNamur), Rue de Bruxelles 61, Namur 5000 (Belgium)
- Department of Pharmaceutical and Chemical Sciences and INSTM UdR Trieste, University of Trieste, Piazzale Europa 1, Trieste 34127 (Italy)
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17
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Rocard L, Berezin A, De Leo F, Bonifazi D. Templated Chromophore Assembly by Dynamic Covalent Bonds. Angew Chem Int Ed Engl 2015; 54:15739-43. [PMID: 26637106 DOI: 10.1002/anie.201507186] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Indexed: 11/10/2022]
Abstract
Through the simultaneous use of three orthogonal dynamic covalent reactions, namely disulfide, boronate, and acyl hydrazone formation, we conceived a facile and versatile protocol to spatially organize tailored chromophores, which absorb in the blue, red, and yellow regions, on a preprogrammed α-helix peptide. This approach allowed the assembly of the dyes in the desired ratio and spacing, as dictated by both the relative positioning and distribution of the recognition units on the peptide scaffold. Steady-state UV/Vis absorption and emission studies suggest an energy transfer from the yellow and red donors to the blue acceptor. A molecular dynamics simulation supports the experimental findings that the helical structure is maintained after the assembly and the three dyes are confined in defined conformational spaces.
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Affiliation(s)
- Lou Rocard
- Namur Research College (NARC) and Department of Chemistry University of Namur (UNamur), Rue de Bruxelles 61, Namur 5000 (Belgium)
| | - Andrey Berezin
- Namur Research College (NARC) and Department of Chemistry University of Namur (UNamur), Rue de Bruxelles 61, Namur 5000 (Belgium)
| | - Federica De Leo
- Namur Research College (NARC) and Department of Chemistry University of Namur (UNamur), Rue de Bruxelles 61, Namur 5000 (Belgium)
| | - Davide Bonifazi
- Namur Research College (NARC) and Department of Chemistry University of Namur (UNamur), Rue de Bruxelles 61, Namur 5000 (Belgium). .,Department of Pharmaceutical and Chemical Sciences and INSTM UdR Trieste, University of Trieste, Piazzale Europa 1, Trieste 34127 (Italy).
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18
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Siebler C, Maryasin B, Kuemin M, Erdmann RS, Rigling C, Grünenfelder C, Ochsenfeld C, Wennemers H. Importance of dipole moments and ambient polarity for the conformation of Xaa-Pro moieties - a combined experimental and theoretical study. Chem Sci 2015; 6:6725-6730. [PMID: 30154996 PMCID: PMC6090429 DOI: 10.1039/c5sc02211h] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 07/27/2015] [Indexed: 12/04/2022] Open
Abstract
NMR spectroscopic studies with a series of proline derivatives revealed that the polarity of the environment has a significant effect on the trans : cis isomer ratio of Xaa-Pro bonds. Computational studies showed that this effect is due to differences in the overall dipole moments of trans and cis conformers. Comparisons between the conformational properties of amide and ester derivatives revealed an intricate balance between polarity effects and n → π* interactions of adjacent carbonyl groups. The findings have important implications for protein folding and signaling as well as the performance of proline-based stereoselective catalysts.
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Affiliation(s)
- Christiane Siebler
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Boris Maryasin
- Chair of Theoretical Chemistry , Department of Chemistry , University of Munich (LMU) , Butenandtstr. 7 , D-81377 Munich , Germany
- Center of Integrated Protein Science (CIPSM) at the Department of Chemistry , University of Munich (LMU) , Butenandtstr. 5-13 , D-81377 Munich , Germany
| | - Michael Kuemin
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Roman S Erdmann
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Carla Rigling
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Claudio Grünenfelder
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry , Department of Chemistry , University of Munich (LMU) , Butenandtstr. 7 , D-81377 Munich , Germany
- Center of Integrated Protein Science (CIPSM) at the Department of Chemistry , University of Munich (LMU) , Butenandtstr. 5-13 , D-81377 Munich , Germany
| | - Helma Wennemers
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
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19
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Martin V, Legrand B, Vezenkov LL, Berthet M, Subra G, Calmès M, Bantignies J, Martinez J, Amblard M. Turning Peptide Sequences into Ribbon Foldamers by a Straightforward Multicyclization Reaction. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506955] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Vincent Martin
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS‐Université Montpellier‐ENSCM, Bâtiment E, Faculté de Pharmacie, 34093 Montpellier cedex 5 (France) http://www.ibmm.univ‐montp1.fr
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS‐Université Montpellier‐ENSCM, Bâtiment E, Faculté de Pharmacie, 34093 Montpellier cedex 5 (France) http://www.ibmm.univ‐montp1.fr
| | - Lubomir L. Vezenkov
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS‐Université Montpellier‐ENSCM, Bâtiment E, Faculté de Pharmacie, 34093 Montpellier cedex 5 (France) http://www.ibmm.univ‐montp1.fr
| | - Mathéo Berthet
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS‐Université Montpellier‐ENSCM, Bâtiment E, Faculté de Pharmacie, 34093 Montpellier cedex 5 (France) http://www.ibmm.univ‐montp1.fr
| | - Gilles Subra
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS‐Université Montpellier‐ENSCM, Bâtiment E, Faculté de Pharmacie, 34093 Montpellier cedex 5 (France) http://www.ibmm.univ‐montp1.fr
| | - Monique Calmès
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS‐Université Montpellier‐ENSCM, Bâtiment E, Faculté de Pharmacie, 34093 Montpellier cedex 5 (France) http://www.ibmm.univ‐montp1.fr
| | - Jean‐Louis Bantignies
- LC2 ‐ UMR 5221 CNRS, Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier (France)
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS‐Université Montpellier‐ENSCM, Bâtiment E, Faculté de Pharmacie, 34093 Montpellier cedex 5 (France) http://www.ibmm.univ‐montp1.fr
| | - Muriel Amblard
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS‐Université Montpellier‐ENSCM, Bâtiment E, Faculté de Pharmacie, 34093 Montpellier cedex 5 (France) http://www.ibmm.univ‐montp1.fr
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20
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Adhikari B, Singh C, Shah A, Lough AJ, Kraatz H. Amino Acid Chirality and Ferrocene Conformation Guided Self‐Assembly and Gelation of Ferrocene–Peptide Conjugates. Chemistry 2015; 21:11560-72. [DOI: 10.1002/chem.201501395] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Bimalendu Adhikari
- Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, M1C 1A4 (Canada)
| | - Charanpreet Singh
- Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, M1C 1A4 (Canada)
| | - Afzal Shah
- Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, M1C 1A4 (Canada)
- Present address: Department of Chemistry, Quaid‐i‐Azam University, 45320 (Pakistan)
| | - Alan J. Lough
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6 (Canada)
| | - Heinz‐Bernhard Kraatz
- Department of Physical and Environmental Sciences, University of Toronto, 1265 Military Trail, Toronto, M1C 1A4 (Canada)
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6 (Canada)
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21
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Wilhelm P, Lewandowski B, Trapp N, Wennemers H. A crystal structure of an oligoproline PPII-helix, at last. J Am Chem Soc 2014; 136:15829-32. [PMID: 25368901 DOI: 10.1021/ja507405j] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The first crystal structure of an oligoproline adopting an all-trans polyproline II (PPII) helix is presented. The high-resolution structure provides detailed insight into the dimensions and conformational properties of oligoprolines that are important for, e.g., their use as "molecular rulers" and "molecular scaffolds". The structure also showed that the amides interact with each other within a PPII helix and that water is not necessary for PPII helicity.
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Affiliation(s)
- Patrick Wilhelm
- Laboratory of Organic Chemistry, ETH Zurich , Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
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