1
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Debnath S, Flood AH, Raghavachari K. Solvent-Dependent Folding Behavior of a Helix-Forming Aryl-Triazole Foldamer. J Phys Chem B 2024; 128:1586-1594. [PMID: 38324342 DOI: 10.1021/acs.jpcb.3c04907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Aromatic foldamers make up a novel class of bioinspired molecules that display helical conformations and have functions that rely on control over their coil-helix folding preferences. While the folding has been extensively examined by experiment, it has rarely been paired with the types of atomic level insights offered by theory. We present the results of all-atom molecular dynamics (MD) simulations to examine the role of solvent polarity on driving the helical folding behavior of the aryl-triazole foldamer. The temperature-dependent enhanced sampling technique, replica-exchange MD simulations, was employed to understand the folding phenomena. The simulation results show that in a low polarity solvent (dichloromethane), the foldamer prefers to stay in the unfolded state. The unfolded state has four dipolar triazoles (5 D) in their favored all-anti geometries and favoring anti-parallel geometries. However, an increase in solvent polarity using acetonitrile resulted in solvophobic collapse, yielding the helically folded form as the predominant state. The folded helix has an all-syn geometry, with triazoles in parallel arrangements. Intermediate conformations with a mixture of syn and anti arrangements of the triazoles are of lower abundance in both the DCM and MeCN solvents. The chiral handedness of the helix observed experimentally is assigned as left-handed by correlation with computed electronic circular dichroism spectra using time-dependent density functional theory.
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Affiliation(s)
- Sibali Debnath
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Amar H Flood
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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2
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Teng B, Mandal PK, Allmendinger L, Douat C, Ferrand Y, Huc I. Controlling aromatic helix dimerization in water by tuning charge repulsions. Chem Sci 2023; 14:11251-11260. [PMID: 37860656 PMCID: PMC10583700 DOI: 10.1039/d3sc02020g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/14/2023] [Indexed: 10/21/2023] Open
Abstract
Several helically folded aromatic oligoamides were designed and synthesized. The sequences were all water-soluble thanks to the charged side chains borne by the monomers. Replacing a few, sometimes only two, charged side chains by neutral methoxy groups was shown to trigger the formation of various aggregates which could be tentatively assigned to head-to-head stacked dimers of single helices, double helical duplexes and a quadruplex, none of which would form in organic solvent with organic-soluble analogues. The nature of the aggregates was supported by concentration and solvent dependent NMR studies, 1H DOSY experiments, mass spectrometry, and X-ray crystallography or energy-minimized models, as well as analogies with earlier studies. The hydrophobic effect appears to be the main driving force for aggregation but it can be finely modulated by the presence or absence of a small number of charges to an extent that had no precedent in aromatic foldamer architectures. These results will serve as a benchmark for future foldamer design in water.
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Affiliation(s)
- Binhao Teng
- Department of Pharmacy, Ludwig-Maximilians-Universität Butenandtstr. 5-13 81377 München Germany
| | - Pradeep K Mandal
- Department of Pharmacy, Ludwig-Maximilians-Universität Butenandtstr. 5-13 81377 München Germany
| | - Lars Allmendinger
- Department of Pharmacy, Ludwig-Maximilians-Universität Butenandtstr. 5-13 81377 München Germany
| | - Céline Douat
- Department of Pharmacy, Ludwig-Maximilians-Universität Butenandtstr. 5-13 81377 München Germany
| | - Yann Ferrand
- Univ. Bordeaux, CNRS, Bordeaux Institut National Polytechnique CBMN UMR 5248, 2 rue Escarpit 33600 Pessac France
| | - Ivan Huc
- Department of Pharmacy, Ludwig-Maximilians-Universität Butenandtstr. 5-13 81377 München Germany
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3
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Meier D, Schoof B, Wang J, Li X, Walz A, Huettig A, Schlichting H, Rosu F, Gabelica V, Maurizot V, Reichert J, Papageorgiou AC, Huc I, Barth JV. Structural adaptations of electrosprayed aromatic oligoamide foldamers on Ag(111). Chem Commun (Camb) 2022; 58:8938-8941. [PMID: 35851385 DOI: 10.1039/d2cc03286d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aromatic foldamers are promising for applications such as molecular recognition and molecular machinery. For many of these, defect free, 2D-crystaline monolayers are needed. To this end, submonolayers were prepared in ultra-high vacuum (UHV) on Ag(111) via electrospray controlled ion beam deposition (ES-CIBD). On the surface, the unfolded state is unambiguously identified by real-space single-molecule imaging using scanning tunnelling microscopy (STM) and it is found to assemble in regular structures.
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Affiliation(s)
- Dennis Meier
- Physics Department E20, Technical University Munich, D-85748 Garching, Germany.
| | - Benedikt Schoof
- Physics Department E20, Technical University Munich, D-85748 Garching, Germany.
| | - Jinhua Wang
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, F-33600 Pessac, France
| | - Xuesong Li
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, F-33600 Pessac, France
| | - Andreas Walz
- Physics Department E20, Technical University Munich, D-85748 Garching, Germany.
| | - Annette Huettig
- Physics Department E20, Technical University Munich, D-85748 Garching, Germany.
| | - Hartmut Schlichting
- Physics Department E20, Technical University Munich, D-85748 Garching, Germany.
| | - Frédéric Rosu
- Institut Européen de Chimie et Biologie (UAR3033/US001), Univ. Bordeaux, CNRS, INSERM, F-33600 Pessac, France
| | - Valérie Gabelica
- Institut Européen de Chimie et Biologie (UAR3033/US001), Univ. Bordeaux, CNRS, INSERM, F-33600 Pessac, France.,ARNA (U1212), Univ. Bordeaux, INSERM, CNRS, F-33600 Pessac, France
| | - Victor Maurizot
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, F-33600 Pessac, France
| | - Joachim Reichert
- Physics Department E20, Technical University Munich, D-85748 Garching, Germany.
| | | | - Ivan Huc
- Department of Pharmacy, Ludwig-Maximilians-University Munich, D-81377 Munich, Germany. .,Cluster of Excellence e-conversion, D-85748 Garching, Germany
| | - Johannes V Barth
- Physics Department E20, Technical University Munich, D-85748 Garching, Germany. .,Cluster of Excellence e-conversion, D-85748 Garching, Germany
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4
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Zhou C, Fan G, Deng L. Theoretical study of the helical conformers and ECD spectra of 8-aminoquinoline polymers. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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5
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Urushibara K, Ferrand Y, Liu Z, Katagiri K, Kawahata M, Morvan E, D'Elia R, Pophristic V, Tanatani A, Huc I. Accessing Improbable Foldamer Shapes with Strained Macrocycles. Chemistry 2021; 27:11205-11215. [PMID: 33905165 PMCID: PMC8453500 DOI: 10.1002/chem.202101201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Indexed: 11/07/2022]
Abstract
The alkylation of some secondary amide functions with a dimethoxybenzyl (DMB) group in oligomers of 8-amino-2-quinolinecarboxylic acid destabilizes the otherwise favored helical conformations, and allows for cyclization to take place. A cyclic hexamer and a cyclic heptamer were produced in this manner. After DMB removal, X-ray crystallography and NMR show that the macrocycles adopt strained conformations that would be improbable in noncyclic species. The high helix folding propensity of the main chain is partly expressed in these conformations, but it remains frustrated by macrocyclization. Despite being homomeric, the macrocycles possess inequivalent monomer units. Experimental and computational studies highlight specific fluxional pathways within these structures. Extensive simulated annealing molecular dynamics allow for the prediction of the conformations for larger macrocycles with up to sixteen monomers.
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Affiliation(s)
- Ko Urushibara
- Department of ChemistryFaculty of ScienceOchanomizu University2-1-1 Otsuka, Bunkyo-kuTokyo112-8610Japan
- CBMN (UMR 5248)Université de BordeauxCNRSBordeaux Institut National Polytechnique2 rue Robert Escarpit33600PessacFrance
| | - Yann Ferrand
- CBMN (UMR 5248)Université de BordeauxCNRSBordeaux Institut National Polytechnique2 rue Robert Escarpit33600PessacFrance
| | - Zhiwei Liu
- Department of Chemistry & BiochemistryUniversity of the Sciences600 South 43rd StreetPhiladelphiaPA19104USA
| | - Kosuke Katagiri
- Department of ChemistryFaculty of Science and EngineeringKonan University8-9-1 Okamoto, Higashinada-kuKobe658-8501Japan
| | - Masatoshi Kawahata
- Faculty of Pharmaceutical SciencesShowa Pharmaceutical University3-3165 Higashi-TamagawagakuenMachidaTokyo194-8543Japan
| | - Estelle Morvan
- IECB (UMS3033/US001)Université de Bordeaux, CNRS, INSERM2 rue Robert Escarpit33600PessacFrance
| | - Ryan D'Elia
- Department of Chemistry & BiochemistryUniversity of the Sciences600 South 43rd StreetPhiladelphiaPA19104USA
| | - Vojislava Pophristic
- Department of Chemistry & BiochemistryUniversity of the Sciences600 South 43rd StreetPhiladelphiaPA19104USA
| | - Aya Tanatani
- Department of ChemistryFaculty of ScienceOchanomizu University2-1-1 Otsuka, Bunkyo-kuTokyo112-8610Japan
| | - Ivan Huc
- CBMN (UMR 5248)Université de BordeauxCNRSBordeaux Institut National Polytechnique2 rue Robert Escarpit33600PessacFrance
- Department of Pharmacy and Center for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstr. 5–1381377MünchenGermany
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6
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Hierarchical communication of chirality for aromatic oligoamide sequences. Nat Commun 2021; 12:2659. [PMID: 33976219 PMCID: PMC8113567 DOI: 10.1038/s41467-021-22984-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 04/07/2021] [Indexed: 11/24/2022] Open
Abstract
The communication of chirality at a molecular and supramolecular level is the fundamental feature capable of transmitting and amplifying chirality information. Yet, the limitation of one-step communication mode in many artificial systems has precluded the ability of further processing the chirality information. Here, we report the chirality communication of aromatic oligoamide sequences within the interpenetrated helicate architecture in a hierarchical manner, specifically, the communication is manipulated by three sequential steps: (i) coordination, (ii) concentration, and (iii) ion stimulus. Such approach enables the information to be implemented progressively and reversibly to different levels. Furthermore, the chiral information on the side chains can be accumulated and transferred to the helical backbones of the sequences, resulting in that one of ten possible diastereoisomers of the interpenetrated helicate is finally selected. The circular dichroism experiments with a mixture of chiral and achiral ligands demonstrate a cooperative behavior of these communications, leading to amplification of chiral information. Communication of chirality at a molecular level is the fundamental for transmitting chirality information but one-step communication modes in many artificial systems limits further processing the chirality information. Here, the authors report chirality communication of aromatic oligoamide sequences within interpenetrated helicate architecture in a hierarchical manner.
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7
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Devaux F, Li X, Sluysmans D, Maurizot V, Bakalis E, Zerbetto F, Huc I, Duwez AS. Single-molecule mechanics of synthetic aromatic amide helices: Ultrafast and robust non-dissipative winding. Chem 2021. [DOI: 10.1016/j.chempr.2021.02.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Wang J, Wicher B, Maurizot V, Huc I. Oligo-Quinolylene-Vinylene Foldamers. Chemistry 2021; 27:1031-1038. [PMID: 32881144 PMCID: PMC7839515 DOI: 10.1002/chem.202003559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/01/2020] [Indexed: 01/26/2023]
Abstract
Quinoline based aromatic amide foldamers are known to adopt stable folded conformations. We have developed a synthetic approach to produce similar oligomers where all amide bonds, or part of them, have been replaced by an isosteric vinylene group. The results of solution and solid state structural studies show that oligomers exclusively containing vinylene linkages are not well folded, and adopt predominantly flat conformations. In contrast, a vinylene segment flanked by helical oligoamides also folds in a helix, albeit with a slightly lower curvature. The presence of vinylene functions also result in an extension of π-conjugation across the oligomer that may change charge transport properties. Altogether, these results pave the way to foldamers in which both structural control and specific electronic properties may be engineered.
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Affiliation(s)
- Jinhua Wang
- CBMN (UMR5248), Univ. Bordeaux–CNRS–IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
| | - Barbara Wicher
- Department of Chemical Technology of DrugsPoznan University of Medical SciencesGrunwaldzka 660-780PoznanPoland
| | - Victor Maurizot
- CBMN (UMR5248), Univ. Bordeaux–CNRS–IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
| | - Ivan Huc
- CBMN (UMR5248), Univ. Bordeaux–CNRS–IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
- Department of Pharmacy and Cluster e-conversionLudwig-Maximilians-UniversiätButenandtstrasse 5–1381377MünchenGermany
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9
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Hu X, Mandal PK, Kauffmann B, Huc I. Hybrid Sequences that Express both Aromatic Amide and α-Peptidic Folding Features. Chempluschem 2020; 85:1580-1586. [PMID: 32729681 PMCID: PMC7496704 DOI: 10.1002/cplu.202000416] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 07/05/2020] [Indexed: 01/28/2023]
Abstract
Foldamers combining aliphatic and aromatic main-chain units often produce atypical structures that cannot easily be accessed from purely aromatic or aliphatic sequences. We report solid-state evidence that sequences comprising α-amino acids and quinoline-based monomers adopt conformations that combine the folding propensities of both components. Foldamers 2 and 3 having an XQQ repeat motif (X=α-amino acid, Q=quinoline) were synthesized. Crystals of 2 (X=Phe, Q with an anionic side chain) obtained from water revealed an aromatic helix where amide groups belonging to the α-amino acids created a hydrogen-bond array typical of peptidic helices. Crystals of 3 (X=Ser, Q with a lipophilic side chain) obtained from organic solvents revealed a helix-turn-helix structure in which α-amino acid side chains interfere with main-chain hydrogen bonding. High sequence-dependency of the conformation is typical of peptides but is shown here to include aromatic folding features.
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Affiliation(s)
- Xiaobo Hu
- CBMN (UMR5248)Univ. Bordeaux-CNRS-IPBInstitut Européen de Chimie et Biologie2 rue Robert Escarpit33600PessacFrance
| | - Pradeep K. Mandal
- Department PharmazieCenter for Integrated Protein ScienceLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MünchenGermany
| | - Brice Kauffmann
- IECB (UMS3033)Univ. Bordeaux-CNRS-INSERMInstitut Européen de Chimie et Biologie2 rue Robert Escarpit33600PessacFrance
| | - Ivan Huc
- Department PharmazieCenter for Integrated Protein ScienceLudwig-Maximilians-Universität MünchenButenandtstr. 5–1381377MünchenGermany
- CBMN (UMR5248)Univ. Bordeaux-CNRS-IPBInstitut Européen de Chimie et Biologie2 rue Robert Escarpit33600PessacFrance
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10
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Enhancing Aromatic Foldamer Helix Dynamics to Probe Interactions with Protein Surfaces. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800855] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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11
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Sproviero EM. Intramolecular Natural Energy Decomposition Analysis: Applications to the Rational Design of Foldamers. J Comput Chem 2018; 39:1367-1386. [PMID: 29962063 DOI: 10.1002/jcc.25127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 10/23/2017] [Accepted: 10/24/2017] [Indexed: 12/24/2022]
Abstract
We describe an intramolecular version of the natural energy decomposition analysis (NEDA), with the aim of evaluating interactions between molecular fragments across covalent bonds. The electronic energy in intramolecular natural energy decomposition analysis (INEDA) is divided into electrical, core, and charge transfer components. The INEDA method describes the fragments using the nonfragmented electronic density, and, therefore, there are no limitations in how to choose the boundary orbital. We used INEDA to evaluate the interaction energies that give origin to barriers of rotation around Camide Caromatic (Cam Car ) and Namide Caromtaic (Nam Car ) bonds in arylamide-foldamer building blocks. We found that differences of barrier height between models with different ortho-aryl substituents stem from charge transfer and core interactions. In three-center hydrogen-bond (H-bond) models with an NH proton donor H-bound to two electronegative ortho-aryl substituents, the interaction energy of the three-center system is larger than in either of the two-center H-bond subsystem alone, indicating an increase of overall rigidity. The combination of INEDA and NEDA allows the evaluation of intermolecular and intramolecular interactions using a consistent theoretical framework. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Eduardo M Sproviero
- Department of Chemistry and Biochemistry, University of the Sciences in Philadelphia, 600 S. 43rd St, Philadelphia, Pennsylvania, 19104
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12
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Urushibara K, Ferrand Y, Liu Z, Masu H, Pophristic V, Tanatani A, Huc I. Frustrierte Helizität: Zusammenführung divergierender Enden einer stabilen aromatischen Amid‐Helix zu einem fluxionalen Makrocyclus. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Ko Urushibara
- Department of Chemistry Faculty of Science Ochanomizu University 2-1-1 Otsuka, Bunkyo-ku Tokyo 112-8610 Japan
- CBMN (UMR5248) Univ. Bordeaux – CNRS – IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
| | - Yann Ferrand
- CBMN (UMR5248) Univ. Bordeaux – CNRS – IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
| | - Zhiwei Liu
- Department of Chemistry &Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
| | - Hyuma Masu
- Center for Analytical Instrumentation Chiba University 1-33 Yayoi, Inage Chiba 263-8522 Japan
| | - Vojislava Pophristic
- Department of Chemistry &Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
| | - Aya Tanatani
- Department of Chemistry Faculty of Science Ochanomizu University 2-1-1 Otsuka, Bunkyo-ku Tokyo 112-8610 Japan
| | - Ivan Huc
- CBMN (UMR5248) Univ. Bordeaux – CNRS – IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
- Department Pharmazie Ludwig-Maximilians-Universität Butenandtstraße 5–13 81377 München Deutschland
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13
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Urushibara K, Ferrand Y, Liu Z, Masu H, Pophristic V, Tanatani A, Huc I. Frustrated Helicity: Joining the Diverging Ends of a Stable Aromatic Amide Helix to Form a Fluxional Macrocycle. Angew Chem Int Ed Engl 2018; 57:7888-7892. [DOI: 10.1002/anie.201802159] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Ko Urushibara
- Department of Chemistry Faculty of Science Ochanomizu University 2-1-1 Otsuka, Bunkyo-ku Tokyo 112-8610 Japan
- CBMN (UMR5248), Univ. Bordeaux—CNRS—IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac France
| | - Yann Ferrand
- CBMN (UMR5248), Univ. Bordeaux—CNRS—IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac France
| | - Zhiwei Liu
- Department of Chemistry &Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
| | - Hyuma Masu
- Center for Analytical Instrumentation Chiba University 1–33 Yayoi, Inage Chiba 263-8522 Japan
| | - Vojislava Pophristic
- Department of Chemistry &Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
| | - Aya Tanatani
- Department of Chemistry Faculty of Science Ochanomizu University 2-1-1 Otsuka, Bunkyo-ku Tokyo 112-8610 Japan
| | - Ivan Huc
- CBMN (UMR5248), Univ. Bordeaux—CNRS—IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac France
- Department Pharmazie Ludwig-Maximilians-Universität Butenandtstr. 5–13 81377 München Germany
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14
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Zhao D, Yang L, Yuan Y, Wang H, Dong H, Li S. Molecular Mechanism of Self-Assembly of Aromatic Oligoamides into Interlocked Double-Helix Foldamers. J Phys Chem B 2017; 121:10064-10072. [PMID: 29019673 DOI: 10.1021/acs.jpcb.7b09067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Foldamer, inspired by the structures and functions of biopolymers, is defined as an artificial molecular architecture that can fold into a three-dimensional structure in solution and has been a growing and active field in supramolecular chemistry. The central issue in foldamer science is to understand how the primary sequence of oligomer folds into conformationally ordered structures as well as how individual subunits self-associate into assembly. For duplex structures, these two issues are always interrelated and inseparable with each other. Although the emergence of new foldamer keeps growing, the detailed mechanism remains elusive. On the basis of an artificially synthesized arylamide oligoamide foldamer with its crystal structure available, we constructed a set of four foldamers with a similar backbone but different substituents and aimed at dissecting the folding and self-association mechanisms of a double-helical foldamer with computations. Using molecular simulations at a microsecond time scale, we observed very consistent processes of the spontaneous self-assembly of two single-helical motifs into an entwined complex. Our results reveal that aggregation of two single-helical motifs driven by extensive π-π interactions is energetically favorable and that this spontaneous self-assembly proceeds through an "unwinding-threading-rewinding" mechanism. The detailed mechanisms about the folding and self-assembly in an aromatic oligoamide foldamer we present here disclose how the sequence is associated with a well-ordered three-dimensional structure at atomic level and therefore may have implications for designing new foldamers with versatile functions.
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Affiliation(s)
| | - Ling Yang
- CAS Key Laboratory of Photochemistry, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, People's Republic of China
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15
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Liu Z, Hu X, Abramyan AM, Mészáros Á, Csékei M, Kotschy A, Huc I, Pophristic V. Computational Prediction and Rationalization, and Experimental Validation of Handedness Induction in Helical Aromatic Oligoamide Foldamers. Chemistry 2017; 23:3605-3615. [DOI: 10.1002/chem.201605082] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Zhiwei Liu
- Department of Chemistry & Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
| | - Xiaobo Hu
- University of Bordeaux, CBMN (UMR 5248) Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac France
- CNRS, CBMN (UMR 5248) France
- Bordeaux Institut National Polytechnique CBMN (UMR 5248) France
| | - Ara M. Abramyan
- Department of Chemistry & Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
| | - Ádám Mészáros
- Servier Research Institute of Medicinal Chemistry Záhony utca 7. 1031 Budapest Hungary
| | - Márton Csékei
- Servier Research Institute of Medicinal Chemistry Záhony utca 7. 1031 Budapest Hungary
| | - András Kotschy
- Servier Research Institute of Medicinal Chemistry Záhony utca 7. 1031 Budapest Hungary
| | - Ivan Huc
- University of Bordeaux, CBMN (UMR 5248) Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac France
- CNRS, CBMN (UMR 5248) France
- Bordeaux Institut National Polytechnique CBMN (UMR 5248) France
| | - Vojislava Pophristic
- Department of Chemistry & Biochemistry University of the Sciences 600 South 43rd Street Philadelphia PA 19104 USA
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16
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Uribe L, Gauss J, Diezemann G. Determining Factors for the Unfolding Pathway of Peptides, Peptoids, and Peptidic Foldamers. J Phys Chem B 2016; 120:10433-10441. [DOI: 10.1021/acs.jpcb.6b06784] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lalita Uribe
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
- Graduate School Materials Science in Mainz, Staudinger Weg 9, 55128 Mainz, Germany
| | - Jürgen Gauss
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
| | - Gregor Diezemann
- Institut für Physikalische Chemie, Universität Mainz, Duesbergweg 10-14, 55128 Mainz, Germany
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17
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Wechsel R, Raftery J, Cavagnat D, Guichard G, Clayden J. The meso
Helix: Symmetry and Symmetry-Breaking in Dynamic Oligourea Foldamers with Reversible Hydrogen-Bond Polarity. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604496] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Romina Wechsel
- School of Chemistry; University of Manchester; Oxford Road Manchester M13 9PL UK
| | - James Raftery
- School of Chemistry; University of Manchester; Oxford Road Manchester M13 9PL UK
| | - Dominique Cavagnat
- ISM, UMR CNRS 5255; Université de Bordeaux; 351 cours de la Libération 33405 Talence France
| | - Gilles Guichard
- Université de Bordeaux, CBMN, UMR 5248; Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33607 Pessac France
- CNRS, CBMN, UMR 5248; 33600 Pessac France
| | - Jonathan Clayden
- School of Chemistry; University of Bristol; Cantock's Close Bristol BS8 1TS UK
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18
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Wechsel R, Raftery J, Cavagnat D, Guichard G, Clayden J. The meso
Helix: Symmetry and Symmetry-Breaking in Dynamic Oligourea Foldamers with Reversible Hydrogen-Bond Polarity. Angew Chem Int Ed Engl 2016; 55:9657-61. [DOI: 10.1002/anie.201604496] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Romina Wechsel
- School of Chemistry; University of Manchester; Oxford Road Manchester M13 9PL UK
| | - James Raftery
- School of Chemistry; University of Manchester; Oxford Road Manchester M13 9PL UK
| | - Dominique Cavagnat
- ISM, UMR CNRS 5255; Université de Bordeaux; 351 cours de la Libération 33405 Talence France
| | - Gilles Guichard
- Université de Bordeaux, CBMN, UMR 5248; Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33607 Pessac France
- CNRS, CBMN, UMR 5248; 33600 Pessac France
| | - Jonathan Clayden
- School of Chemistry; University of Bristol; Cantock's Close Bristol BS8 1TS UK
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19
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Tsiamantas C, de Hatten X, Douat C, Kauffmann B, Maurizot V, Ihara H, Takafuji M, Metzler-Nolte N, Huc I. Selective Dynamic Assembly of Disulfide Macrocyclic Helical Foldamers with Remote Communication of Handedness. Angew Chem Int Ed Engl 2016; 55:6848-52. [DOI: 10.1002/anie.201601156] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Christos Tsiamantas
- University of Bordeaux, CBMN (UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS, CBMN (UMR 5248); France
| | - Xavier de Hatten
- University of Bordeaux, CBMN (UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS, CBMN (UMR 5248); France
| | - Céline Douat
- University of Bordeaux, CBMN (UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS, CBMN (UMR 5248); France
| | - Brice Kauffmann
- University of Bordeaux; Institut Européen de Chimie et Biologie (UMS3033); 2 rue Escarpit 33600 Pessac France
- CNRS, IECB (UMS 3033); Pessac France
- INSERM, IECB (US 001); Pessac France
| | - Victor Maurizot
- University of Bordeaux, CBMN (UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS, CBMN (UMR 5248); France
| | - Hirotaka Ihara
- Kumamoto University; Department of Applied Chemistry and Biochemistry; 2-39-1 Kurokami Kumamoto 860-8555 Japan
| | - Makoto Takafuji
- Kumamoto University; Department of Applied Chemistry and Biochemistry; 2-39-1 Kurokami Kumamoto 860-8555 Japan
| | - Nils Metzler-Nolte
- Ruhr University Bochum; Faculty for Chemistry and Biochemistry; Universitätstrasse 150 44801 Bochum Germany
| | - Ivan Huc
- University of Bordeaux, CBMN (UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS, CBMN (UMR 5248); France
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20
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Tsiamantas C, de Hatten X, Douat C, Kauffmann B, Maurizot V, Ihara H, Takafuji M, Metzler-Nolte N, Huc I. Selective Dynamic Assembly of Disulfide Macrocyclic Helical Foldamers with Remote Communication of Handedness. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601156] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Christos Tsiamantas
- University of Bordeaux, CBMN (UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS, CBMN (UMR 5248); France
| | - Xavier de Hatten
- University of Bordeaux, CBMN (UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS, CBMN (UMR 5248); France
| | - Céline Douat
- University of Bordeaux, CBMN (UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS, CBMN (UMR 5248); France
| | - Brice Kauffmann
- University of Bordeaux; Institut Européen de Chimie et Biologie (UMS3033); 2 rue Escarpit 33600 Pessac France
- CNRS, IECB (UMS 3033); Pessac France
- INSERM, IECB (US 001); Pessac France
| | - Victor Maurizot
- University of Bordeaux, CBMN (UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS, CBMN (UMR 5248); France
| | - Hirotaka Ihara
- Kumamoto University; Department of Applied Chemistry and Biochemistry; 2-39-1 Kurokami Kumamoto 860-8555 Japan
| | - Makoto Takafuji
- Kumamoto University; Department of Applied Chemistry and Biochemistry; 2-39-1 Kurokami Kumamoto 860-8555 Japan
| | - Nils Metzler-Nolte
- Ruhr University Bochum; Faculty for Chemistry and Biochemistry; Universitätstrasse 150 44801 Bochum Germany
| | - Ivan Huc
- University of Bordeaux, CBMN (UMR 5248); Institut Européen de Chimie et Biologie; 2 rue Escarpit 33600 Pessac France
- CNRS, CBMN (UMR 5248); France
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Abstract
In nature, the folding of oligomers and polymers is used to generate complex three-dimensional structures, yielding macromolecules with diverse functions in catalysis, recognition, transport, and charge- and energy-transfer. Over the past 20-30 years, chemists have sought to replicate this strategy by developing new foldamers: oligomers that fold into well-defined secondary structures in solution. A wide array of abiotic foldamers have been developed, ranging from non-natural peptides to aromatics. The ortho-phenylenes represent a recent addition to the family of aromatic foldamers. Despite their structural simplicity (chains of benzenes connected at the ortho positions), it was not until 2010 that systematic studies of o-phenylenes showed that they reliably fold into helices in solution (and in the solid state). This conformational behavior is of fundamental interest: o-Arylene and o-heteroarylene structures are found embedded within many other systems, part of an emerging interest in sterically congested polyphenylenes. Further, o-phenylenes are increasingly straightforward to synthesize because of continuing developments in arene-arene coupling, the Asao-Yamamoto benzannulation, and benzyne polymerization. In this Account, we discuss the folding of o-phenylenes with emphasis on features that make them unique among aromatic foldamers. Interconversion between their different backbone conformers is slow on the NMR time scale around room temperature. The (1)H NMR spectra of oligomers can therefore be deconvoluted to give sets of chemical shifts for different folding states. The chemical shifts are both highly sensitive to conformation and readily predicted using ab initio methods, affording critical information about the conformational distribution. The picture that emerges is that o-phenylenes fold into helices with offset stacking between every third repeat unit. In general, misfolding occurs primarily at the oligomer termini (i.e., "frayed ends"). Because of their structural simplicity, the folding can be described by straightforward models. The overall population can be divided into two enantiomeric pools, with racemization and misfolding as two distinct processes. Examination of substituent effects on folding reveals that the determinant of the relative stability of different conformers is (offset) aromatic stacking interactions parallel to the helical axis. That is, the folding of o-phenylenes is analogous to that of α-helices, with aromatic stacking in place of hydrogen bonding. The folding propensity can be tuned using well-known substituent effects on aromatic stacking, with moderate electron-withdrawing substituents giving nearly perfect folding. The combination of a simple folding mechanism and readily characterized conformational populations makes o-phenylenes attractive structural motifs for incorporation into more-complex architectures, an important part of the next phase of foldamer research.
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Affiliation(s)
- C. Scott Hartley
- Department of Chemistry & Biochemistry, Miami University, Oxford, Ohio 45056, United States
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22
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Chandramouli N, El-Behairy MF, Lautrette G, Ferrand Y, Huc I. Polar solvent effects on tartaric acid binding by aromatic oligoamide foldamer capsules. Org Biomol Chem 2016; 14:2466-72. [DOI: 10.1039/c5ob02641e] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aromatic amide foldamer capsules hold polar guests in protic solvents.
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Affiliation(s)
- Nagula Chandramouli
- Univ. Bordeaux
- CBMN (UMR 5248)
- Institut Européen de Chimie Biologie
- 33607 Pessac
- France
| | | | - Guillaume Lautrette
- Univ. Bordeaux
- CBMN (UMR 5248)
- Institut Européen de Chimie Biologie
- 33607 Pessac
- France
| | - Yann Ferrand
- Univ. Bordeaux
- CBMN (UMR 5248)
- Institut Européen de Chimie Biologie
- 33607 Pessac
- France
| | - Ivan Huc
- Univ. Bordeaux
- CBMN (UMR 5248)
- Institut Européen de Chimie Biologie
- 33607 Pessac
- France
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