1
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Fobe TL, Walker CC, Meek GA, Shirts MR. Folding Coarse-Grained Oligomer Models with PyRosetta. J Chem Theory Comput 2022; 18:6354-6369. [PMID: 36179376 DOI: 10.1021/acs.jctc.2c00519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Non-biological foldamers are a promising class of macromolecules that share similarities to classical biopolymers such as proteins and nucleic acids. Currently, designing novel foldamers is a non-trivial process, often involving many iterations of trial synthesis and characterization until folded structures are observed. In this work, we aim to tackle these foldamer design challenges using computational modeling techniques. We developed CG PyRosetta, an extension to the popular protein folding python package, PyRosetta, which introduces coarse-grained (CG) residues into PyRosetta, enabling the folding of toy CG foldamer models. Although these models are simplified, they can help explore overarching physical hypotheses about how oligomers can form. Through systematic variation of CG parameters in these models, we can investigate various folding hypotheses at the CG scale to inform the design process of new foldamer chemistries. In this study, we demonstrate CG PyRosetta's ability to identify minimum energy structures with a diverse structural search over a range of simple models, as well as two hypothesis-driven parameter scans investigating the effects of side-chain size and internal backbone angle on secondary structures. We are able to identify several types of secondary structures from single- and double-helices to sheet-like and knot-like structures. We show how side-chain size and backbone bond angle both play an important role in the structure and energetics of these toy models. Optimal side-chain sizes promote favorable packing of side chains, while specific backbone bond angles influence the specific helix type found in folded structures.
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Affiliation(s)
- Theodore L Fobe
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Christopher C Walker
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Garrett A Meek
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
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2
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Sobiech TA, Zhong Y, Gong B. Cavity-containing aromatic oligoamide foldamers and macrocycles: progress and future perspectives. Org Biomol Chem 2022; 20:6962-6978. [PMID: 36040143 DOI: 10.1039/d2ob01467j] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
As a major class of foldamers, aromatic oligoamide foldamers have attracted intense interest. The rigidity of aromatic residues and amide linkages allows the development of foldamers with readily predictable, stable conformations. Aromatic oligoamide foldamers having backbones fully constrained by intramolecular hydrogen bonds have attracted wide attention. Depending on their lengths, such foldamers adopt crescent or helical conformations with highly negative inner cavities. Cyclizing the backbone of the aromatic oligoamides affords the corresponding macrocycles which are characterised by persistent shapes and non-deformable inner cavities. With their defined, inner cavities, such aromatic oligoamide foldamers and macrocycles have served as hosts for cationic and polar guests, and as transmembrane channels for transporting ions and molecules. Recent synthetic progress resulted in the construction of multi-turn hollow helices that offer three-dimensional inner pores with adjustable depth. Reducing the number of backbone-constraining hydrogen bonds leads to oligoamides which, with their partially constrained backbones, undergo either solvent- or guest-dependent folding. One class of such aromatic olgioamide foldamders, which offer multiple backbone amide NH groups as hydrogen-bond donors, are designed to bind anions with adjustable affinities.
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Affiliation(s)
- Thomas A Sobiech
- Department of Chemistry, University at Buffalo, the State University of New York, Buffalo, NY 14260, USA.
| | - Yulong Zhong
- Department of Chemistry, University at Buffalo, the State University of New York, Buffalo, NY 14260, USA.
| | - Bing Gong
- Department of Chemistry, University at Buffalo, the State University of New York, Buffalo, NY 14260, USA.
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3
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Yao C, Kauffmann B, Huc I, Ferrand Y. Self-assembling figure-of-eight and pseudoplectoneme aromatic oligoamide ribbons. Chem Commun (Camb) 2022; 58:5789-5792. [PMID: 35466334 DOI: 10.1039/d2cc01696f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two oligoamide macrocycles composed of eight and twelve 7-amino-8-fluoro-2-quinolinecarboxylic acid monomers were synthesised despite the propensity of their acyclic precursors to fold and self-assemble into double helices. Macrocyclisations were made possible through the transient use of helicity disruptors. The resulting macrocyclic ribbons were found to adopt figure-of-eight and pseudoplectoneme shapes that maintain an ability to self-assemble.
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Affiliation(s)
- Chenhao Yao
- Univ. Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN UMR 5248, 2 rue Escarpit, 33600 Pessac, France.
| | - Brice Kauffmann
- Univ. Bordeaux, CNRS, INSERM, Institut Européen de Chimie Biologie (UMS3033/US001), 2 rue Escarpit, 33600 Pessac, France
| | - Ivan Huc
- Department Pharmazie, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377 München, Germany.,Cluster of Excellence e-conversion, 85748 Garching, Germany.
| | - Yann Ferrand
- Univ. Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN UMR 5248, 2 rue Escarpit, 33600 Pessac, France.
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4
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Xing P, Liu Y, Li B, Dong ZY, Qian HJ, Wang L. Promoting a desired conformational preference of an aromatic amide in various crystals by rational design of intramolecular hydrogen bonding. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.120854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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5
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Xu Y, Liu C, Wang H, Zhang D, Li Z. Intermolecular Halogen Bonding-Controlled Self-Assembly of Hydrogen Bonded Aromatic Amide Foldamers. CHINESE J ORG CHEM 2021. [DOI: 10.6023/cjoc202102012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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6
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Meunier A, Singleton ML, Kauffmann B, Granier T, Lautrette G, Ferrand Y, Huc I. Aromatic foldamers as scaffolds for metal second coordination sphere design. Chem Sci 2020; 11:12178-12186. [PMID: 34094430 PMCID: PMC8162952 DOI: 10.1039/d0sc05143h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 10/11/2020] [Indexed: 11/21/2022] Open
Abstract
As metalloproteins exemplify, the chemical and physical properties of metal centers depend not only on their first but also on their second coordination sphere. Installing arrays of functional groups around the first coordination sphere of synthetic metal complexes is thus highly desirable, but it remains a challenging objective. Here we introduce a novel approach to produce tailored second coordination spheres. We used bioinspired artificial architectures based on aromatic oligoamide foldamers to construct a rigid, modular and well-defined environment around a metal complex. Specifically, aza-aromatic monomers having a tethered [2Fe-2S] cluster have been synthesized and incorporated in conical helical foldamer sequences. Exploiting the modularity and predictability of aromatic oligoamide structures allowed for the straightforward design of a conical architecture able to sequester the metal complex in a confined environment. Even though no direct metal complex-foldamer interactions were purposely designed in this first generation model, crystallography, NMR and IR spectroscopy concurred to show that the aromatic oligoamide backbone alters the structure and fluxional processes of the metal cluster.
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Affiliation(s)
- Antoine Meunier
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), IECB 2 Rue Robert Escarpit 33600 Pessac France
| | - Michael L Singleton
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), IECB 2 Rue Robert Escarpit 33600 Pessac France
| | - Brice Kauffmann
- Université de Bordeaux, CNRS, INSERM, Institut Européen de Chimie et Biologie (UMS 3033) 2 Rue Robert Escarpit 33600 Pessac France
| | - Thierry Granier
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), IECB 2 Rue Robert Escarpit 33600 Pessac France
| | - Guillaume Lautrette
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), IECB 2 Rue Robert Escarpit 33600 Pessac France
| | - Yann Ferrand
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), IECB 2 Rue Robert Escarpit 33600 Pessac France
| | - Ivan Huc
- Université de Bordeaux, CNRS, Bordeaux Institut National Polytechnique, CBMN (UMR 5248), IECB 2 Rue Robert Escarpit 33600 Pessac France
- Department of Pharmacy, Centre for Integrated Protein Science, Ludwig-Maximilians-Universität Butenandtstraße 5-13 D-81377 Munich Germany
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7
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Zhong Y, Kauffmann B, Xu W, Lu ZL, Ferrand Y, Huc I, Zeng XC, Liu R, Gong B. Multiturn Hollow Helices: Synthesis and Folding of Long Aromatic Oligoamides. Org Lett 2020; 22:6938-6942. [PMID: 32794403 DOI: 10.1021/acs.orglett.0c02481] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aromatic oligoamides adopting helical conformations are synthesized by coupling carboxyl-terminated basic units having two, four, and eight residues to amine-terminated oligomer precursors. Coupling yields show no noticeable reduction with the size of the basic units or the final product. One- and two-dimensional NMR spectroscopy and computational studies demonstrate the reliable helical folding of these oligomers. The X-ray structure of 16mer 7 reveals a compact, multiturn helix having a 9 Å inner pore.
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Affiliation(s)
- Yulong Zhong
- Department of Chemistry, University at Buffalo, the State University of New York, Buffalo, New York 14260, United States
| | - Brice Kauffmann
- Institut Européen de Chimie et Biologie, UMS3011/US001 CNRS, Inserm, Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Wenwu Xu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Zhong-Lin Lu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yann Ferrand
- Institut de Chimie et Biologie des Membranes et des Nano-objets, UMR 5248 CNRS, Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Ivan Huc
- Department Pharmazie, Ludwig-Maximilians-Universität München, Butenandtstraße 5-13, D-81377 Munich, Germany
| | - Xiao Cheng Zeng
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Rui Liu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Bing Gong
- Department of Chemistry, University at Buffalo, the State University of New York, Buffalo, New York 14260, United States
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8
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Saha S, Kauffmann B, Ferrand Y, Huc I. Selective Encapsulation of Disaccharide Xylobiose by an Aromatic Foldamer Helical Capsule. Angew Chem Int Ed Engl 2018; 57:13542-13546. [DOI: 10.1002/anie.201808370] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Subrata Saha
- UMR 5248-CBMN, Univ. Bordeaux-CNRS-; Institut Polytechnique de Bordeaux; Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33600 Pessac France
| | - Brice Kauffmann
- Université de Bordeaux; CNRS; INSERM, UMS3033; Institut Européen de Chimie et Biologie (IECB); 2 rue Escarpit 33600 Pessac France
| | - Yann Ferrand
- UMR 5248-CBMN, Univ. Bordeaux-CNRS-; Institut Polytechnique de Bordeaux; Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33600 Pessac France
| | - Ivan Huc
- UMR 5248-CBMN, Univ. Bordeaux-CNRS-; Institut Polytechnique de Bordeaux; Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33600 Pessac France
- Department Pharmazie; Ludwig-Maximilians-Universität; Butenandtstr. 5-13 81377 München Germany
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9
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Saha S, Kauffmann B, Ferrand Y, Huc I. Selective Encapsulation of Disaccharide Xylobiose by an Aromatic Foldamer Helical Capsule. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808370] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Subrata Saha
- UMR 5248-CBMN, Univ. Bordeaux-CNRS-; Institut Polytechnique de Bordeaux; Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33600 Pessac France
| | - Brice Kauffmann
- Université de Bordeaux; CNRS; INSERM, UMS3033; Institut Européen de Chimie et Biologie (IECB); 2 rue Escarpit 33600 Pessac France
| | - Yann Ferrand
- UMR 5248-CBMN, Univ. Bordeaux-CNRS-; Institut Polytechnique de Bordeaux; Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33600 Pessac France
| | - Ivan Huc
- UMR 5248-CBMN, Univ. Bordeaux-CNRS-; Institut Polytechnique de Bordeaux; Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33600 Pessac France
- Department Pharmazie; Ludwig-Maximilians-Universität; Butenandtstr. 5-13 81377 München Germany
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10
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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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11
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Liu CZ, Yan M, Wang H, Zhang DW, Li ZT. Making Molecular and Macromolecular Helical Tubes: Covalent and Noncovalent Approaches. ACS OMEGA 2018; 3:5165-5176. [PMID: 31458731 PMCID: PMC6641876 DOI: 10.1021/acsomega.8b00681] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 04/30/2018] [Indexed: 05/21/2023]
Abstract
Aromatic foldamers possess well-defined cavity that can be stabilized by discrete intramolecular interactions including hydrogen bonding, solvophobicity, electrostatic repulsion, or coordination. Long foldamers can form dynamic deep helical tubular architectures that are not only structurally attractive but also useful hosts for guest encapsulation, chirality induction, delivery, and catalysis. This kind of helical tubular structures can be formed by single molecules or macromolecules or by connecting short-folded or helical segments through noncovalent or covalent forces. This perspective summarizes the recent advances on the construction of helical tubes and their properties and functions.
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Affiliation(s)
- Chuan-Zhi Liu
- Department
of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and
Innovative Materials, andCollaborative Innovation Centre of Chemistry for Energy
Materials (iChEM), Fudan University, 2205 Songhu Road, Shanghai 200438, China
| | - Meng Yan
- Department
of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and
Innovative Materials, andCollaborative Innovation Centre of Chemistry for Energy
Materials (iChEM), Fudan University, 2205 Songhu Road, Shanghai 200438, China
| | - Hui Wang
- Department
of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and
Innovative Materials, andCollaborative Innovation Centre of Chemistry for Energy
Materials (iChEM), Fudan University, 2205 Songhu Road, Shanghai 200438, China
| | - Dan-Wei Zhang
- Department
of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and
Innovative Materials, andCollaborative Innovation Centre of Chemistry for Energy
Materials (iChEM), Fudan University, 2205 Songhu Road, Shanghai 200438, China
- E-mail: (D.-W.Z.)
| | - Zhan-Ting Li
- Department
of Chemistry, Shanghai Key Laboratory of Molecular Catalysis and
Innovative Materials, andCollaborative Innovation Centre of Chemistry for Energy
Materials (iChEM), Fudan University, 2205 Songhu Road, Shanghai 200438, China
- E-mail: (Z.-T.L.)
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12
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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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13
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Zhang DW, Wang H, Li ZT. Polymeric Tubular Aromatic Amide Helices. Macromol Rapid Commun 2017; 38. [DOI: 10.1002/marc.201700179] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Revised: 04/10/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Dan-Wei Zhang
- Department of Chemistry; Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Fudan University; Shanghai 200433 China
| | - Hui Wang
- Department of Chemistry; Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Fudan University; Shanghai 200433 China
| | - Zhan-Ting Li
- Department of Chemistry; Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials; Collaborative Innovation Center of Chemistry for Energy Materials (iChEM); Fudan University; Shanghai 200433 China
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14
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Yang L, Wang Y, Che Y, Jiang H. An aryl-triazole foldamer containing a 1,8-naphthalimide fluorescent motif for monitoring and enhancing the anion-induced folding. Org Biomol Chem 2017; 15:7747-7752. [DOI: 10.1039/c7ob01736g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A 1,8-naphthalimide fluorescent motif was found to facilitate folding and to largely enhance halogen anion binding for an aryl-triazole foldamer.
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Affiliation(s)
- Ling Yang
- CAS Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Ying Wang
- College of Chemistry
- Beijing Normal University
- Beijing 100875
- China
| | - Yanke Che
- CAS Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
| | - Hua Jiang
- CAS Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- China
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15
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Abstract
Nature makes use of tubular structures for the spatial separation of matter on many different length scales, ranging from the nanometer scale (selective channels based on folded proteins) up to the centimeter scale (blood vessels). Today, polymer chemists and engineers can prepare polymeric tubular structures via a variety of different methods also covering many lengthscales, from nanometers to meters. The synthetic approaches described in this chapter vary significantly from the folding of single polymer chains via the self-assembly of DNA fragments to coordinative metal-organic nanotubes to tubes engineerd from bulk polymers using a range of porous or fibrous templates. While all examples reported in this chapter form tubular structures and thereby mimic their naturally occuring counterparts, it is mainly the engineered tubes that are more straightforward to prepare that also show some bio-inspired function.
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Affiliation(s)
- Samantha Doninelli
- Department of Chemistry, University of Fribourg Chemin du Musée 9 CH-1700 Fribourg Switzerland
| | - Michael Badoux
- Department of Chemistry, University of Fribourg Chemin du Musée 9 CH-1700 Fribourg Switzerland
| | - Andreas F. M. Kilbinger
- Department of Chemistry, University of Fribourg Chemin du Musée 9 CH-1700 Fribourg Switzerland
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16
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Zhang P, Zhang L, Wang ZK, Zhang YC, Guo R, Wang H, Zhang DW, Li ZT. Guest-Induced Arylamide Polymer Helicity: Twist-Sense Bias and Solvent-Dependent Helicity Inversion. Chem Asian J 2016; 11:1725-30. [DOI: 10.1002/asia.201600289] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Peng Zhang
- Department of Chemistry, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM); Fudan University; 220 Handan Road Shanghai 200433 China
| | - Liang Zhang
- Department of Chemistry, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM); Fudan University; 220 Handan Road Shanghai 200433 China
| | - Ze-Kun Wang
- Department of Chemistry, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM); Fudan University; 220 Handan Road Shanghai 200433 China
| | - Yun-Chang Zhang
- Department of Chemistry, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM); Fudan University; 220 Handan Road Shanghai 200433 China
| | - Rong Guo
- Department of Chemistry, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM); Fudan University; 220 Handan Road Shanghai 200433 China
| | - Hui Wang
- Department of Chemistry, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM); Fudan University; 220 Handan Road Shanghai 200433 China
| | - Dan-Wei Zhang
- Department of Chemistry, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM); Fudan University; 220 Handan Road Shanghai 200433 China
| | - Zhan-Ting Li
- Department of Chemistry, Collaborative Innovation Centre of Chemistry for Energy Materials (iChEM); Fudan University; 220 Handan Road Shanghai 200433 China
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17
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Li X, Qi T, Srinivas K, Massip S, Maurizot V, Huc I. Synthesis and Multibromination of Nanosized Helical Aromatic Amide Foldamers via Segment-Doubling Condensation. Org Lett 2016; 18:1044-7. [DOI: 10.1021/acs.orglett.6b00165] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xuesong Li
- Department
of Chemistry, University of Liège, B6a Sart-Tilman, 4000 Liège, Belgium
| | - Ting Qi
- CBMN
(UMR 5248), CNRS, 33600 Pessac, France
| | | | - Stéphane Massip
- IECB
(UMS 3033), CNRS, 33600 Pessac, France
- IECB (US001), INSERM, 33600 Pessac, France
| | | | - Ivan Huc
- CBMN
(UMR 5248), CNRS, 33600 Pessac, France
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18
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Liu R, Connor AL, Al-mkhaizim FY, Gong B. Aromatic oligoamides with increased backbone flexibility: improved synthetic efficiencies, solvent-dependent folding and cooperative conformational transitions. NEW J CHEM 2015. [DOI: 10.1039/c4nj01820f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A 15-residue aromatic oligoamide with a backbone of increased flexibility exhibits solvent- and temperature-dependent folding and highly cooperative conformational transition.
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Affiliation(s)
- Rui Liu
- Department of Chemistry
- the State University of New York at Buffalo
- Buffalo
- USA
- College of Chemistry
| | - Alan L. Connor
- Department of Chemistry
- the State University of New York at Buffalo
- Buffalo
- USA
| | | | - Bing Gong
- Department of Chemistry
- the State University of New York at Buffalo
- Buffalo
- USA
- College of Chemistry
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Qi T, Deschrijver T, Huc I. Large-scale and chromatography-free synthesis of an octameric quinoline-based aromatic amide helical foldamer. Nat Protoc 2013; 8:693-708. [DOI: 10.1038/nprot.2013.029] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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20
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Zhang DW, Zhao X, Hou JL, Li ZT. Aromatic Amide Foldamers: Structures, Properties, and Functions. Chem Rev 2012; 112:5271-316. [PMID: 22871167 DOI: 10.1021/cr300116k] [Citation(s) in RCA: 509] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Dan-Wei Zhang
- Department of Chemistry, Fudan
University, 220 Handan Road, Shanghai 200433, China
| | - Xin Zhao
- Shanghai Institute of Organic
Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai
200032, China
| | - Jun-Li Hou
- Department of Chemistry, Fudan
University, 220 Handan Road, Shanghai 200433, China
| | - Zhan-Ting Li
- Department of Chemistry, Fudan
University, 220 Handan Road, Shanghai 200433, China
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21
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Yamato K, Kline M, Gong B. Cavity-containing, backbone-rigidified foldamers and macrocycles. Chem Commun (Camb) 2012; 48:12142-58. [PMID: 23104157 DOI: 10.1039/c2cc36391g] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Kazuhiro Yamato
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY 14260, USA
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22
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Baptiste B, Douat-Casassus C, Laxmi-Reddy K, Godde F, Huc I. Solid Phase Synthesis of Aromatic Oligoamides: Application to Helical Water-Soluble Foldamers. J Org Chem 2010; 75:7175-85. [DOI: 10.1021/jo101360h] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Benoît Baptiste
- Université de Bordeaux, EA 4138-Pharmacochimie, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Céline Douat-Casassus
- Institut Européen de Chimie et Biologie, Université de Bordeaux-CNRS UMR 5248, 2 rue Robert Escarpit, 33607 Pessac Cedex, France
| | - Katta Laxmi-Reddy
- Institut Européen de Chimie et Biologie, Université de Bordeaux-CNRS UMR 5248, 2 rue Robert Escarpit, 33607 Pessac Cedex, France
| | - Frédéric Godde
- Institut Européen de Chimie et Biologie, Université de Bordeaux-CNRS UMR 5248, 2 rue Robert Escarpit, 33607 Pessac Cedex, France
| | - Ivan Huc
- Institut Européen de Chimie et Biologie, Université de Bordeaux-CNRS UMR 5248, 2 rue Robert Escarpit, 33607 Pessac Cedex, France
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23
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Baptiste B, Zhu J, Haldar D, Kauffmann B, Léger JM, Huc I. Hybridization of Long Pyridine-Dicarboxamide Oligomers into Multi-Turn Double Helices: Slow Strand Association and Dissociation, Solvent Dependence, and Solid State Structures. Chem Asian J 2010; 5:1364-75. [DOI: 10.1002/asia.200900713] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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24
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Yan Y, Qin B, Ren C, Chen X, Yip YK, Ye R, Zhang D, Su H, Zeng H. Synthesis, Structural Investigations, Hydrogen−Deuterium Exchange Studies, and Molecular Modeling of Conformationally Stablilized Aromatic Oligoamides. J Am Chem Soc 2010; 132:5869-79. [DOI: 10.1021/ja100579z] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yan Yan
- Department of Chemistry and MedChem Programme, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Department of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, and Department of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371
| | - Bo Qin
- Department of Chemistry and MedChem Programme, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Department of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, and Department of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371
| | - Changliang Ren
- Department of Chemistry and MedChem Programme, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Department of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, and Department of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371
| | - Xiuying Chen
- Department of Chemistry and MedChem Programme, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Department of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, and Department of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371
| | - Yeow Kwan Yip
- Department of Chemistry and MedChem Programme, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Department of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, and Department of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371
| | - Ruijuan Ye
- Department of Chemistry and MedChem Programme, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Department of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, and Department of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371
| | - Dawei Zhang
- Department of Chemistry and MedChem Programme, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Department of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, and Department of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371
| | - Haibin Su
- Department of Chemistry and MedChem Programme, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Department of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, and Department of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371
| | - Huaqiang Zeng
- Department of Chemistry and MedChem Programme, National University of Singapore, 3 Science Drive 3, Singapore, 117543, Department of Materials Science, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, and Department of Chemistry and Biological Chemistry, Nanyang Technological University, 21 Nanyang Link, Singapore, 637371
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25
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Wang W, Joyner S, Khoury KAS, Dömling A. (-)-Bacillamide C: the convergent approach. Org Biomol Chem 2009; 8:529-32. [PMID: 20090966 DOI: 10.1039/b918214d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The newly discovered natural product bacillamide C and several derivatives were convergently synthesized for the first time and in only three steps. The key transformation constitutes a thiazole Ugi multicomponent reaction. These compounds will serve to elucidate chemical biology and SAR of this potent anti-algae natural product and shows the synthetic pathway to related natural products.
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Affiliation(s)
- Wei Wang
- University of Pittsburgh, Drug Discovery Institute, Pittsburgh, PA 15261, USA
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26
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Mousseau J, Xing L, Tang N, Cuccia L. Design and Synthesis of Urea-Linked Aromatic Oligomers-A Route Towards Convoluted Foldamers. Chemistry 2009; 15:10030-8. [DOI: 10.1002/chem.200901094] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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27
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Sánchez-García D, Kauffmann B, Kawanami T, Ihara H, Takafuji M, Delville MH, Huc I. Nanosized hybrid oligoamide foldamers: aromatic templates for the folding of multiple aliphatic units. J Am Chem Soc 2009; 131:8642-8. [PMID: 19530733 DOI: 10.1021/ja9019758] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligoamide sequences comprised of both 8-amino-2-quinolinecarboxylic acid "Q" and 6-aminomethyl-2-pyridinecarboxylic acid "P" have been synthesized. It was found that the aliphatic amine of P greatly facilitates amide couplings, as opposed to the aromatic amine of Q, which enabled us to prepare sequences having up to 40 units. The conformation and conformational stability of these oligomers were characterized in the solid state using X-ray crystallography and in solution using NMR and various chromatographic techniques. Q(n) oligomers adopt very stable helically folded conformations whereas P(n) oligomers do not fold and impart conformational preferences distinct from those of Q units. When a P(n) segments is attached at the end of a Q(4) segment, a couple P units appear to follow the folding pattern imposed by the Q(n) segment, but P units remote from the Q(n) segment do not fold. When a P(n) segment is inserted between two Q(4) segments, the P(n) segment adopts the canonical helical conformation imposed by the Q units at least up to two full helical turns (n = 5). However, the overall stability of the helix tends to decrease as the number of P units increases. When noncontiguous P units separated by Q(4) segments are incorporated in a sequence, they all adopt the helical conformation imposed by Q monomers and the overall helix stability increases when helix length increases. For example, a 40mer with a sequence (PQ(4))(8) folds into a rod-like helix spanning over 16 turns with a length of 5.6 nm. This investigation thus demonstrates that remarkably long (nanometers) yet well-defined foldamers can be efficiently synthesized stepwise and that their helical stability may be continuously tuned upon controlling the ratio and sequence of P and Q monomers.
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Affiliation(s)
- David Sánchez-García
- Institut Européen de Chimie et Biologie, Université de Bordeaux-CNRS UMR5248, 2 rue Robert Escarpit, 33607 Pessac, France
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Yamato K, Gong B. Folding and aggregation of backbone-rigidified oligo(m-phenylene ethynylenes) in polar and nonpolar media. Supramol Chem 2009. [DOI: 10.1080/10610270802527002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Kazuhiro Yamato
- a Department of Chemistry , University at Buffalo, The State University of New York , Buffalo, NY, USA
| | - Bing Gong
- a Department of Chemistry , University at Buffalo, The State University of New York , Buffalo, NY, USA
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29
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Feng W, Yamato K, Yang L, Ferguson JS, Zhong L, Zou S, Yuan L, Zeng XC, Gong B. Efficient Kinetic Macrocyclization. J Am Chem Soc 2009; 131:2629-37. [DOI: 10.1021/ja807935y] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wen Feng
- College of Chemistry, Key Laboratory for Radiation Physics and Technology of Ministry of Education, and Institute of Nuclear Science and Technology, Sichuan University, Chengdu, 610064, Sichuan, China, Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, and Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588
| | - Kazuhiro Yamato
- College of Chemistry, Key Laboratory for Radiation Physics and Technology of Ministry of Education, and Institute of Nuclear Science and Technology, Sichuan University, Chengdu, 610064, Sichuan, China, Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, and Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588
| | - Liuqing Yang
- College of Chemistry, Key Laboratory for Radiation Physics and Technology of Ministry of Education, and Institute of Nuclear Science and Technology, Sichuan University, Chengdu, 610064, Sichuan, China, Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, and Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588
| | - Joseph S. Ferguson
- College of Chemistry, Key Laboratory for Radiation Physics and Technology of Ministry of Education, and Institute of Nuclear Science and Technology, Sichuan University, Chengdu, 610064, Sichuan, China, Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, and Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588
| | - Lijian Zhong
- College of Chemistry, Key Laboratory for Radiation Physics and Technology of Ministry of Education, and Institute of Nuclear Science and Technology, Sichuan University, Chengdu, 610064, Sichuan, China, Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, and Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588
| | - Shuliang Zou
- College of Chemistry, Key Laboratory for Radiation Physics and Technology of Ministry of Education, and Institute of Nuclear Science and Technology, Sichuan University, Chengdu, 610064, Sichuan, China, Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, and Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588
| | - Lihua Yuan
- College of Chemistry, Key Laboratory for Radiation Physics and Technology of Ministry of Education, and Institute of Nuclear Science and Technology, Sichuan University, Chengdu, 610064, Sichuan, China, Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, and Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588
| | - Xiao Cheng Zeng
- College of Chemistry, Key Laboratory for Radiation Physics and Technology of Ministry of Education, and Institute of Nuclear Science and Technology, Sichuan University, Chengdu, 610064, Sichuan, China, Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, and Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588
| | - Bing Gong
- College of Chemistry, Key Laboratory for Radiation Physics and Technology of Ministry of Education, and Institute of Nuclear Science and Technology, Sichuan University, Chengdu, 610064, Sichuan, China, Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, and Department of Chemistry, University of Nebraska−Lincoln, Lincoln, Nebraska 68588
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Saraogi I, Hamilton AD. Recent advances in the development of aryl-based foldamers. Chem Soc Rev 2009; 38:1726-43. [DOI: 10.1039/b819597h] [Citation(s) in RCA: 295] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kim UI, Suk JM, Naidu V, Jeong KS. Folding and Anion-Binding Properties of Fluorescent Oligoindole Foldamers. Chemistry 2008; 14:11406-14. [DOI: 10.1002/chem.200801713] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Delsuc N, Kawanami T, Lefeuvre J, Shundo A, Ihara H, Takafuji M, Huc I. Kinetics of helix-handedness inversion: folding and unfolding in aromatic amide oligomers. Chemphyschem 2008; 9:1882-90. [PMID: 18726966 DOI: 10.1002/cphc.200800310] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A series of helically folded oligoamides of 8-amino-2-quinoline carboxylic acid possessing 6, 7, 8, 9, 10 or 16 units are prepared following convergent synthetic schemes. The right-handed (P) and the left-handed (M) helical conformers of these oligomers undergo an exchange slow enough to allow their chromatographic separation on a chiral stationary phase. Thus, the M conformer is isolated for each of these oligomers and its slow racemization in hexane/CHCl(3) solutions is monitored at various temperatures using chiral HPLC. The kinetics of racemization at different temperatures in hexane/CHCl(3) (75:25 vol/vol) are fitted to a first order kinetic model to yield the kinetic constant and the Gibbs energy of activation for oligomers having 6, 7, 8, 9, 10 or 16 quinoline units. This energy gives the first quantitative measure of the exceptional stability of the helical conformers of an aromatic amide foldamer with respect to its partly unfolded conformations that occur between an M helix and a P helix. The trend of the Gibbs energy as a function of oligomer length suggests that helix-handedness inversion does not require a complete unfolding of a helical strand and may instead occur through the propagation of a local unfolding separating two segments of opposite handedness.
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Affiliation(s)
- Nicolas Delsuc
- Institut Européen de Chimie et Biologie, Université de Bordeaux - CNRS UMR 5248, 2 rue Escarpit, 33607 Pessac, France
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Gong B. Hollow crescents, helices, and macrocycles from enforced folding and folding-assisted macrocyclization. Acc Chem Res 2008; 41:1376-86. [PMID: 18459803 DOI: 10.1021/ar700266f] [Citation(s) in RCA: 237] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This Account reviews the progress made by us on creating porous molecular crescents, helices, and macrocycles based on aromatic oligoamides. Inspired by natural pore- or cavity-containing secondary structures, work described in this Account stemmed from the development of foldamers consisting of benzene rings linked by secondary amide groups. Highly stable, three-center intramolecular hydrogen bonds involving the amide linkages are incorporated into these aromatic oligoamides, which, along with meta-linked benzene units that introduce curvatures into the corresponding backbones, leads to tape-like, curved backbones. Depending on their chain lengths, aromatic oligoamides that fold into crescent and helical conformations have been obtained. Combining results from modeling and experimentally measured data indicates that the folding of these oligomers is readily predictable, determined by the localized intramolecular three-center H-bonds and is independent of side-chain substitution. As a result, a variety of reliably folded, modifiable scaffolds can now be constructed. The well-defined crescent or helical conformations contain noncollapsible internal cavities having multiple introverted amide oxygen atoms. Changing the backbone curvature by tuning the ratio of meta- to para-linked benzene units leads to crescents or helices with cavities of tunable sizes. For example, oligoamides consisting of meta-linked units contain cavities of approximately 9 A across, while those with alternating meta- and para-linked units have cavities of over 30 A across. The generality of such a folding and cavity-creating strategy has also been demonstrated by the enforced folding of other types of aromatic oligomers such as oligo(phenylene ethynylene)s, aromatic oligoureas, and aromatic oligosulfonamides. More recently, the folding of aromatic oligoamides was found to assist efficient macrocyclization reactions, which has provided a convenient method for preparing a new class of large shape-persistent macrocycles in high yields. The folded and cyclic structures were extensively characterized based on multiple techniques such as one- and two-dimensional NMR, mass spectrometry, and X-ray crystallography, as well as theoretical calculations. The enforced folding and folding-assisted cyclization of oligomers have provided a predictable strategy for developing crescent, helical, and cyclic structures containing nanosized voids that are mostly associated with the tertiary and quaternary structures of proteins. The availability of these porous molecules has supplied a new class of nanosized building blocks that provide both opportunities and challenges for creating the next-generation nanostructures capable of presenting multiple introverted functional groups, forming various pores and channels, and finally, developing protein-like pockets.
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Affiliation(s)
- Bing Gong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260
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Velázquez DG, Díaz DD, Ravelo ÁG, Marrero-Tellado JJ. Hunter's Oligoamide: A FunctionalC2-Symmetric Molecule with Unusual Topology for Selective Organic Gel Formation. European J Org Chem 2007. [DOI: 10.1002/ejoc.200700007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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