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Grafskaia K, Qin Q, Li J, Magnin D, Dellemme D, Surin M, Glinel K, Jonas AM. Chain stretching in brushes favors sequence recognition for nucleobase-functionalized flexible precise oligomers. SOFT MATTER 2024. [PMID: 39387435 DOI: 10.1039/d4sm00866a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2024]
Abstract
Six different flexible stereocontrolled oligo(triazole-urethane)s substituted by precise sequences of nucleobases or analogs are synthesized. Molecular dynamics simulations indicate that the flexibility of the backbone leads to unspecific complexation of pairs of oligomers, irrespective of the complementarity of their sequences. This is ascribed to the existence of other interactions between pairs of oligomers, as well as to the spatial blurring of the sequence order encoded in the chemical structure of the chain due to its flexibility. The same conclusions are drawn when investigating the irreversible adsorption of different probe oligomers onto a layer of target oligomers grafted by click chemistry in a mushroom configuration on a silicon substrate. In contrast, when the target oligomers are grafted in denser brush configurations, irreversible adsorption becomes more specific, with it being twice as probable that probe chains of complementary sequence would be irreversibly-bound to the layer of target chains than those of non-complementary sequence. This is ascribed to lateral excluded volume interactions between chains in the brush, leading to partial chain stretching and increased spatial preservation of the information contained in the monomer sequence of the chains. At even higher grafting densities, however, the penetration of the probe chains in the brush becomes increasingly difficult, resulting in a loss of binding efficiency. Our work thus demonstrates the adverse role of chain flexibility in the specificity of complexation between nucleobase-functionalized oligomers and provides directions for an improvement of specificity by tuning the grafting density of target chains on a substrate.
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Affiliation(s)
- Kseniia Grafskaia
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, Croix du Sud 1 L7.04.02, Louvain-la-Neuve, Belgium.
| | - Qian Qin
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, Croix du Sud 1 L7.04.02, Louvain-la-Neuve, Belgium.
| | - Jie Li
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, Croix du Sud 1 L7.04.02, Louvain-la-Neuve, Belgium.
| | - Delphine Magnin
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, Croix du Sud 1 L7.04.02, Louvain-la-Neuve, Belgium.
| | - David Dellemme
- Laboratory for Chemistry of Novel Materials, Université de Mons - UMONS, Avenue Maistriau, 17, B-7000 Mons, Belgium
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials, Université de Mons - UMONS, Avenue Maistriau, 17, B-7000 Mons, Belgium
| | - Karine Glinel
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, Croix du Sud 1 L7.04.02, Louvain-la-Neuve, Belgium.
| | - Alain M Jonas
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain, Croix du Sud 1 L7.04.02, Louvain-la-Neuve, Belgium.
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2
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Qin Q, Li J, Dellemme D, Fossépré M, Barozzino-Consiglio G, Nekkaa I, Boborodea A, Fernandes AE, Glinel K, Surin M, Jonas AM. Dynamic self-assembly of supramolecular catalysts from precision macromolecules. Chem Sci 2023; 14:9283-9292. [PMID: 37712032 PMCID: PMC10498719 DOI: 10.1039/d3sc03133k] [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: 06/20/2023] [Accepted: 08/15/2023] [Indexed: 09/16/2023] Open
Abstract
We show the emergence of strong catalytic activity at low concentrations in dynamic libraries of complementary sequence-defined oligomeric chains comprising pendant functional catalytic groups and terminal recognition units. In solution, the dynamic constitutional library created from pairs of such complementary oligomers comprises free oligomers, self-assembled di(oligomeric) macrocycles, and a virtually infinite collection of linear poly(oligomeric) chains. We demonstrate, on an exemplary catalytic system requiring the cooperation of no less than five chemical groups, that supramolecular di(oligomeric) macrocycles exhibit a catalytic turnover frequency ca. 20 times larger than the whole collection of linear poly(oligomers) and free chains. Molecular dynamics simulations and network analysis indicate that self-assembled supramolecular di(oligomeric) macrocycles are stabilized by different interactions, among which chain end pairing. We mathematically model the catalytic properties of such complex dynamic libraries with a small set of physically relevant parameters, which provides guidelines for the synthesis of oligomers capable to self-assemble into functionally-active supramolecular macrocycles over a larger range of concentrations.
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Affiliation(s)
- Qian Qin
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain Croix du Sud 1 L7.04.02, Louvain-la-Neuve Belgium
| | - Jie Li
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain Croix du Sud 1 L7.04.02, Louvain-la-Neuve Belgium
| | - David Dellemme
- Laboratory for Chemistry of Novel Materials, Université de Mons - UMONS Avenue Maistriau, 17 B-7000 Mons Belgium
| | - Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials, Université de Mons - UMONS Avenue Maistriau, 17 B-7000 Mons Belgium
| | - Gabriella Barozzino-Consiglio
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain Croix du Sud 1 L7.04.02, Louvain-la-Neuve Belgium
| | - Imane Nekkaa
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain Croix du Sud 1 L7.04.02, Louvain-la-Neuve Belgium
| | | | - Antony E Fernandes
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain Croix du Sud 1 L7.04.02, Louvain-la-Neuve Belgium
- Certech rue Jules Bordet 45 7180 Seneffe Belgium
| | - Karine Glinel
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain Croix du Sud 1 L7.04.02, Louvain-la-Neuve Belgium
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials, Université de Mons - UMONS Avenue Maistriau, 17 B-7000 Mons Belgium
| | - Alain M Jonas
- Institute of Condensed Matter and Nanosciences, Université catholique de Louvain Croix du Sud 1 L7.04.02, Louvain-la-Neuve Belgium
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3
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Ren X, Guo C, Li X, Wu Y, Zhang Y, Li S, Zhang K. Protecting-Group-Free Iterative Divergent/Convergent Method for Preparing Sequence-Defined Polymers. Macromolecules 2023. [DOI: 10.1021/acs.macromol.2c02090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Xiangzhu Ren
- State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changjuan Guo
- State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xijuan Li
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ying Wu
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Yu Zhang
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Shumu Li
- State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Ke Zhang
- State Key Laboratory of Polymer Physics and Chemistry, Institute of Chemistry, The Chinese Academy of Sciences, Beijing 100190, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Engineering synergistic effects of immobilized cooperative catalysts. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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5
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Chandra P. A Review on the Consequence of 3D-Orienation of Cu/TEMPO/Imidazole Sequence on Selective Alcohol Oxidation. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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6
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Kardas S, Fossépré M, Lemaur V, Fernandes AE, Glinel K, Jonas AM, Surin M. Revealing the Organization of Catalytic Sequence-Defined Oligomers via Combined Molecular Dynamics Simulations and Network Analysis. J Chem Inf Model 2022; 62:2761-2770. [PMID: 35608867 DOI: 10.1021/acs.jcim.2c00101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Similar to biological macromolecules such as DNA and proteins, the precise control over the monomer position in sequence-defined polymers is of paramount importance for tuning their structures and properties toward achieving specific functions. Here, we apply molecular network analysis on three-dimensional structures issued from molecular dynamics simulations to decipher how the chain organization of trifunctional catalytic oligomers is influenced by the oligomer sequence and the length of oligo(ethylene oxide) spacers. Our findings demonstrate that the tuning of their primary structures is crucial for favoring cooperative interactions between the catalytic units and thus higher catalytic activities. This combined approach can assist in establishing structure-property relationships, leading to a more rational design of sequence-defined catalytic oligomers via computational chemistry.
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Affiliation(s)
- Sinan Kardas
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, University of Mons-UMONS, Place du Parc 20, Mons B-7000, Belgium.,Institute for Complex Molecular Systems, Eindhoven University of Technology-TU/e, P.O. Box 513, Eindhoven 5600 MB, The Netherlands
| | - Mathieu Fossépré
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, University of Mons-UMONS, Place du Parc 20, Mons B-7000, Belgium
| | - Vincent Lemaur
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, University of Mons-UMONS, Place du Parc 20, Mons B-7000, Belgium
| | - Antony E Fernandes
- Institute of Condensed Matter and Nanosciences, Bio- and Soft Matter, Université catholique de Louvain-UCLouvain, Louvain-la-Neuve B-1348, Belgium.,Certech, Rue Jules Bordet 45, Zone Industrielle C, Seneffe B-7180, Belgium
| | - Karine Glinel
- Institute of Condensed Matter and Nanosciences, Bio- and Soft Matter, Université catholique de Louvain-UCLouvain, Louvain-la-Neuve B-1348, Belgium
| | - Alain M Jonas
- Institute of Condensed Matter and Nanosciences, Bio- and Soft Matter, Université catholique de Louvain-UCLouvain, Louvain-la-Neuve B-1348, Belgium
| | - Mathieu Surin
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, University of Mons-UMONS, Place du Parc 20, Mons B-7000, Belgium
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7
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De Franceschi I, Mertens C, Badi N, Du Prez F. Uniform soluble support for the large-scale synthesis of sequence-defined macromolecules. Polym Chem 2022. [DOI: 10.1039/d2py00883a] [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
A monodisperse soluble support is used as an effective tool for the large-scale, liquid-phase synthesis of sequence-defined macromolecules. This uniform support allows for direct characterisation and leads to a single peak in mass spectrometry.
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Affiliation(s)
- Irene De Franceschi
- Polymer Chemistry Research group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium
| | - Chiel Mertens
- Polymer Chemistry Research group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium
| | - Nezha Badi
- Polymer Chemistry Research group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium
| | - Filip Du Prez
- Polymer Chemistry Research group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium
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