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Acosta-Calle S, Huebsch EZ, Kolmar SS, Whited MT, Chen CH, Miller AJM. Regulating Access to Active Sites via Hydrogen Bonding and Cation-Dipole Interactions: A Dual Cofactor Approach to Switchable Catalysis. J Am Chem Soc 2024. [PMID: 38598724 DOI: 10.1021/jacs.3c10877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Hydrogen bonding networks are ubiquitous in biological systems and play a key role in controlling the conformational dynamics and allosteric interactions of enzymes. Yet in small organometallic catalysts, hydrogen bonding rarely controls ligand binding to the metal center. In this work, a hydrogen bonding network within a well-defined organometallic catalyst works in concert with cation-dipole interactions to gate substrate access to the active site. An ammine ligand acts as one cofactor, templating a hydrogen bonding network within a pendent crown ether and preventing the binding of strong donor ligands, such as nitriles, to the nickel center. Sodium ions are the second cofactor, disrupting hydrogen bonding to enable switchable ligand substitution reactions. Thermodynamic analyses provide insight into the energetic requirements of the different supramolecular interactions that enable substrate gating. The dual cofactor approach enables switchable catalytic hydroamination of crotononitrile. Systematic comparisons of catalysts with varying structural features provide support for the critical role of the dual cofactors in achieving on/off catalysis with substrates containing strongly donating functional groups that might otherwise interfere with switchable catalysts.
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Affiliation(s)
- Sebastian Acosta-Calle
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Elsa Z Huebsch
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Scott S Kolmar
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Matthew T Whited
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
- Department of Chemistry, Carleton College, Northfield, Minnesota 55057, United States
| | - Chun-Hsing Chen
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Alexander J M Miller
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
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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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Abstract
We report DNA-scaffolded synergistic catalysis, a concept that combines the diverse reaction scope of synergistic catalysis with the ability of DNA to precisely preorganize abiotic groups and undergo stimuli-triggered conformational changes. As an initial demonstration of this concept, we focus on Cu-TEMPO-catalyzed aerobic alcohol oxidation, using DNA as a scaffold to hold a copper cocatalyst and an organic radical cocatalyst (TEMPO) in proximity. The DNA-scaffolded catalyst maintained a high turnover number upon dilution and exhibited 190-fold improvement in catalyst turnover number relative to the unscaffolded cocatalysts. By incorporating the cocatalysts into a DNA hairpin-containing scaffold, we demonstrate that the rate of the synergistic catalytic reaction can be controlled through a reversible DNA conformational change that alters the distance between the cocatalysts. This work demonstrates the compatibility of synergistic catalytic reactions with DNA scaffolding, opening future avenues in reaction discovery, sensing, responsive materials, and chemical biology.
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Affiliation(s)
- Edward B. Pimentel
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI, 53706, USA
- Morgridge Institute for Research, Madison, WI, 53515, USA
| | - Jeffrey D. Martell
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, WI, 53705, USA
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Guo Y, Lv M, Ren J, Wang E. Regulating Catalytic Activity of DNA-Templated Silver Nanoclusters Based on their Differential Interactions with DNA Structures and Stimuli-Responsive Structural Transition. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2006553. [PMID: 33350148 DOI: 10.1002/smll.202006553] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/05/2020] [Indexed: 05/21/2023]
Abstract
This work reports exquisite engineering of catalytic activity of DNA-templated silver nanoclusters (DNA-AgNCs) based on unique adsorption phenomena of DNAs on DNA-AgNCs and reversible transition between double and triple-stranded DNAs. Four DNA homopolymers exhibit different inhibition effects on the catalytic activity of DNA-AgNCs, poly adenine (polyA) > poly guanine (polyG) > poly cytosine (polyC) > poly thymine (polyT), demonstrating that polyA strands have the strongest adsorption affinity on DNA-AgNCs. Through the formation of T-A•T triplex DNAs, catalytic activity of DNA-AgNCs is restored from the deactivated state by double or single-stranded DNAs, indicating the participation of N7 groups of adenine bases in binding to DNA-AgNCs and blocking active sites. Accordingly, reversibly regulating catalytic activity of DNA-AgNCs can be realized based on DNA input-stimulated transition between duplex and triplex structures. In the end, two low-cost and facile biosensing methods are presented, which are derived from the activity-switchable platform. It is worthy to anticipate that the DNA-AgNCs with controlled catalytic activity will inspire researchers to devise more functionalized nanocatalysts and contribute to the exploration of intelligent biomedicine in the future.
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Affiliation(s)
- Yuchun Guo
- College of Chemistry, Jilin University, Changchun, Jilin, 130012, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Mengmeng Lv
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Jiangtao Ren
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Erkang Wang
- College of Chemistry, Jilin University, Changchun, Jilin, 130012, China
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
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Mukherjee P, Maiti D. Evolution of strept(avidin)-based artificial metalloenzymes in organometallic catalysis. Chem Commun (Camb) 2020; 56:14519-14540. [PMID: 33150893 DOI: 10.1039/d0cc05450j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Artificial metalloenzymes have been recently established as efficient alternatives to traditional transition metal catalysts. The presence of a secondary coordination sphere in artificial metalloenzymes makes them advantageous over transition metal catalysts, which rely essentially on their first coordination sphere to exhibit their catalytic activity. Recent developments on streptavidin- and avidin-based artificial metalloenzymes have made them highly chemically and genetically evolved for selective organometallic transformations. In this review, we discuss the chemo-genetic optimization of streptavidin- and avidin-based artificial metalloenzymes for the enhancement of their catalytic activities towards a wide range of synthetic transformations. Considering the high impact in vivo applications of artificial metalloenzymes, their catalytic efficacies to promote abiological reactions in intracellular as well as periplasmic environment are also discussed. Overall, this review can provide an insight to readers regarding the design and systematic optimization of strept(avidin)-based artificial metalloenzymes for specific reactions.
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Affiliation(s)
- Prasun Mukherjee
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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