1
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Piskorz T, Lee B, Zhan S, Duarte F. Metallicious: Automated Force-Field Parameterization of Covalently Bound Metals for Supramolecular Structures. J Chem Theory Comput 2024; 20:9060-9071. [PMID: 39373209 PMCID: PMC11500408 DOI: 10.1021/acs.jctc.4c00850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 09/20/2024] [Accepted: 09/25/2024] [Indexed: 10/08/2024]
Abstract
Metal ions play a central, functional, and structural role in many molecular structures, from small catalysts to metal-organic frameworks (MOFs) and proteins. Computational studies of these systems typically employ classical or quantum mechanical approaches or a combination of both. Among classical models, only the covalent metal model reproduces both geometries and charge transfer effects but requires time-consuming parameterization, especially for supramolecular systems containing repetitive units. To streamline this process, we introduce metallicious, a Python tool designed for efficient force-field parameterization of supramolecular structures. Metallicious has been tested on diverse systems including supramolecular cages, knots, and MOFs. Our benchmarks demonstrate that parameters accurately reproduce the reference properties obtained from quantum calculations and crystal structures. Molecular dynamics simulations of the generated structures consistently yield stable simulations in explicit solvent, in contrast to similar simulations performed with nonbonded and cationic dummy models. Overall, metallicious facilitates the atomistic modeling of supramolecular systems, key for understanding their dynamic properties and host-guest interactions. The tool is freely available on GitHub (https://github.com/duartegroup/metallicious).
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Affiliation(s)
| | - Bernadette Lee
- Department
of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K.
| | - Shaoqi Zhan
- Department
of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K.
- Department
of Chemistry—Ångström, Ångströmlaboratoriet Box
523, Uppsala S-751 20, Sweden
| | - Fernanda Duarte
- Department
of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K.
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2
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Tiemann JKS, Szczuka M, Bouarroudj L, Oussaren M, Garcia S, Howard RJ, Delemotte L, Lindahl E, Baaden M, Lindorff-Larsen K, Chavent M, Poulain P. MDverse, shedding light on the dark matter of molecular dynamics simulations. eLife 2024; 12:RP90061. [PMID: 39212001 PMCID: PMC11364437 DOI: 10.7554/elife.90061] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024] Open
Abstract
The rise of open science and the absence of a global dedicated data repository for molecular dynamics (MD) simulations has led to the accumulation of MD files in generalist data repositories, constituting the dark matter of MD - data that is technically accessible, but neither indexed, curated, or easily searchable. Leveraging an original search strategy, we found and indexed about 250,000 files and 2000 datasets from Zenodo, Figshare and Open Science Framework. With a focus on files produced by the Gromacs MD software, we illustrate the potential offered by the mining of publicly available MD data. We identified systems with specific molecular composition and were able to characterize essential parameters of MD simulation such as temperature and simulation length, and could identify model resolution, such as all-atom and coarse-grain. Based on this analysis, we inferred metadata to propose a search engine prototype to explore the MD data. To continue in this direction, we call on the community to pursue the effort of sharing MD data, and to report and standardize metadata to reuse this valuable matter.
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Affiliation(s)
- Johanna KS Tiemann
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of CopenhagenCopenhagenDenmark
| | - Magdalena Szczuka
- Institut de Pharmacologie et Biologie Structurale, CNRS, Université de ToulouseToulouseFrance
| | - Lisa Bouarroudj
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
| | | | | | - Rebecca J Howard
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm UniversityStockholmSweden
| | - Lucie Delemotte
- Department of applied physics, Science for Life Laboratory, KTH Royal Institute of TechnologyStockholmSweden
| | - Erik Lindahl
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm UniversityStockholmSweden
- Department of applied physics, Science for Life Laboratory, KTH Royal Institute of TechnologyStockholmSweden
| | - Marc Baaden
- Laboratoire de Biochimie Théorique, CNRS, Université Paris CitéParisFrance
| | - Kresten Lindorff-Larsen
- Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of CopenhagenCopenhagenDenmark
| | - Matthieu Chavent
- Institut de Pharmacologie et Biologie Structurale, CNRS, Université de ToulouseToulouseFrance
| | - Pierre Poulain
- Université Paris Cité, CNRS, Institut Jacques MonodParisFrance
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3
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Li MY, Wang S, Li XT, Zhu B, Guan W. Origin of Manipulating Selectivity in Prins Cyclization by [Ga 4L 6] 12- Supramolecular Catalysis through Host-Guest Interactions. Inorg Chem 2024; 63:15906-15914. [PMID: 39119932 DOI: 10.1021/acs.inorgchem.4c02224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
The host effect of the supramolecular [Ga4L6]12- tetrahedral metallocage on Prins cyclization reaction of the substrate by encapsulated citronellal has been investigated by means of molecular dynamics and quantum mechanics. The encapsulation process of the substrate into the [Ga4L6]12- cavity was simulated via attach-pull-release (APR) methods. Thermodynamic calculations and classical molecular dynamics simulations assessed the substrate's microenvironment inside the cavity, guiding DFT-level modeling of the reaction. DFT calculations show diol product predominance in acidic solution but high enol selectivity inside [Ga4L6]12-, consistent with experimental findings. [Ga4L6]12- alters the selectivity of the Prins cyclization reaction by inhibiting diol formation. The activation strain model-based decomposition analysis (ASM-DA) of the barrier difference among distortion and interaction terms indicates that the more positive interaction between a host and guest in the diol transition state than enol determines the product selectivity, particularly the fewer C-H···O and O-H···O hydrogen-bonding interactions. These theoretical insights could contribute to a deeper understanding of the nature of supramolecular catalysis and to further develop new supramolecular catalysts.
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Affiliation(s)
- Mo-Yao Li
- Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Shuang Wang
- Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Xue-Tao Li
- Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Bo Zhu
- Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
| | - Wei Guan
- Key Laboratory of Polyoxometalate and Reticular Material Chemistry of Ministry of Education, Faculty of Chemistry, Northeast Normal University, Changchun 130024, P. R. China
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4
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Reinhardt CR, Manetsch MT, Li WL, Román-Leshkov Y, Head-Gordon T, Kulik HJ. Computational Screening of Putative Catalyst Transition Metal Complexes as Guests in a Ga 4L 612- Nanocage. Inorg Chem 2024; 63:14609-14622. [PMID: 39049593 DOI: 10.1021/acs.inorgchem.4c02113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Metal-organic cages form well-defined microenvironments that can enhance the catalytic proficiency of encapsulated transition metal complexes (TMCs). We introduce a screening protocol to efficiently identify TMCs that are promising candidates for encapsulation in the Ga4L612- nanocage. We obtain TMCs from the Cambridge Structural Database with geometric and electronic characteristics amenable to encapsulation and mine the text of associated manuscripts to curate TMCs with documented catalytic functionality. By docking candidate TMCs inside the nanocage cavity and carrying out electronic structure calculations, we identify a subset of successfully optimized candidates (TMC-34) and observe that encapsulated guests occupy an average of 60% of the cavity volume, in line with previous observations. Notably, some guests occupy as much as 72% of the cavity as a result of linker rotation. Encapsulation has a universal effect on the electrostatic potential (ESP), systematically decreasing the ESP at the metal center of each TMC in the TMC-34 data set, while minimally altering TMC metal partial charges. Collectively these observations support geometry-based screening of potential guests and suggest that encapsulation in Ga4L612- cages could electrostatically stabilize diverse cationic or electropositive intermediates. We highlight candidate guests with associated known reactivity and solubility most amenable for encapsulation in experimental follow-up studies.
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Affiliation(s)
- Clorice R Reinhardt
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Melissa T Manetsch
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Wan-Lu Li
- Kenneth S. Pitzer Center for Theoretical Chemistry, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yuriy Román-Leshkov
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Berkeley, California 94720, United States
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
- Department of Bioengineering, University of California, Berkeley, California 94720, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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5
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Martí-Centelles V, Piskorz TK, Duarte F. CageCavityCalc ( C3): A Computational Tool for Calculating and Visualizing Cavities in Molecular Cages. J Chem Inf Model 2024; 64:5604-5616. [PMID: 38980812 PMCID: PMC11267575 DOI: 10.1021/acs.jcim.4c00355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/05/2024] [Accepted: 06/26/2024] [Indexed: 07/11/2024]
Abstract
Organic(porous) and metal-organic cages are promising biomimetic platforms with diverse applications spanning recognition, sensing, and catalysis. The key to the emergence of these functions is the presence of well-defined inner cavities capable of binding a wide range of guest molecules and modulating their properties. However, despite the myriad cage architectures currently available, the rational design of structurally diverse and functional cages with specific host-guest properties remains challenging. Efficiently predicting such properties is critical for accelerating the discovery of novel functional cages. Herein, we introduce CageCavityCalc (C3), a Python-based tool for calculating the cavity size of molecular cages. The code is available on GitHub at https://github.com/VicenteMartiCentelles/CageCavityCalc. C3 utilizes a novel algorithm that enables the rapid calculation of cavity sizes for a wide range of molecular structures and porous systems. Moreover, C3 facilitates easy visualization of the computed cavity size alongside hydrophobic and electrostatic potentials, providing insights into host-guest interactions within the cage. Furthermore, the calculated cavity can be visualized using widely available visualization software, such as PyMol, VMD, or ChimeraX. To enhance user accessibility, a PyMol plugin has been created, allowing nonspecialists to use this tool without requiring computer programming expertise. We anticipate that the deployment of this computational tool will significantly streamline cage cavity calculations, thereby accelerating the discovery of functional cages.
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Affiliation(s)
- Vicente Martí-Centelles
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Camino de Vera s/n, Valencia 46022, Spain
- CIBER
de Bioingeniería Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid 28029, Spain
- Departamento
de Química, Universitat Politècnica
de València, Camino de Vera
s/n, Valencia 46022, Spain
| | - Tomasz K. Piskorz
- Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Fernanda Duarte
- Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
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6
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Boaler P, Piskorz TK, Bickerton LE, Wang J, Duarte F, Lloyd-Jones GC, Lusby PJ. Origins of High-Activity Cage-Catalyzed Michael Addition. J Am Chem Soc 2024; 146:19317-19326. [PMID: 38976816 PMCID: PMC11258793 DOI: 10.1021/jacs.4c05160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/23/2024] [Accepted: 05/24/2024] [Indexed: 07/10/2024]
Abstract
Cage catalysis continues to create significant interest, yet catalyst function remains poorly understood. Herein, we report mechanistic insights into coordination-cage-catalyzed Michael addition using kinetic and computational methods. The study has been enabled by the detection of identifiable catalyst intermediates, which allow the evolution of different cage species to be monitored and modeled alongside reactants and products. The investigations show that the overall acceleration results from two distinct effects. First, the cage reaction shows a thousand-fold increase in the rate constant for the turnover-limiting C-C bond-forming step compared to a reference state. Computational modeling and experimental analysis of activation parameters indicate that this stems from a significant reduction in entropy, suggesting substrate coencapsulation. Second, the cage markedly acidifies the bound pronucleophile, shifting this equilibrium by up to 6 orders of magnitude. The combination of these two factors results in accelerations up to 109 relative to bulk-phase reference reactions. We also show that the catalyst can fundamentally alter the reaction mechanism, leading to intermediates and products that are not observable outside of the cage. Collectively, the results show that cage catalysis can proceed with very high activity and unique selectivity by harnessing a series of individually weak noncovalent interactions.
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Affiliation(s)
- Patrick
J. Boaler
- EaStCHEM
School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh, Scotland EH9 3FJ, U.K.
| | - Tomasz K. Piskorz
- Chemistry
Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K.
| | - Laura E. Bickerton
- EaStCHEM
School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh, Scotland EH9 3FJ, U.K.
| | - Jianzhu Wang
- EaStCHEM
School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh, Scotland EH9 3FJ, U.K.
| | - Fernanda Duarte
- Chemistry
Research Laboratory, University of Oxford, Oxford OX1 3TA, U.K.
| | - Guy C. Lloyd-Jones
- EaStCHEM
School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh, Scotland EH9 3FJ, U.K.
| | - Paul J. Lusby
- EaStCHEM
School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh, Scotland EH9 3FJ, U.K.
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7
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Tiemann JKS, Szczuka M, Bouarroudj L, Oussaren M, Garcia S, Howard RJ, Delemotte L, Lindahl E, Baaden M, Lindorff-Larsen K, Chavent M, Poulain P. MDverse: Shedding Light on the Dark Matter of Molecular Dynamics Simulations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.02.538537. [PMID: 37205542 PMCID: PMC10187166 DOI: 10.1101/2023.05.02.538537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The rise of open science and the absence of a global dedicated data repository for molecular dynamics (MD) simulations has led to the accumulation of MD files in generalist data repositories, constituting the dark matter of MD - data that is technically accessible, but neither indexed, curated, or easily searchable. Leveraging an original search strategy, we found and indexed about 250,000 files and 2,000 datasets from Zenodo, Figshare and Open Science Framework. With a focus on files produced by the Gromacs MD software, we illustrate the potential offered by the mining of publicly available MD data. We identified systems with specific molecular composition and were able to characterize essential parameters of MD simulation such as temperature and simulation length, and could identify model resolution, such as all-atom and coarse-grain. Based on this analysis, we inferred metadata to propose a search engine prototype to explore the MD data. To continue in this direction, we call on the community to pursue the effort of sharing MD data, and to report and standardize metadata to reuse this valuable matter.
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8
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Stracke K, Evans JD. The use of collective variables and enhanced sampling in the simulations of existing and emerging microporous materials. NANOSCALE 2024. [PMID: 38647659 DOI: 10.1039/d4nr01024h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
Microporous materials, including zeolites, metal-organic frameworks, and cage compounds, offer diverse functionalities due to their unique dynamics and guest confinement properties. These materials play a significant role in separation, catalysis, and sensing, but their complexity hinders exploration using traditional atomistic simulations. This review explores collective variables (CVs) paired with enhanced sampling as a powerful approach to enable efficient investigation of key features in microporous materials. We highlight successful applications of CVs in studying adsorption, diffusion, phase transitions, and mechanical properties, demonstrating their crucial role in guiding material design and optimisation. The future of CVs lies in integration with techniques like machine learning, allowing for enhanced efficiency and accuracy. By tailoring CVs to specific materials and developing multi-scale approaches we can further unlock the intricacies of these fascinating materials. Simulations are a cornerstone in unravelling the complexities of microporous materials and are crucial for our future understanding.
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Affiliation(s)
- Konstantin Stracke
- School of Physics, Chemistry and Earth Science, The University of Adelaide, 5005 Australia.
| | - Jack D Evans
- School of Physics, Chemistry and Earth Science, The University of Adelaide, 5005 Australia.
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9
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Gao K, Cheng Y, Zhang Z, Huo X, Guo C, Fu W, Xu J, Hou GL, Shang X, Zhang M. Guest-Regulated Generation of Reactive Oxygen Species from Porphyrin-Based Multicomponent Metallacages for Selective Photocatalysis. Angew Chem Int Ed Engl 2024; 63:e202319488. [PMID: 38305830 DOI: 10.1002/anie.202319488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/03/2024]
Abstract
The development of novel materials for highly efficient and selective photocatalysis is crucial for their practical applications. Herein, we employ the host-guest chemistry of porphyrin-based metallacages to regulate the generation of reactive oxygen species and further use them for the selective photocatalytic oxidation of benzyl alcohols. Upon irradiation, the sole metallacage (6) can generate singlet oxygen (1O2) effectively via excited energy transfer, while its complex with C70 (6⊃C70) opens a pathway for electron transfer to promote the formation of superoxide anion (O2⋅-), producing both 1O2 and O2⋅-. The addition of 4,4'-bipyridine (BPY) to complex 6⊃C70 forms a more stable complex (6⊃BPY) via the coordination of the Zn-porphyrin faces of 6 and BPY, which drives fullerenes out of the cavities and restores the ability of 1O2 generation. Therefore, benzyl alcohols are oxidized into benzyl aldehydes upon irradiation in the presence of 6 or 6⊃BPY, while they are oxidized into benzoic acids when 6⊃C70 is employed as the photosensitizing agent. This study demonstrates a highly efficient strategy that utilizes the host-guest chemistry of metallacages to regulate the generation of reactive oxygen species for selective photooxidation reactions, which could promote the utilization of metallacages and their related host-guest complexes for photocatalytic applications.
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Affiliation(s)
- Ke Gao
- State Key Laboratory for Mechanical Behavior of Materials, Shaanxi International Research Center for Soft Matter, School of Materials Science and Engineering, Xi'an Jiaotong University, 710049, Xi'an, P. R. China
| | - Ying Cheng
- State Key Laboratory for Mechanical Behavior of Materials, Shaanxi International Research Center for Soft Matter, School of Materials Science and Engineering, Xi'an Jiaotong University, 710049, Xi'an, P. R. China
| | - Zeyuan Zhang
- State Key Laboratory for Mechanical Behavior of Materials, Shaanxi International Research Center for Soft Matter, School of Materials Science and Engineering, Xi'an Jiaotong University, 710049, Xi'an, P. R. China
| | - Xingda Huo
- State Key Laboratory for Mechanical Behavior of Materials, Shaanxi International Research Center for Soft Matter, School of Materials Science and Engineering, Xi'an Jiaotong University, 710049, Xi'an, P. R. China
| | - Chenxing Guo
- College of Chemistry and Environmental Engineering, Shenzhen University, 518055, Shenzhen, P. R. China
| | - Wenlong Fu
- State Key Laboratory for Mechanical Behavior of Materials, Shaanxi International Research Center for Soft Matter, School of Materials Science and Engineering, Xi'an Jiaotong University, 710049, Xi'an, P. R. China
| | - Jianzhi Xu
- MOE Key Laboratory for Non-Equilibrium Synthesis and Modulation of Condensed Matter, School of, Physics, Xi'an Jiaotong University, 710049, Xi'an, P. R. China
| | - Gao-Lei Hou
- MOE Key Laboratory for Non-Equilibrium Synthesis and Modulation of Condensed Matter, School of, Physics, Xi'an Jiaotong University, 710049, Xi'an, P. R. China
| | - Xiaobo Shang
- State Key Laboratory for Mechanical Behavior of Materials, Shaanxi International Research Center for Soft Matter, School of Materials Science and Engineering, Xi'an Jiaotong University, 710049, Xi'an, P. R. China
| | - Mingming Zhang
- State Key Laboratory for Mechanical Behavior of Materials, Shaanxi International Research Center for Soft Matter, School of Materials Science and Engineering, Xi'an Jiaotong University, 710049, Xi'an, P. R. China
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10
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Mishra SS, Krishnaswamy S, Chand DK. Neighboring Cage Participation for Assisted Construction of Self-Assembled Multicavity Conjoined Cages and Augmented Guest Binding. J Am Chem Soc 2024; 146:4473-4488. [PMID: 38334098 DOI: 10.1021/jacs.3c10565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
A set of Pd2L4, Pd3L4, and Pd4L4-type single-, double-, and triple-cavity cages are prepared by complexation of Pd(NO3)2 with designer bis-monodentate (L1), tris-monodentate (L2), and tetrakis-monodentate (L3) ligands. The Pd2L4 cage exists in equilibrium with a Pd3L6 cage; the equilibrium shifted to Pd2L4 at 70 °C or upon addition of pyrazine-N,N'-dioxide (PZDO). The Pd2L4 cage binds a PZDO molecule using electrostatic, bifurcated H-bonding and overcoordinated H-bonding interactions. The discrete Pd3L4 and Pd4L4 compounds are conjoined cages comprising of unequal sized Pd2L4 cages (bigger and smaller). The bigger unit of Pd3L4 cage selectively binds a PZDO, and the smaller one binds a nitrate, fluoride, chloride, or bromide. The Pd4L4 cage, having a central bigger Pd2L4 cavity and two smaller peripheral Pd2L4 cavities, binds one PZDO and two nitrate, fluoride, chloride, or bromide. The smaller cavity can be prepared individually from Pd(II) and bis-monodentate ligand (L4), however, in the presence of template like a nitrate, fluoride, chloride, or bromide; otherwise, it forms an oligomeric mixture. Notably, the conjoined Pd3L4 and Pd4L4 cages could be prepared with (preferably) or without using a template for smaller cavity, and the bigger Pd2L4 is formed by sacrificing the possibility of the Pd3L6 moiety. Thus, the conjoined cages are formed in a symbiotic manner where the neighboring cages participate in the formation of each other. The binding of PZDO shows that the presence of one neighboring cage (as in Pd3L4) augments the binding affinity and that is further augmented in the presence of two neighboring cages (as in Pd4L4).
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Affiliation(s)
- Srabani S Mishra
- IoE Center of Molecular Architecture, Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Shobhana Krishnaswamy
- IoE Center of Molecular Architecture, Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Dillip Kumar Chand
- IoE Center of Molecular Architecture, Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
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11
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Norjmaa G, Rebek J, Himo F. Modeling Amine Methylation in Methyl Ester Cavitand. Chemistry 2024:e202303911. [PMID: 38224206 DOI: 10.1002/chem.202303911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Indexed: 01/16/2024]
Abstract
Methylation of amines inside an introverted resorcinarene-based deep methyl ester cavitand is investigated by means of molecular dynamics simulations and quantum chemical calculations. Experimentally, the cavitand has been shown to bind a number of amines and accelerate the methylation reaction by more than four orders of magnitude for some of them. Eight different amines are considered in the present study, and the geometries and energies of their binding to the cavitand are first characterized and analyzed. Next, the methyl transfer reactions are investigated and the calculated barriers are found to be in generally good agreement with experimental results. In particular, the experimentally-observed rate acceleration in the cavitand as compared to the solution reaction is well reproduced by the calculations. The origins of this rate acceleration are analyzed by computational modifications made to the structure of the cavitand, and the role of the solvent is discussed.
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Affiliation(s)
- Gantulga Norjmaa
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
| | - Julius Rebek
- The Skaggs Institute for Chemical Biology and Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, 92037, La Jolla, California, United States
- Center for Supramolecular Chemistry and Catalysis, Shanghai University, 200444, Shanghai, P. R. China
| | - Fahmi Himo
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden
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12
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Tarzia A, Wolpert EH, Jelfs KE, Pavan GM. Systematic exploration of accessible topologies of cage molecules via minimalistic models. Chem Sci 2023; 14:12506-12517. [PMID: 38020374 PMCID: PMC10646940 DOI: 10.1039/d3sc03991a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023] Open
Abstract
Cages are macrocyclic structures with an intrinsic internal cavity that support applications in separations, sensing and catalysis. These materials can be synthesised via self-assembly of organic or metal-organic building blocks. Their bottom-up synthesis and the diversity in building block chemistry allows for fine-tuning of their shape and properties towards a target property. However, it is not straightforward to predict the outcome of self-assembly, and, thus, the structures that are practically accessible during synthesis. Indeed, such a prediction becomes more difficult as problems related to the flexibility of the building blocks or increased combinatorics lead to a higher level of complexity and increased computational costs. Molecular models, and their coarse-graining into simplified representations, may be very useful to this end. Here, we develop a minimalistic toy model of cage-like molecules to explore the stable space of different cage topologies based on a few fundamental geometric building block parameters. Our results capture, despite the simplifications of the model, known geometrical design rules in synthetic cage molecules and uncover the role of building block coordination number and flexibility on the stability of cage topologies. This leads to a large-scale and systematic exploration of design principles, generating data that we expect could be analysed through expandable approaches towards the rational design of self-assembled porous architectures.
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Affiliation(s)
- Andrew Tarzia
- Department of Applied Science and Technology, Politecnico di Torino Corso Duca degli Abruzzi 24 10129 Torino Italy
| | - Emma H Wolpert
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus Wood Lane London W12 0BZ UK
| | - Kim E Jelfs
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus Wood Lane London W12 0BZ UK
| | - Giovanni M Pavan
- Department of Applied Science and Technology, Politecnico di Torino Corso Duca degli Abruzzi 24 10129 Torino Italy
- Department of Innovative Technologies, University of Applied Sciences and Arts of Southern Switzerland, Polo Universitario Lugano Campus Est, Via la Santa 1 6962 Lugano-Viganello Switzerland
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13
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Piskorz TK, Martí-Centelles V, Spicer RL, Duarte F, Lusby PJ. Picking the lock of coordination cage catalysis. Chem Sci 2023; 14:11300-11331. [PMID: 37886081 PMCID: PMC10599471 DOI: 10.1039/d3sc02586a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/29/2023] [Indexed: 10/28/2023] Open
Abstract
The design principles of metallo-organic assembly reactions have facilitated access to hundreds of coordination cages of varying size and shape. Many of these assemblies possess a well-defined cavity capable of hosting a guest, pictorially mimicking the action of a substrate binding to the active site of an enzyme. While there are now a growing collection of coordination cages that show highly proficient catalysis, exhibiting both excellent activity and efficient turnover, this number is still small compared to the vast library of metal-organic structures that are known. In this review, we will attempt to unpick and discuss the key features that make an effective coordination cage catalyst, linking structure to activity (and selectivity) using lessons learnt from both experimental and computational analysis of the most notable exemplars. We will also provide an outlook for this area, reasoning why coordination cages have the potential to become the gold-standard in (synthetic) non-covalent catalysis.
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Affiliation(s)
- Tomasz K Piskorz
- Chemistry Research Laboratory, University of Oxford Oxford OX1 3TA UK
| | - Vicente Martí-Centelles
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València Camino de Vera, s/n 46022 Valencia Spain
| | - Rebecca L Spicer
- Department of Chemistry, Lancaster University Lancaster LA14YB UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, University of Oxford Oxford OX1 3TA UK
| | - Paul J Lusby
- EaStCHEM School of Chemistry, University of Edinburgh Edinburgh Scotland EH9 3FJ UK
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14
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Jahović I, Yang Y, Ronson TK, Nitschke JR. Capture of Singlet Oxygen Modulates Host-Guest Behavior of Coordination Cages. Angew Chem Int Ed Engl 2023; 62:e202309589. [PMID: 37610599 PMCID: PMC10952966 DOI: 10.1002/anie.202309589] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Indexed: 08/24/2023]
Abstract
The anthracene panels of two tetrahedral MII 4 L6 cages, where MII =CoII or FeII , were found to react with photogenerated singlet oxygen (1 O2 ) in a hetero-Diels-Alder reaction. ESI-MS analysis showed the cobalt(II) cages to undergo complete transformation of all anthracene panels into endoperoxides, whereas the iron(II) congeners underwent incomplete conversion. The reaction was found to be partially reversible in the case of the 1-FeII cage. The dioxygen-cage cycloadducts were found to bind a set of guest molecules more weakly than the parent cages, with affinity dropping by more than two orders of magnitude in some cases. The light-driven cycloaddition reaction between cage and 1 O2 thus served as a stimulus for guest release and reuptake.
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Affiliation(s)
- Ilma Jahović
- Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
| | - Yuchong Yang
- Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
| | - Tanya K. Ronson
- Department of ChemistryUniversity of CambridgeLensfield RoadCB2 1EWCambridgeUK
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15
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Liang R, Zhou Q, Li X, Wong MW, Chung LW. A Computational Study on the Reaction Mechanism of Stereocontrolled Synthesis of β-Lactam within [2]Rotaxane. J Org Chem 2023. [PMID: 37257155 DOI: 10.1021/acs.joc.3c00330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The macrocycle effect of [2]rotaxane on the highly trans-stereoselective cyclization reaction of N-benzylfumaramide was extensively investigated by various computational methods, including DFT and high-level DLPNO-CCSD(T) methods. Our computational results suggest that the most favorable mechanism of the CsOH-promoted cyclization of the fumaramide into trans-β-lactam within [2]rotaxane initiates with deprotonation of a N-benzyl group of the interlocked fumaramide substrate by CsOH, followed by the trans-selective C-C bond formation and protonation by one amide functional group of the macrocycle. Our distortion/interaction analysis further shows that the uncommon trans-stereoselective cyclization forming β-lactam within the rotaxane may be attributed to a higher distortion energy (mainly from the distortion of the twisted cis-fumaramide conformation enforced by the rotaxane). Our systematic study should give deeper mechanistic insight into the reaction mechanism influenced by a supramolecular host.
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Affiliation(s)
- Rong Liang
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
| | - Qinghai Zhou
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
- The Education Ministry Key Lab of Resource Chemistry, Joint International Research Laboratory of Resource Chemistry of Ministry of Education, Shanghai Key Laboratory of Rare Earth Functional Materials, Shanghai Frontiers Science Center of Biomimetic Catalysis, College of Chemistry and Materials Science, Shanghai Normal University, Shanghai 200234, China
| | - Xin Li
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ming Wah Wong
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, 117543, Singapore
| | - Lung Wa Chung
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
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16
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Ghanbari B, Asadi Mofarrah L, Clegg JK. Selective Supramolecular Recognition of Nitroaromatics by a Fluorescent Metal-Organic Cage Based on a Pyridine-Decorated Dibenzodiaza-Crown Macrocyclic Co(II) Complex. Inorg Chem 2023; 62:7434-7445. [PMID: 37134276 DOI: 10.1021/acs.inorgchem.3c00693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Two isomorphous fluorescent (FL) lantern-shaped metal-organic cages 1 and 2 were prepared by coordination-directed self-assembly of Co(II) centers with a new aza-crown macrocyclic ligand bearing pyridine pendant arms (Lpy). The cage structures were determined using single-crystal X-ray diffraction analysis, thermogravimetric, elemental microanalysis, FT-IR spectroscopy, and powder X-ray diffraction. The crystal structures of 1 and 2 show that anions (Cl- in 1 and Br- in 2) are encapsulated within the cage cavity. 1 and 2 bear two coordinated water molecules that are directed inside the cages, surrounded by the eight pyridine rings at the "bottom" and the "roof" of the cage. These hydrogen bond donors, π systems, and the cationic nature of the cages enable 1 and 2 to encapsulate the anions. FL experiments revealed that 1 could detect nitroaromatic compounds by exhibiting selective and sensitive fluorescence quenching toward p-nitroaniline (PNA), recommending a limit of detection of 4.24 ppm. Moreover, the addition of 50 μL of PNA and o-nitrophenol to the ethanolic suspension of 1 led to a significant large FL red shift, namely, 87 and 24 nm, respectively, which were significantly higher than the corresponding values observed in the presence of other nitroaromatic compounds. The titration of the ethanolic suspension of 1, with various concentrations of PNA (>12 μM) demonstrated a concentration-dependent emission red shift. Hence, the efficient FL quenching of 1 was capable of distinguishing the dinitrobenzene isomers. Meanwhile, the observed red shift (10 nm) and quenching of this emission band under the influence of a trace amount of o- and p-nitrophenol isomers also showed that 1 could discriminate between o- and p-nitrophenol. Replacement of the chlorido with a bromido ligand in 1 generated cage 2 which was a more electron-donating cage than 1. The FL experiments showed that 2 was partially more sensitive and less selective toward NACs than 1.
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Affiliation(s)
- Bahram Ghanbari
- Department of Chemistry, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran
| | - Leila Asadi Mofarrah
- Department of Chemistry, Sharif University of Technology, P.O. Box 11155-3516, Tehran, Iran
| | - Jack K Clegg
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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17
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Martí-Rujas J, Elli S, Famulari A. Kinetic trapping of 2,4,6-tris(4-pyridyl)benzene and ZnI 2 into M 12L 8 poly-[n]-catenanes using solution and solid-state processes. Sci Rep 2023; 13:5605. [PMID: 37019947 PMCID: PMC10076325 DOI: 10.1038/s41598-023-32661-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/30/2023] [Indexed: 04/07/2023] Open
Abstract
Here, we show that in a supramolecular system with more than 20 building blocks forming large icosahedral M12L8 metal-organic cages (MOCs), using the instant synthesis method, it is possible to kinetically trap and control the formation of interlocking M12L8 nanocages, giving rare M12L8 TPB-ZnI2 poly-[n]-catenane. The catenanes are obtained in a one-pot reaction, selectively as amorphous (a1) or crystalline states, as demonstrated by powder X-ray diffraction (powder XRD), thermogravimetric (TG) analysis and 1H NMR. The 300 K M12L8 poly-[n]-catenane single crystal X-ray diffraction (SC-XRD) structure including nitrobenzene (1) indicates strong guest binding with the large M12L8 cage (i.e., internal volume ca. 2600 Å3), allowing its structural resolution. Conversely, slow self-assembly (5 days) leads to a mixture of the M12L8 poly-[n]-catenane and a new TPB-ZnI2 (2) coordination polymer (i.e., thermodynamic product), as revealed by SC-XRD. The neat grinding solid-state synthesis also yields amorphous M12L8 poly-[n]-catenane (a1'), but not coordination polymers, selectively in 15 min. The dynamic behavior of the M12L8 poly-[n]-catenanes demonstrated by the amorphous-to-crystalline transformation upon the uptake of ortho-, meta- and para-xylenes shows the potential of M12L8 poly-[n]-catenanes as functional materials in molecular separation. Finally, combining SC-XRD of 1 and DFT calculations specific for the solid-state, the role of the guests in the stability of the 1D chains of M12L8 nanocages is reported. Energy interactions such as interaction energies (E), lattice energies (E*), host-guest energies (Ehost-guest) and guest-guest energies (Eguest-guest) were analysed considering the X-ray structure with and without the nitrobenzene guest. Not only the synthetic control achieved in the synthesis of the M12L8 MOCs but also their dynamic behavior either in the crystalline or amorphous phase are sufficient to raise scientific interest in areas ranging from fundamental to applied sides of chemistry and material sciences.
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Affiliation(s)
- Javier Martí-Rujas
- Dipartimento di Chimica Materiali e Ingegneria Chimica, ''Giulio Natta'', Politecnico di Milano, Via L. Mancinelli 7, 20131, Milan, Italy.
- Center for Nano Science and Technology@Polimi, Istituto Italiano di Tecnologia, Via Pascoli 70/3, 20133, Milan, Italy.
| | - Stefano Elli
- Dipartimento di Chimica Materiali e Ingegneria Chimica, ''Giulio Natta'', Politecnico di Milano, Via L. Mancinelli 7, 20131, Milan, Italy
| | - Antonino Famulari
- Dipartimento di Chimica Materiali e Ingegneria Chimica, ''Giulio Natta'', Politecnico di Milano, Via L. Mancinelli 7, 20131, Milan, Italy
- INSTM, Consorzio Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali, Florence, Italy
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18
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Mao XR, Wang Q, Zhuo SP, Xu LP. Reactivity and Selectivity of the Diels-Alder Reaction of Anthracene in [Pd 6L 4] 12+ Supramolecular Cages: A Computational Study. Inorg Chem 2023; 62:4330-4340. [PMID: 36863004 DOI: 10.1021/acs.inorgchem.3c00005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
The field of supramolecular metal-organic cage catalysis has grown rapidly in recent years. However, theoretical studies regarding the reaction mechanism and reactivity and selectivity controlling factors for supramolecular catalysis are still underdeveloped. Herein, we demonstrate a detailed density functional theory study on the mechanism, catalytic efficiency, and regioselectivity of the Diels-Alder reaction in bulk solution and within two [Pd6L4]12+ supramolecular cages. Our calculations are consistent with experiments. The origins of the catalytic efficiency of the bowl-shaped cage 1 have been elucidated to be the host-guest stabilization of the transition states and the favorable entropy effect. The reasons for the switch of the regioselectivity from 9,10-addition to 1,4-addition within the octahedral cage 2 were attributed to the confinement effect and the noncovalent interactions. This work would shed light on the understanding of [Pd6L4]12+ metallocage-catalyzed reactions and provide a detailed mechanistic profile otherwise difficult to obtain from experiments. The findings of this study could also aid to the improvement and development of more efficient and selective supramolecular catalysis.
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Affiliation(s)
- Xin-Rui Mao
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255049, China
| | - Qian Wang
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255049, China
| | - Shu-Ping Zhuo
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255049, China
| | - Li-Ping Xu
- School of Chemistry and Chemical Engineering, Shandong University of Technology, Zibo 255049, China
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19
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Metallocavitins as Advanced Enzyme Mimics and Promising Chemical Catalysts. Catalysts 2023. [DOI: 10.3390/catal13020415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023] Open
Abstract
The supramolecular approach is becoming increasingly dominant in biomimetics and chemical catalysis due to the expansion of the enzyme active center idea, which now includes binding cavities (hydrophobic pockets), channels and canals for transporting substrates and products. For a long time, the mimetic strategy was mainly focused on the first coordination sphere of the metal ion. Understanding that a highly organized cavity-like enzymatic pocket plays a key role in the sophisticated functionality of enzymes and that the activity and selectivity of natural metalloenzymes are due to the effects of the second coordination sphere, created by the protein framework, opens up new perspectives in biomimetic chemistry and catalysis. There are two main goals of mimicking enzymatic catalysis: (1) scientific curiosity to gain insight into the mysterious nature of enzymes, and (2) practical tasks of mankind: to learn from nature and adopt from its many years of evolutionary experience. Understanding the chemistry within the enzyme nanocavity (confinement effect) requires the use of relatively simple model systems. The performance of the transition metal catalyst increases due to its retention in molecular nanocontainers (cavitins). Given the greater potential of chemical synthesis, it is hoped that these promising bioinspired catalysts will achieve catalytic efficiency and selectivity comparable to and even superior to the creations of nature. Now it is obvious that the cavity structure of molecular nanocontainers and the real possibility of modifying their cavities provide unlimited possibilities for simulating the active centers of metalloenzymes. This review will focus on how chemical reactivity is controlled in a well-defined cavitin nanospace. The author also intends to discuss advanced metal–cavitin catalysts related to the study of the main stages of artificial photosynthesis, including energy transfer and storage, water oxidation and proton reduction, as well as highlight the current challenges of activating small molecules, such as H2O, CO2, N2, O2, H2, and CH4.
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20
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Vasdev RAS, Preston D, Casey-Stevens CA, Martí-Centelles V, Lusby PJ, Garden AL, Crowley JD. Exploiting Supramolecular Interactions to Control Isomer Distributions in Reduced-Symmetry [Pd 2L 4] 4+ Cages. Inorg Chem 2023; 62:1833-1844. [PMID: 35604785 DOI: 10.1021/acs.inorgchem.2c00937] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
High-symmetry metallosupramolecular architectures (MSAs) have been exploited for a range of applications including molecular recognition, catalysis, and drug delivery. Recently, there have been increasing efforts to enhance those applications by generating reduced-symmetry MSAs. Here we report our attempts to use supramolecular (dispersion and hydrogen-bonding) forces and solvophobic effects to generate isomerically pure [Pd2(L)4]4+ cage architectures from a family of new reduced-symmetry ditopic tripyridyl ligands. The reduced-symmetry tripyridyl ligands featured either solvophilic polyether chains, solvophobic alkyl chains, or amino substituents. We show using NMR spectroscopy, high-performance liquid chromatography, X-ray diffraction data, and density functional theory calculations that the combination of dispersion forces and solvophobic effects does not provide any control of the [Pd2(L)4]4+ isomer distribution with mixtures of all four cage isomers (HHHH, HHHT, cis-HHTT, or trans-HTHT, where H = head and T = tail) obtained in each case. More control was obtained by exploiting hydrogen-bonding interactions between amino units. While the cage assembly with a 3-amino-substituted tripyridyl ligand leads to a mixture of all four possible isomers, the related 2-amino-substituted tripyridyl ligand generated a cis-HHTT cage architecture. Formation of the cis-HHTT [Pd2(L)4]4+ cage was confirmed using NMR studies and X-ray crystallography.
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Affiliation(s)
- Roan A S Vasdev
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand.,MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6012, New Zealand
| | - Dan Preston
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand.,MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6012, New Zealand
| | - Caitlin A Casey-Stevens
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand.,MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6012, New Zealand
| | - Vicente Martí-Centelles
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, Scotland
| | - Paul J Lusby
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, Scotland
| | - Anna L Garden
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand.,MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6012, New Zealand
| | - James D Crowley
- Department of Chemistry, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand.,MacDiarmid Institute for Advanced Materials and Nanotechnology, Wellington 6012, New Zealand
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21
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Ghorai S, Natarajan R. Anion-Driven Programmable Chiral Self-Sorting in Metal-Organic Cages and Structural Transformations between Heterochiral and Homochiral Cages. Chemistry 2023; 29:e202203085. [PMID: 36300703 DOI: 10.1002/chem.202203085] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Indexed: 12/12/2022]
Abstract
When a racemic mixture of chiral building blocks self-assembles to form discrete molecular or supramolecular cages, the system can adopt either social or narcissistic chiral self-sorting. However, control over such chiral self-sorting is hard to achieve with a desired choice of outcome. Herein, we report anion templated high-fidelity chiral self-sorting during the coordination-driven self-assembly of [Pd2 L4 ] metal-organic cages, with a racemic mixture of an axially chiral ligand. Upon varying the counter-anions, the outcome of the choice of chiral self-sorting, whether social or narcissistic, leading to kinetically favored heterochiral or thermodynamically favored homochiral cages, can be controlled through specific anion encapsulation. Non-encapsulating anion afforded a mixture of all possible diastereomers. Anion exchange enabled structural transformations between the diastereomers and the conversion of the mixture of diastereomers into homochiral diastereomers.
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Affiliation(s)
- Sandipan Ghorai
- Organic and Medicinal Chemistry Division, CSIR Indian Institute of Chemical Biology, 4 Raja S C Mullick Road, 700031, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Ramalingam Natarajan
- Organic and Medicinal Chemistry Division, CSIR Indian Institute of Chemical Biology, 4 Raja S C Mullick Road, 700031, Kolkata, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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22
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Norjmaa G, Himo F, Maréchal J, Ujaque G. Catalysis by [Ga 4 L 6 ] 12- Metallocage on the Nazarov Cyclization: The Basicity of Complexed Alcohol is Key. Chemistry 2022; 28:e202201792. [PMID: 35859038 PMCID: PMC9804567 DOI: 10.1002/chem.202201792] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Indexed: 01/05/2023]
Abstract
The Nazarov cyclization is investigated in solution and within K12 [Ga4 L6 ] supramolecular organometallic cage by means of computational methods. The reaction needs acidic condition in solution but works at neutral pH in the presence of the metallocage. The reaction steps for the process are analogous in both media: (a) protonation of the alcohol group, (b) water loss and (c) cyclization. The relative Gibbs energies of all the steps are affected by changing the environment from solvent to the metallocage. The first step in the mechanism, the alcohol protonation, turns out to be the most critical one for the acceleration of the reaction inside the metallocage. In order to calculate the relative stability of protonated alcohol inside the cavity, we propose a computational scheme for the calculation of basicity for species inside cavities and can be of general use. These results are in excellent agreement with the experiments, identifying key steps of catalysis and providing an in-depth understanding of the impact of the metallocage on all the reaction steps.
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Affiliation(s)
- Gantulga Norjmaa
- Departament de Química and Centro de Innovación en Química Avanzada (ORFEO-CINQA)Universitat Autònoma de Barcelona08193Cerdanyola del VallesBarcelona, CataloniaSpain
| | - Fahmi Himo
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
| | - Jean‐Didier Maréchal
- Departament de Química and Centro de Innovación en Química Avanzada (ORFEO-CINQA)Universitat Autònoma de Barcelona08193Cerdanyola del VallesBarcelona, CataloniaSpain
| | - Gregori Ujaque
- Departament de Química and Centro de Innovación en Química Avanzada (ORFEO-CINQA)Universitat Autònoma de Barcelona08193Cerdanyola del VallesBarcelona, CataloniaSpain
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23
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Synthesis of cyclodextrin derivatives for enantiodifferentiating photocyclodimerization of 2-anthracenecarboxylate. Nat Protoc 2022; 17:2494-2516. [PMID: 36045225 DOI: 10.1038/s41596-022-00722-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 05/02/2022] [Indexed: 11/08/2022]
Abstract
Photochemical methods are increasingly being used in organic synthesis. They are especially useful for preparing many compounds that are not readily accessible through thermal or enzymatic reactions. The supramolecular strategy has proved highly promising in recent years for manipulating the stereochemical outcome of chiral photoreactions through relatively strong and long-lasting noncovalent interactions in both ground and excited states. Among the numerous chiral photochemical reactions, photocyclodimerization of 2-anthracenecarboxylate (AC) is the most comprehensively studied supramolecular chiral photoreaction and has essentially become a benchmark reaction for evaluating supramolecular photochirogenesis. Cyclodextrin (CD) derivatives were the earliest and are the most widely applied chiral host for mediating photoreactions. Herein, we use CD-mediated photocyclodimerization of AC as an example to introduce the operation process of supramolecular chiral photoreactions. The protocol includes the following contents: (i) the preparation, purification and characterization of β-CD derivatives; (ii) methods for investigating the host-guest inclusion behavior between AC and β-CD derivatives; (iii) the photochemical reaction operation flow under different solvent and temperature conditions; (iv) chiral high-performance liquid chromatography (HPLC) analyses of the product distribution and enantioselectivity. The protocol is introduced by using representative examples of the synthesis of β-CD derivatives and the manipulation of environmental factors that give excellent regio- and enantioselectivities in the photocyclodimerization of AC. The synthesis and purification of β-CD derivatives require 3-5 d of work. The photoirradiation of AC with β-CD derivatives can be done within 1 h. The product analysis requires 5 h.
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24
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McTernan C, Davies JA, Nitschke JR. Beyond Platonic: How to Build Metal-Organic Polyhedra Capable of Binding Low-Symmetry, Information-Rich Molecular Cargoes. Chem Rev 2022; 122:10393-10437. [PMID: 35436092 PMCID: PMC9185692 DOI: 10.1021/acs.chemrev.1c00763] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Indexed: 12/17/2022]
Abstract
The field of metallosupramolecular chemistry has advanced rapidly in recent years. Much work in this area has focused on the formation of hollow self-assembled metal-organic architectures and exploration of the applications of their confined nanospaces. These discrete, soluble structures incorporate metal ions as 'glue' to link organic ligands together into polyhedra.Most of the architectures employed thus far have been highly symmetrical, as these have been the easiest to prepare. Such high-symmetry structures contain pseudospherical cavities, and so typically bind roughly spherical guests. Biomolecules and high-value synthetic compounds are rarely isotropic, highly-symmetrical species. To bind, sense, separate, and transform such substrates, new, lower-symmetry, metal-organic cages are needed. Herein we summarize recent approaches, which taken together form the first draft of a handbook for the design of higher-complexity, lower-symmetry, self-assembled metal-organic architectures.
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Affiliation(s)
| | | | - Jonathan R. Nitschke
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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25
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Piskorz TK, Martí-Centelles V, Young TA, Lusby PJ, Duarte F. Computational Modeling of Supramolecular Metallo-organic Cages-Challenges and Opportunities. ACS Catal 2022; 12:5806-5826. [PMID: 35633896 PMCID: PMC9127791 DOI: 10.1021/acscatal.2c00837] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/09/2022] [Indexed: 01/18/2023]
Abstract
Self-assembled metallo-organic cages have emerged as promising biomimetic platforms that can encapsulate whole substrates akin to an enzyme active site. Extensive experimental work has enabled access to a variety of structures, with a few notable examples showing catalytic behavior. However, computational investigations of metallo-organic cages are scarce, not least due to the challenges associated with their modeling and the lack of accurate and efficient protocols to evaluate these systems. In this review, we discuss key molecular principles governing the design of functional metallo-organic cages, from the assembly of building blocks through binding and catalysis. For each of these processes, computational protocols will be reviewed, considering their inherent strengths and weaknesses. We will demonstrate that while each approach may have its own specific pitfalls, they can be a powerful tool for rationalizing experimental observables and to guide synthetic efforts. To illustrate this point, we present several examples where modeling has helped to elucidate fundamental principles behind molecular recognition and reactivity. We highlight the importance of combining computational and experimental efforts to speed up supramolecular catalyst design while reducing time and resources.
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Affiliation(s)
- Tomasz K. Piskorz
- Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Vicente Martí-Centelles
- Instituto
Interuniversitario de Investigación de Reconocimiento Molecular
y Desarrollo Tecnológico (IDM), Universitat
Politècnica de València, Universitat de València, Valencia 46022, Spain
| | - Tom A. Young
- Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
| | - Paul J. Lusby
- EaStCHEM
School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster
Road, Edinburgh, Scotland EH9 3FJ, United Kingdom
| | - Fernanda Duarte
- Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United
Kingdom
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26
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Lu YL, Song JQ, Qin YH, Guo J, Huang YH, Zhang XD, Pan M, Su CY. A Redox-Active Supramolecular Fe 4L 6 Cage Based on Organic Vertices with Acid-Base-Dependent Charge Tunability for Dehydrogenation Catalysis. J Am Chem Soc 2022; 144:8778-8788. [PMID: 35507479 DOI: 10.1021/jacs.2c02692] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Supramolecular cage chemistry is of lasting interest because, as artificial blueprints of natural enzymes, the self-assembled cage structures not only provide substrate-hosting biomimetic environments but also can integrate active sites in the confined nanospaces for function synergism. Herein, we demonstrate a vertex-directed organic-clip chelation assembly strategy to construct a metal-organic cage Fe4L68+ (MOC-63) incorporating 12 imidazole proton donor-acceptor motifs and four redox-active Fe centers in an octahedral coordination nanospace. Different from regular supramolecular cages assembled with coordination metal vertices, MOC-63 comprises six ditopic organic-clip ligands as vertices and four tris-chelating Fe(N∩N)3 moieties as faces, thus improving its acid, base, and redox robustness by virtue of cage-stabilized dynamics in solution. Improved dehydrogenation catalysis of 1,2,3,4-tetrahydroquinoline derivatives is accomplished by MOC-63 owing to a supramolecular cage effect that synergizes multiple Fe centers and radical species to expedite intermediate conversion of the multistep reactions in a cage-confined nanospace. The acid-base buffering imidazole motifs play a vital role in modulating the total charge state to resist pH variation and tune the solubility among varied solvents, thereby enhancing reaction acceleration in acidic conditions and rendering a facile recycling catalytic process.
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Affiliation(s)
- Yu-Lin Lu
- MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jia-Qi Song
- MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yu-Han Qin
- MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jing Guo
- MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yin-Hui Huang
- MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xiao-Dong Zhang
- MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Mei Pan
- MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China
| | - Cheng-Yong Su
- MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou 510275, China.,State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
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27
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Vatsadze SZ, Maximov AL, Bukhtiyarov VI. Supramolecular Effects and Systems in Catalysis. A Review. DOKLADY CHEMISTRY 2022. [DOI: 10.1134/s0012500822010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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McConnell AJ. Metallosupramolecular cages: from design principles and characterisation techniques to applications. Chem Soc Rev 2022; 51:2957-2971. [PMID: 35356956 DOI: 10.1039/d1cs01143j] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Although metallosupramolecular cages are self-assembled from seemingly simple building blocks, metal ions and organic ligands, architectures of increasingly large size and complexity are accessible and exploited in applications from catalysis to the stabilisation of reactive species. This Tutorial Review gives an introduction to the principles for designing metallosupramolecular cages and highlights advances in the design of large and lower symmetry cages. The characterisation and identification of cages relies on a number of complementary techniques with NMR spectroscopy, mass spectrometry, X-ray crystallography and computational methods being the focus of this review. Finally, examples of cages are discussed where these design principles and characterisation techniques are put into practice for an application or function of the cage.
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Affiliation(s)
- Anna J McConnell
- Otto Diels Institute of Organic Chemistry, Christian-Albrechts-Universität zu Kiel, Kiel 24098, Germany.
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29
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Tarzia A, Jelfs KE. Unlocking the computational design of metal-organic cages. Chem Commun (Camb) 2022; 58:3717-3730. [PMID: 35229861 PMCID: PMC8932387 DOI: 10.1039/d2cc00532h] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/22/2022] [Indexed: 12/11/2022]
Abstract
Metal-organic cages are macrocyclic structures that can possess an intrinsic void that can hold molecules for encapsulation, adsorption, sensing, and catalysis applications. As metal-organic cages may be comprised from nearly any combination of organic and metal-containing components, cages can form with diverse shapes and sizes, allowing for tuning toward targeted properties. Therefore, their near-infinite design space is almost impossible to explore through experimentation alone and computational design can play a crucial role in exploring new systems. Although high-throughput computational design and screening workflows have long been known as powerful tools in drug and materials discovery, their application in exploring metal-organic cages is more recent. We show examples of structure prediction and host-guest/catalytic property evaluation of metal-organic cages. These examples are facilitated by advances in methods that handle metal-containing systems with improved accuracy and are the beginning of the development of automated cage design workflows. We finally outline a scope for how high-throughput computational methods can assist and drive experimental decisions as the field pushes toward functional and complex metal-organic cages. In particular, we highlight the importance of considering realistic, flexible systems.
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Affiliation(s)
- Andrew Tarzia
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, London, W12 0BZ, UK.
| | - Kim E Jelfs
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, London, W12 0BZ, UK.
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30
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Liu C, Chen Z, Teng K, Tong W, Zhang Y, Chee W, An Q. Enzyme‐Mimetic Molecular Selective Catalysis via Single Zr Atom Catalysis in Chelated Cage Embedded in a Flexible Piezoelectrical Matrix. Chemistry 2022; 28:e202104287. [DOI: 10.1002/chem.202104287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Indexed: 11/08/2022]
Affiliation(s)
- Chao Liu
- Beijing Key Laboratory of Materials Utilization of Nonmetallic Minerals and Solid Wastes National Laboratory of Mineral Materials School of Materials Science and Technology China University of Geosciences, Beijing Beijing 100083 P. R. China
| | - Zhensheng Chen
- Beijing Key Laboratory of Materials Utilization of Nonmetallic Minerals and Solid Wastes National Laboratory of Mineral Materials School of Materials Science and Technology China University of Geosciences, Beijing Beijing 100083 P. R. China
| | - Kaixuan Teng
- Beijing Key Laboratory of Materials Utilization of Nonmetallic Minerals and Solid Wastes National Laboratory of Mineral Materials School of Materials Science and Technology China University of Geosciences, Beijing Beijing 100083 P. R. China
| | - Wangshu Tong
- Beijing Key Laboratory of Materials Utilization of Nonmetallic Minerals and Solid Wastes National Laboratory of Mineral Materials School of Materials Science and Technology China University of Geosciences, Beijing Beijing 100083 P. R. China
| | - Yihe Zhang
- Beijing Key Laboratory of Materials Utilization of Nonmetallic Minerals and Solid Wastes National Laboratory of Mineral Materials School of Materials Science and Technology China University of Geosciences, Beijing Beijing 100083 P. R. China
| | - Whowwei Chee
- Micron Semiconductor Asia 75743 Singapore Singapore
| | - Qi An
- Beijing Key Laboratory of Materials Utilization of Nonmetallic Minerals and Solid Wastes National Laboratory of Mineral Materials School of Materials Science and Technology China University of Geosciences, Beijing Beijing 100083 P. R. China
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31
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Tehrani FN, Assaf KI, Hein R, Jensen CME, Nugent TC, Nau WM. Supramolecular Catalysis of a Catalysis-Resistant Diels–Alder Reaction: Almost Theoretical Acceleration of Cyclopentadiene Dimerization inside Cucurbit[7]uril. ACS Catal 2022. [DOI: 10.1021/acscatal.1c05659] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Foad N. Tehrani
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Khaleel I. Assaf
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
- Department of Chemistry, Faculty of Science, Al-Balqa Applied University, 19117 Al-Salt, Jordan
| | - Robert Hein
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Casper M. E. Jensen
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Thomas C. Nugent
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Werner M. Nau
- Department of Life Sciences and Chemistry, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
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32
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Li K, Wu K, Lu Y, Guo J, Hu P, Su C. Creating Dynamic Nanospaces in Solution by Cationic Cages as Multirole Catalytic Platform for Unconventional C(sp)−H Activation Beyond Enzyme Mimics. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202114070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Kang Li
- School of Chemistry South China Normal University Guangzhou 510006 China
- MOE Laboratory of Bioinorganic and Synthetic Chemistry Lehn Institute of Functional Materials School of Chemistry Sun Yat-Sen University Guangzhou 510275 China
| | - Kai Wu
- MOE Laboratory of Bioinorganic and Synthetic Chemistry Lehn Institute of Functional Materials School of Chemistry Sun Yat-Sen University Guangzhou 510275 China
| | - Yu‐Lin Lu
- MOE Laboratory of Bioinorganic and Synthetic Chemistry Lehn Institute of Functional Materials School of Chemistry Sun Yat-Sen University Guangzhou 510275 China
| | - Jing Guo
- MOE Laboratory of Bioinorganic and Synthetic Chemistry Lehn Institute of Functional Materials School of Chemistry Sun Yat-Sen University Guangzhou 510275 China
| | - Peng Hu
- MOE Laboratory of Bioinorganic and Synthetic Chemistry Lehn Institute of Functional Materials School of Chemistry Sun Yat-Sen University Guangzhou 510275 China
| | - Cheng‐Yong Su
- MOE Laboratory of Bioinorganic and Synthetic Chemistry Lehn Institute of Functional Materials School of Chemistry Sun Yat-Sen University Guangzhou 510275 China
- State Key Laboratory of Organometallic Chemistry Shanghai Institute of Organic Chemistry Chinese Academy of Sciences Shanghai 200032 China
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33
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Li D, Han Y, Jiang Y, Jiang G, Sun H, Sun Z, Zhang QW, Tian Y. Achieving Adjustable Multifunction Based on Host-Guest Interaction-Manipulated Reversible Molecular Conformational Switching. ACS APPLIED MATERIALS & INTERFACES 2022; 14:1807-1816. [PMID: 34955010 DOI: 10.1021/acsami.1c22172] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Small molecules that are capable of toggling between multiple and definite conformational states under external stimuli have great potential for use in molecular switches or sensors. However, currently developed regulation approaches for these switchable molecules mostly involve covalent bond-breaking/reforming processes, thereby inevitably producing byproducts or causing fatigue accumulation. Herein, we report a simple but successful model whose molecular conformation can be precisely manipulated between stretched and folded forms by employing host-guest interactions with rigid macrocycles, thus avoiding possible side reactions and fatigue accumulation and possessing excellent reversibility. Moreover, the conformation states of this molecule can be visualized and identified by luminous readout, endowing it with real-time self-reporting features. Furthermore, this controllable and reversible conformational conversion is accompanied by various valuable functions, including controllable multicolor emission; ratiometric fluorescent thermosensing with high temperature resolution, excellent reversibility, lock/unlock switching, and especially linear detection range tunability; and in addition real-time intracellular temperature sensing and imaging, disclosing the intriguing microscopic "conformation-function" relationship based on a single molecule.
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Affiliation(s)
- Dong Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, P. R. China
| | - Yujie Han
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, P. R. China
| | - Yanrong Jiang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, P. R. China
| | - Guanyu Jiang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, P. R. China
| | - Haitao Sun
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, P. R. China
| | - Zhenrong Sun
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, P. R. China
| | - Qi-Wei Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, P. R. China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, Department of Chemistry, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, P. R. China
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34
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Lewis JEM. Molecular engineering of confined space in metal–organic cages. Chem Commun (Camb) 2022; 58:13873-13886. [DOI: 10.1039/d2cc05560k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
The host–guest chemistry of metal–organic cages can be modified through tailoring of structural aspects such as size, shape and functionality. In this review, strategies, opportunities and challenges of such molecular engineering are discussed.
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Affiliation(s)
- James E. M. Lewis
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
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35
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Norjmaa G, Maréchal J, Ujaque G. Origin of the Rate Acceleration in the C-C Reductive Elimination from Pt(IV)-complex in a [Ga 4 L 6 ] 12- Supramolecular Metallocage. Chemistry 2021; 27:15973-15980. [PMID: 34545974 PMCID: PMC9293218 DOI: 10.1002/chem.202102250] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Indexed: 12/29/2022]
Abstract
The reductive elimination on [(Me3 P)2 Pt(MeOH)(CH3 )3 ]+ , 2P, complex performed in MeOH solution and inside a [Ga4 L6 ]12- metallocage are computationally analysed by mean of QM and MD simulations and compared with the mechanism of gold parent systems previously reported [Et3 PAu(MeOH)(CH3 )2 ]+ , 2Au. The comparative analysis between the encapsulated Au(III) and Pt(IV)-counterparts shows that there are no additional solvent MeOH molecules inside the cavity of the metallocage for both systems. The Gibbs energy barriers for the 2P reductive elimination calculated at DFT level are in good agreement with the experimental values for both environments. The effect of microsolvation and encapsulation on the rate acceleration are evaluated and shows that the latter is far more relevant, conversely to 2Au. Energy decomposition analysis indicates that the encapsulation is the main responsible for most of the energy barrier reduction. Microsolvation and encapsulation effects are not equally contributing for both metal systems and consequently, the reasons of the rate acceleration are not the same for both metallic systems despite the similarity between them.
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Affiliation(s)
- Gantulga Norjmaa
- Departament de Química and Centro de Innovación en Química Avanzada (ORFEO-CINQA)Universitat Autònoma de Barcelona08193Cerdanyola del VallesBarcelonaCataloniaSpain
| | - Jean‐Didier Maréchal
- Departament de Química and Centro de Innovación en Química Avanzada (ORFEO-CINQA)Universitat Autònoma de Barcelona08193Cerdanyola del VallesBarcelonaCataloniaSpain
| | - Gregori Ujaque
- Departament de Química and Centro de Innovación en Química Avanzada (ORFEO-CINQA)Universitat Autònoma de Barcelona08193Cerdanyola del VallesBarcelonaCataloniaSpain
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36
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Li K, Wu K, Lu YL, Guo J, Hu P, Su CY. Creating Dynamic Nanospaces in Solution by Cationic Cages as Multirole Catalytic Platform for Unconventional C(sp)-H Activation Beyond Enzyme Mimics. Angew Chem Int Ed Engl 2021; 61:e202114070. [PMID: 34779551 DOI: 10.1002/anie.202114070] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Indexed: 01/10/2023]
Abstract
Herein we demonstrate that, based on the creation of dynamic nanospaces in solution by highly charged positive coordination cage of [Pd6 (RuL3 )8 ]28+ , multirole and multi-way cage-confined catalysis is accomplishable for versatile functions and anomalous reactivities with the aid of the biomimetic cage effect. The high cationic-host charges drive partial deprotonation of 24 imidazole-NHs on cage sphere alike imidazole-residuals in proteins, generating amphoteric heterogeneity in solution to enforce effective cavity-basicity against solution-acidity. Synergistic actions arisen from cage hydrophobicity, host-guest electrostatic interactions and imidazole-N coordination facilitate C(sp)-H activation and carbanionic intermediate stabilization of terminal alkynes to achieve unusual H/D-exchange and Glaser coupling under acidic conditions, and enable phase transfers of water-insoluble substrates/products/co-catalysts to make immiscible-phase and bi-phase catalysis feasible, thus providing a useful catalytic protocol to combine merits from homogeneous, heterogeneous, enzymatic and phase transfer catalysis.
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Affiliation(s)
- Kang Li
- School of Chemistry, South China Normal University, Guangzhou, 510006, China.,MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Kai Wu
- MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Yu-Lin Lu
- MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Jing Guo
- MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Peng Hu
- MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Cheng-Yong Su
- MOE Laboratory of Bioinorganic and Synthetic Chemistry, Lehn Institute of Functional Materials, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China.,State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China
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37
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Balović J, Ćoćić D, Đorđević S, Radenković S, Eldik R, Puchta R. A theoretical mechanistic study of [K ⊂ [2.2.2]]
+
enantiomerization. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Jelena Balović
- Inorganic Chemistry, Department of Chemistry and Pharmacy University of Erlangen‐Nuremberg Erlangen Germany
- Computer Chemistry Center, Department of Chemistry and Pharmacy University of Erlangen‐Nuremberg Erlangen Germany
- Central Institute for Scientific Computing (ZISC) University of Erlangen‐Nuremberg Erlangen Germany
- Department of Chemistry, Faculty of Science University of Kragujevac Kragujevac Serbia
| | - Dušan Ćoćić
- Department of Chemistry, Faculty of Science University of Kragujevac Kragujevac Serbia
| | - Slađana Đorđević
- Department of Chemistry, Faculty of Science University of Kragujevac Kragujevac Serbia
| | - Slavko Radenković
- Department of Chemistry, Faculty of Science University of Kragujevac Kragujevac Serbia
| | - Rudi Eldik
- Inorganic Chemistry, Department of Chemistry and Pharmacy University of Erlangen‐Nuremberg Erlangen Germany
- Faculty of Chemistry Nicolaus Copernicus University Toruń Poland
- Faculty of Chemistry Jagiellonian University Krakow Poland
| | - Ralph Puchta
- Inorganic Chemistry, Department of Chemistry and Pharmacy University of Erlangen‐Nuremberg Erlangen Germany
- Computer Chemistry Center, Department of Chemistry and Pharmacy University of Erlangen‐Nuremberg Erlangen Germany
- Central Institute for Scientific Computing (ZISC) University of Erlangen‐Nuremberg Erlangen Germany
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38
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Tarzia A, Lewis JEM, Jelfs KE. High‐Throughput Computational Evaluation of Low Symmetry Pd
2
L
4
Cages to Aid in System Design**. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106721] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Andrew Tarzia
- Department of Chemistry Molecular Sciences Research Hub Imperial College London White City Campus, Wood Lane London W12 0BZ UK
| | - James E. M. Lewis
- Department of Chemistry Molecular Sciences Research Hub Imperial College London White City Campus, Wood Lane London W12 0BZ UK
| | - Kim E. Jelfs
- Department of Chemistry Molecular Sciences Research Hub Imperial College London White City Campus, Wood Lane London W12 0BZ UK
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39
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Tarzia A, Lewis JEM, Jelfs KE. High-Throughput Computational Evaluation of Low Symmetry Pd 2 L 4 Cages to Aid in System Design*. Angew Chem Int Ed Engl 2021; 60:20879-20887. [PMID: 34254713 PMCID: PMC8518684 DOI: 10.1002/anie.202106721] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/07/2021] [Indexed: 12/12/2022]
Abstract
Unsymmetrical ditopic ligands can self-assemble into reduced-symmetry Pd2 L4 metallo-cages with anisotropic cavities, with implications for high specificity and affinity guest-binding. Mixtures of cage isomers can form, however, resulting in undesirable system heterogeneity. It is paramount to be able to design components that preferentially form a single isomer. Previous data suggested that computational methods could predict with reasonable accuracy whether unsymmetrical ligands would preferentially self-assemble into single cage isomers under constraints of geometrical mismatch. We successfully apply a collaborative computational and experimental workflow to mitigate costly trial-and-error synthetic approaches. Our rapid computational workflow constructs unsymmetrical ligands and their Pd2 L4 cage isomers, ranking the likelihood for exclusively forming cis-Pd2 L4 assemblies. From this narrowed search space, we successfully synthesised four new, low-symmetry, cis-Pd2 L4 cages.
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Affiliation(s)
- Andrew Tarzia
- Department of ChemistryMolecular Sciences Research HubImperial College LondonWhite City Campus, Wood LaneLondonW12 0BZUK
| | - James E. M. Lewis
- Department of ChemistryMolecular Sciences Research HubImperial College LondonWhite City Campus, Wood LaneLondonW12 0BZUK
| | - Kim E. Jelfs
- Department of ChemistryMolecular Sciences Research HubImperial College LondonWhite City Campus, Wood LaneLondonW12 0BZUK
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40
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Mao D, Li W, Zhang F, Yang S, Isak AN, Song Y, Guo Y, Cao S, Zhang R, Feng C, Zhu X, Li G. Nanocomposite of Peroxidase-Like Cucurbit[6]uril with Enzyme-Encapsulated ZIF-8 and Application for Colorimetric Biosensing. ACS APPLIED MATERIALS & INTERFACES 2021; 13:39719-39729. [PMID: 34392680 DOI: 10.1021/acsami.1c09340] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In this work, cucurbiturils (CBs), a class of macrocyclic supramolecules, were observed to have an interesting peroxidase-like activity, which is metal-free, substrate-specific, thermophilic, acidophilic, and insensitive to ionic strength. By coating CBs on enzyme-encapsulated zeolitic imidazolate framework-8 (ZIF-8), a composite nanozyme was constructed, which retains the catalytic ability of CBs and enzymes and makes them cascade. On addition of the substrate, i.e., the detection target, a highly efficient cascade catalysis can be launched in all the spatial directions to generate sensitive and visible signals. Convenient detection of glucose and cholesterol as models is thereby achieved. More importantly, we have also successfully constructed a composite nanozyme-based sensor array (6 × 8 wells) and thereby achieved simultaneous colorimetric analysis of multiple samples. The concept and successful practice of the construction of the unique core-shell supramolecule/biomolecule@nanomaterial architecture provide the possibility to fabricate next-generation multifunctional materials and create new applications by integrating their unique functions.
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Affiliation(s)
- Dongsheng Mao
- School of Environmental and Chemical Engineering, Shanghai University, Shanghai 200444, P.R. China
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Wenxing Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Fan Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Shiqi Yang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Albertina N Isak
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Yuchen Song
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Yi Guo
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Siyu Cao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Runchi Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai 200072, P.R. China
| | - Genxi Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, China
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, P.R. China
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41
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Young TA, Johnston-Wood T, Deringer VL, Duarte F. A transferable active-learning strategy for reactive molecular force fields. Chem Sci 2021; 12:10944-10955. [PMID: 34476072 PMCID: PMC8372546 DOI: 10.1039/d1sc01825f] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/04/2021] [Indexed: 11/25/2022] Open
Abstract
Predictive molecular simulations require fast, accurate and reactive interatomic potentials. Machine learning offers a promising approach to construct such potentials by fitting energies and forces to high-level quantum-mechanical data, but doing so typically requires considerable human intervention and data volume. Here we show that, by leveraging hierarchical and active learning, accurate Gaussian Approximation Potential (GAP) models can be developed for diverse chemical systems in an autonomous manner, requiring only hundreds to a few thousand energy and gradient evaluations on a reference potential-energy surface. The approach uses separate intra- and inter-molecular fits and employs a prospective error metric to assess the accuracy of the potentials. We demonstrate applications to a range of molecular systems with relevance to computational organic chemistry: ranging from bulk solvents, a solvated metal ion and a metallocage onwards to chemical reactivity, including a bifurcating Diels-Alder reaction in the gas phase and non-equilibrium dynamics (a model SN2 reaction) in explicit solvent. The method provides a route to routinely generating machine-learned force fields for reactive molecular systems.
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Affiliation(s)
- Tom A Young
- Chemistry Research Laboratory, University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Tristan Johnston-Wood
- Chemistry Research Laboratory, University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Volker L Deringer
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford Oxford OX1 3QR UK
| | - Fernanda Duarte
- Chemistry Research Laboratory, University of Oxford Mansfield Road Oxford OX1 3TA UK
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42
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Timmer BJJ, Mooibroek TJ. A Simple Strategy to Obtain Synthetic Ca
2+
‐Dependent Lectin Mimics. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Brian J. J. Timmer
- Van ‘t Hoff Institute for Molecular Sciences University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Tiddo J. Mooibroek
- Van ‘t Hoff Institute for Molecular Sciences University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
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43
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Schaapkens X, Bobylev EO, Reek JNH, Mooibroek TJ. A [Pd 2L 4] 4+ cage complex for n-octyl-β-d-glycoside recognition. Org Biomol Chem 2021; 18:4734-4738. [PMID: 32608444 DOI: 10.1039/d0ob01081b] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The cage complex [Pd294]4+ (3') binds n-octyl glycosides in DCM/DMSO (9 : 1) solution with Ka ≈ 51 M-1 for n-Oct-β-d-Glc and Ka ≈ 29 M-1 for n-Oct-β-d-Gal.
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Affiliation(s)
- Xander Schaapkens
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
| | - Eduard O Bobylev
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
| | - Joost N H Reek
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
| | - Tiddo J Mooibroek
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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44
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Turcani L, Tarzia A, Szczypiński FT, Jelfs KE. stk: An extendable Python framework for automated molecular and supramolecular structure assembly and discovery. J Chem Phys 2021; 154:214102. [PMID: 34240979 DOI: 10.1063/5.0049708] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Computational software workflows are emerging as all-in-one solutions to speed up the discovery of new materials. Many computational approaches require the generation of realistic structural models for property prediction and candidate screening. However, molecular and supramolecular materials represent classes of materials with many potential applications for which there is no go-to database of existing structures or general protocol for generating structures. Here, we report a new version of the supramolecular toolkit, stk, an open-source, extendable, and modular Python framework for general structure generation of (supra)molecular structures. Our construction approach works on arbitrary building blocks and topologies and minimizes the input required from the user, making stk user-friendly and applicable to many material classes. This version of stk includes metal-containing structures and rotaxanes as well as general implementation and interface improvements. Additionally, this version includes built-in tools for exploring chemical space with an evolutionary algorithm and tools for database generation and visualization. The latest version of stk is freely available at github.com/lukasturcani/stk.
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Affiliation(s)
- Lukas Turcani
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, London W12 0BZ, United Kingdom
| | - Andrew Tarzia
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, London W12 0BZ, United Kingdom
| | - Filip T Szczypiński
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, London W12 0BZ, United Kingdom
| | - Kim E Jelfs
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, White City Campus, Wood Lane, London W12 0BZ, United Kingdom
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45
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Timmer BJJ, Kooijman A, Schaapkens X, Mooibroek TJ. A Synthetic Galectin Mimic. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202104924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Brian J. J. Timmer
- Van't Hoff Institute for Molecular Sciences University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Arjaan Kooijman
- Van't Hoff Institute for Molecular Sciences University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Xander Schaapkens
- Van't Hoff Institute for Molecular Sciences University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
| | - Tiddo J. Mooibroek
- Van't Hoff Institute for Molecular Sciences University of Amsterdam Science Park 904 1098 XH Amsterdam The Netherlands
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46
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Timmer BJJ, Kooijman A, Schaapkens X, Mooibroek TJ. A Synthetic Galectin Mimic. Angew Chem Int Ed Engl 2021; 60:16178-16183. [PMID: 33964110 PMCID: PMC8361779 DOI: 10.1002/anie.202104924] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 04/30/2021] [Indexed: 12/30/2022]
Abstract
Galectins are a galactoside specific subclass of carbohydrate binding proteins (lectins) involved in various cellular activities, certain cancers, infections, inflammations, and many other biological processes. The molecular basis for the selectivity of galectins is well-documented and revolves around appropriate interaction complementarity: an aromatic residue for C-H⋅⋅⋅π interactions and polar residues for (charge assisted) hydrogen bonds with the axial hydroxyl group of a galactoside. However, no synthetic mimics are currently available. We now report on the design and synthesis of the first galectin mimic (6), and show that it has a higher than 65-fold preference for n-octyl-β-galactoside (8) over n-octyl-β-glucoside (7) in CD2 Cl2 containing 5 % [D6 ]DMSO (with Ka ≥4500 M-1 for 6:8). Molecular modeling informed by nOe studies reveal a high degree of interaction complementarity between 6 and galactoside 8, which is very similar to the interaction complementarity found in natural galectins.
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Affiliation(s)
- Brian J. J. Timmer
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Arjaan Kooijman
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Xander Schaapkens
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
| | - Tiddo J. Mooibroek
- Van't Hoff Institute for Molecular SciencesUniversity of AmsterdamScience Park 9041098 XHAmsterdamThe Netherlands
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47
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Hasegawa S, Meichsner SL, Holstein JJ, Baksi A, Kasanmascheff M, Clever GH. Long-Lived C 60 Radical Anion Stabilized Inside an Electron-Deficient Coordination Cage. J Am Chem Soc 2021; 143:9718-9723. [PMID: 34156243 DOI: 10.1021/jacs.1c02860] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Fullerene C60 and its derivatives are widely used in molecular electronics, photovoltaics, and battery materials, because of their exceptional suitability as electron acceptors. In this context, single-electron transfer on C60 generates the C60• - radical anion. However, the short lifetime of free C60• - hampers its investigation and application. In this work, we dramatically stabilize the usually short-lived C60• - species within a self-assembled M2L4 coordination cage consisting of a triptycene-based ligand and Pd(II) cations. The electron-deficient cage strongly binds C60 by providing a curved inner π-surface complementary to the fullerene's globular shape. Cyclic voltammetry revealed a positive potential shift for the first reduction of encapsulated C60, which is indicative of a strong interaction between confined C60• - and the cationic cage. Photochemical one-electron reduction with 1-benzyl-1,4-dihydronicotinamide allows selective and quantitative conversion of the confined C60 molecule in millimolar acetonitrile solution at room temperature. Radical generation was confirmed by nuclear magnetic resonance, electron paramagnetic resonance, ultraviolet-visible-near-infrared spectroscopy and electrospray ionization mass spectrometry. The lifetime of C60• - within the cage was determined to be so large that it could still be detected after one month under an inert atmosphere.
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Affiliation(s)
- Shota Hasegawa
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Shari L Meichsner
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Julian J Holstein
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Ananya Baksi
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Müge Kasanmascheff
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
| | - Guido H Clever
- Department of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn-Str. 6, 44227 Dortmund, Germany
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48
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Martín Díaz AE, Lewis JEM. Structural Flexibility in Metal-Organic Cages. Front Chem 2021; 9:706462. [PMID: 34336791 PMCID: PMC8317845 DOI: 10.3389/fchem.2021.706462] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 06/02/2021] [Indexed: 01/23/2023] Open
Abstract
Metal-organic cages (MOCs) have emerged as a diverse class of molecular hosts with potential utility across a vast spectrum of applications. With advances in single-crystal X-ray diffraction and economic methods of computational structure optimisation, cavity sizes can be readily determined. In combination with a chemist's intuition, educated guesses about the likelihood of particular guests being bound within these porous structures can be made. Whilst practically very useful, simple rules-of-thumb, such as Rebek's 55% rule, fail to take into account structural flexibility inherent to MOCs that can allow hosts to significantly adapt their internal cavity. An often unappreciated facet of MOC structures is that, even though relatively rigid building blocks may be employed, conformational freedom can enable large structural changes. If it could be exploited, this flexibility might lead to behavior analogous to the induced-fit of substrates within the active sites of enzymes. To this end, in-roads have already been made to prepare MOCs incorporating ligands with large degrees of conformational freedom. Whilst this may make the constitution of MOCs harder to predict, it has the potential to lead to highly sophisticated and functional synthetic hosts.
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Affiliation(s)
| | - James E. M. Lewis
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, United Kingdom
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49
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Sumida R, Tanaka Y, Niki K, Sei Y, Toyota S, Yoshizawa M. Cyclic monoterpenes trapped in a polyaromatic capsule: unusual selectivity, isomerization, and volatility suppression. Chem Sci 2021; 12:9946-9951. [PMID: 34377391 PMCID: PMC8317663 DOI: 10.1039/d1sc01987b] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 05/17/2021] [Indexed: 12/14/2022] Open
Abstract
Cyclic monoterpenes (CMTs) are intractable natural products with high volatility and strong odors so that there has been no molecular receptor capable of selectively and tightly trapping CMTs in both solution and the solid state. We herein report that a polyaromatic capsule acts as a functional nanoflask for CMTs with the following five features: (i) the capsule can selectively bind menthone from mixtures with other saturated CMTs in water. In contrast, (ii) treatment of the capsule with mixtures of menthone and π-conjugated CMTs gives rise to ternary host–guest complexes with high pair-selectivity. Notably, (iii) the encapsulated menthone displays unusual isomerization from a typical chair conformer to otherwise unstable conformers upon heating. (iv) The selective binding of volatilized CMTs is demonstrated by the capsule even in the solid state at atmospheric pressure. Furthermore, (v) the volatilities of CMTs are significantly suppressed at elevated temperatures by the capsule upon encapsulation in solution as well as in the solid state. A polyaromatic capsule demonstrated its unique host functions toward cyclic monoterpenes, i.e., selective binding in water, pair-selective encapsulation, unusual isomerization, selective binding in the solid state, and remarkable volatility suppression.![]()
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Affiliation(s)
- Ryuki Sumida
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
| | - Yuya Tanaka
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
| | - Keita Niki
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
| | - Yoshihisa Sei
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
| | - Shinji Toyota
- Department of Chemistry, School of Science, Tokyo Institute of Technology 2-12-1 Ookayama, Meguro-ku Tokyo 152-8551 Japan
| | - Michito Yoshizawa
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology 4259 Nagatsuta, Midori-ku Yokohama 226-8503 Japan
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50
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