1
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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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2
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Lee J, Ahn Y, Kim M, Seo J. Isomerism of Cyclodextrin Tetramer Induced by Alkali Halide Cluster Ions Observed by Ion Mobility Spectrometry-Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:622-630. [PMID: 38330264 DOI: 10.1021/jasms.3c00441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
Cyclodextrins (CDs) exhibit versatile self-assembly properties due to their hydrophilic and hydrophobic components, with applications such as drug delivery and selective binding. While research on CD self-assembly is extensive, limited studies have explored their aggregation behavior, particularly in interactions with small ionic guests. The present work investigates the structure of β-CD tetramers aggregated with alkali metal chloride clusters using ion mobility spectrometry-mass spectrometry (IMS-MS). The results revealed that diverse structures emerge in the tetramer depending on the alkali metal cluster size. Notably, the doubly charged tetramer exhibits distinct aggregation trends with specific numbers of MCl clusters for Na+ and K+ ions. After initially adopting a bucket-wheel structure with two internal cations, the structure transforms into a new isomer with a tetrahedral configuration upon cluster addition. The formation of the new isomer structure is closely linked to filling the cavity volume with MCl clusters and ionic interactions, which possibly compensate for the weakened hydrogen bonds between CDs. Theoretical calculations further support the structures, showing well-matched collision cross-section (CCS) values compared with the experimental CCS values. This study highlights the role of alkali metal chloride clusters as potential templates, leading to the formation of novel CD assemblies.
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Affiliation(s)
- Jiyeon Lee
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Republic of Korea
| | - Yunyoung Ahn
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Republic of Korea
| | - Minsu Kim
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Republic of Korea
| | - Jongcheol Seo
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongsangbuk-do 37673, Republic of Korea
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3
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Montà-González G, Sancenón F, Martínez-Máñez R, Martí-Centelles V. Purely Covalent Molecular Cages and Containers for Guest Encapsulation. Chem Rev 2022; 122:13636-13708. [PMID: 35867555 PMCID: PMC9413269 DOI: 10.1021/acs.chemrev.2c00198] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Cage compounds offer unique binding pockets similar to enzyme-binding sites, which can be customized in terms of size, shape, and functional groups to point toward the cavity and many other parameters. Different synthetic strategies have been developed to create a toolkit of methods that allow preparing tailor-made organic cages for a number of distinct applications, such as gas separation, molecular recognition, molecular encapsulation, hosts for catalysis, etc. These examples show the versatility and high selectivity that can be achieved using cages, which is impossible by employing other molecular systems. This review explores the progress made in the field of fully organic molecular cages and containers by focusing on the properties of the cavity and their application to encapsulate guests.
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Affiliation(s)
- Giovanni Montà-González
- 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
| | - Félix Sancenón
- 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,CIBER
de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain,Centro
de Investigación Príncipe Felipe, Unidad Mixta UPV-CIPF
de Investigación de Mecanismos de Enfermedades y Nanomedicina,
Valencia, Universitat Politècnica
de València, 46012 Valencia, Spain,Instituto
de Investigación Sanitaria la Fe, Unidad Mixta de Investigación
en Nanomedicina y Sensores, Universitat
Politènica de València, 46026 València, Spain,Departamento
de Química, Universitat Politècnica
de València, 46022 Valencia, Spain
| | - Ramón Martínez-Máñez
- 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,CIBER
de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, 28029 Madrid, Spain,Centro
de Investigación Príncipe Felipe, Unidad Mixta UPV-CIPF
de Investigación de Mecanismos de Enfermedades y Nanomedicina,
Valencia, Universitat Politècnica
de València, 46012 Valencia, Spain,Instituto
de Investigación Sanitaria la Fe, Unidad Mixta de Investigación
en Nanomedicina y Sensores, Universitat
Politènica de València, 46026 València, Spain,Departamento
de Química, Universitat Politècnica
de València, 46022 Valencia, Spain,R.M.-M.: email,
| | - 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,V.M.-C.:
email,
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4
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Kunde T, Pausch T, Schmidt BM. Porous Organic Compounds – Small Pores on the Rise. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100892] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Tom Kunde
- Institut für Organische Chemie und Makromolekulare Chemie Heinrich-Heine-Universität Düsseldorf Universitätsstraße 1 40225 Düsseldorf Germany
| | - Tobias Pausch
- Institut für Organische Chemie und Makromolekulare Chemie Heinrich-Heine-Universität Düsseldorf Universitätsstraße 1 40225 Düsseldorf Germany
| | - Bernd M. Schmidt
- Institut für Organische Chemie und Makromolekulare Chemie Heinrich-Heine-Universität Düsseldorf Universitätsstraße 1 40225 Düsseldorf Germany
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5
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Cohen Y, Slovak S, Avram L. Solution NMR of synthetic cavity containing supramolecular systems: what have we learned on and from? Chem Commun (Camb) 2021; 57:8856-8884. [PMID: 34486595 DOI: 10.1039/d1cc02906a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
NMR has been instrumental in studies of both the structure and dynamics of molecular systems for decades, so it is not surprising that NMR has played a pivotal role in the study of host-guest complexes and supramolecular systems. In this mini-review, selected examples will be used to demonstrate the added value of using (multiparametric) NMR for studying macrocycle-based host-guest and supramolecular systems. We will restrict the discussion to synthetic host systems having a cavity that can engulf their guests thus restricting them into confined spaces. So discussion of selected examples of cavitands, cages, capsules and their complexes, aggregates and polymers as well as organic cages and porous liquids and other porous materials will be used to demonstrate the insights that have been gathered from the extracted NMR parameters when studying such systems emphasizing the information obtained from somewhat less routine NMR methods such as diffusion NMR, diffusion ordered spectroscopy (DOSY) and chemical exchange saturation transfer (CEST) and their variants. These selected examples demonstrate the impact that the results and findings from these NMR studies have had on our understanding of such systems and on the developments in various research fields.
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Affiliation(s)
- Yoram Cohen
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv, 699781, Tel Aviv, Israel.
| | - Sarit Slovak
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv, 699781, Tel Aviv, Israel.
| | - Liat Avram
- Faculty of Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel
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6
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Hähsler M, Mastalerz M. A Giant [8+12] Boronic Ester Cage with 48 Terminal Alkene Units in the Periphery for Postsynthetic Alkene Metathesis. Chemistry 2021; 27:233-237. [PMID: 32840913 PMCID: PMC7839526 DOI: 10.1002/chem.202003675] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/24/2020] [Indexed: 11/21/2022]
Abstract
Dynamic covalent chemistry (DCC) is a powerful synthetic tool to construct large defined molecules in one step from rather simple precursors. The advantage of the intrinsic dynamics of the applied reversible reaction steps is a self‐correction under the chosen conditions, to achieve high yields of the target compound. To date, only a few examples are known, in which DCC was used to build up a molecular defined but larger product that was chemically transferred to a more stable congener in a second (irreversible) step. Here, we present a nanometer‐sized [8+12] boronic ester cage containing 48 peripheral terminal alkene units which allows to put a hydrocarbon exoskeleton around the cage via alkene metathesis.
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Affiliation(s)
- Martin Hähsler
- Institute of Organic Chemistry, Heidelberg University, Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Michael Mastalerz
- Institute of Organic Chemistry, Heidelberg University, Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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7
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Gayen KS, Das T, Chatterjee N. Recent Advances in Tris‐Primary Amine Based Organic Imine Cages and Related Amine Macrocycles. European J Org Chem 2020. [DOI: 10.1002/ejoc.202001194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Titiksha Das
- Kanchrapara College University of Kalyani Kalyani West Bengal India
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8
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Schick THG, Rominger F, Mastalerz M. Examination of the Dynamic Covalent Chemistry of [2 + 3]-Imine Cages. J Org Chem 2020; 85:13757-13771. [PMID: 32933246 PMCID: PMC7659045 DOI: 10.1021/acs.joc.0c01887] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The synthesis of shape-persistent organic cage compounds by the formation of imine bonds opens the possibility to realize cages of different sizes, geometries, topologies, and functions. It is generally assumed that the imine bond is rather chemically labile allowing a self-correction mechanism until thermodynamic equilibrium is reached, which is often the case if a cage is formed. However, there are some contradictory experimental data to this assumption. To get a deeper insight into the imine bond dynamics of covalent organic cages, we studied the formation and exchange of both dialdehydes and triamines of two different [2 + 3] imine cages with the aid of a deuterated dialdehyde molecular building block.
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Affiliation(s)
- Tobias H G Schick
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Frank Rominger
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Michael Mastalerz
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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9
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Abet V, Szczypiński FT, Little MA, Santolini V, Jones CD, Evans R, Wilson C, Wu X, Thorne MF, Bennison MJ, Cui P, Cooper AI, Jelfs KE, Slater AG. Inducing Social Self-Sorting in Organic Cages To Tune The Shape of The Internal Cavity. Angew Chem Int Ed Engl 2020; 59:16755-16763. [PMID: 32542926 PMCID: PMC7540416 DOI: 10.1002/anie.202007571] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Indexed: 12/22/2022]
Abstract
Many interesting target guest molecules have low symmetry, yet most methods for synthesising hosts result in highly symmetrical capsules. Methods of generating lower symmetry pores are thus required to maximise the binding affinity in host-guest complexes. Herein, we use mixtures of tetraaldehyde building blocks with cyclohexanediamine to access low-symmetry imine cages. Whether a low-energy cage is isolated can be correctly predicted from the thermodynamic preference observed in computational models. The stability of the observed structures depends on the geometrical match of the aldehyde building blocks. One bent aldehyde stands out as unable to assemble into high-symmetry cages-and the same aldehyde generates low-symmetry socially self-sorted cages when combined with a linear aldehyde. We exploit this finding to synthesise a family of low-symmetry cages containing heteroatoms, illustrating that pores of varying geometries and surface chemistries may be reliably accessed through computational prediction and self-sorting.
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Affiliation(s)
- Valentina Abet
- Department of Chemistry and Materials Innovation FactoryUniversity of LiverpoolCrown StreetLiverpoolL69 7ZDUK
| | - Filip T. Szczypiński
- Department of ChemistryImperial College LondonMolecular Sciences Research HubWhite City CampusLondonW12 0BZUK
| | - Marc A. Little
- Department of Chemistry and Materials Innovation FactoryUniversity of LiverpoolCrown StreetLiverpoolL69 7ZDUK
| | - Valentina Santolini
- Department of ChemistryImperial College LondonMolecular Sciences Research HubWhite City CampusLondonW12 0BZUK
| | - Christopher D. Jones
- Department of Chemistry and Materials Innovation FactoryUniversity of LiverpoolCrown StreetLiverpoolL69 7ZDUK
| | - Robert Evans
- Aston Institute of Materials Research, School of Engineering and Applied ScienceAston UniversityBirminghamB4 7ETUK
| | - Craig Wilson
- Department of Chemistry and Materials Innovation FactoryUniversity of LiverpoolCrown StreetLiverpoolL69 7ZDUK
| | - Xiaofeng Wu
- Department of Chemistry and Materials Innovation FactoryUniversity of LiverpoolCrown StreetLiverpoolL69 7ZDUK
| | - Michael F. Thorne
- Department of Chemistry and Materials Innovation FactoryUniversity of LiverpoolCrown StreetLiverpoolL69 7ZDUK
| | - Michael J. Bennison
- Department of Chemistry and Materials Innovation FactoryUniversity of LiverpoolCrown StreetLiverpoolL69 7ZDUK
| | - Peng Cui
- Department of Chemistry and Materials Innovation FactoryUniversity of LiverpoolCrown StreetLiverpoolL69 7ZDUK
| | - Andrew I. Cooper
- Department of Chemistry and Materials Innovation FactoryUniversity of LiverpoolCrown StreetLiverpoolL69 7ZDUK
| | - Kim E. Jelfs
- Department of ChemistryImperial College LondonMolecular Sciences Research HubWhite City CampusLondonW12 0BZUK
| | - Anna G. Slater
- Department of Chemistry and Materials Innovation FactoryUniversity of LiverpoolCrown StreetLiverpoolL69 7ZDUK
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10
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Abet V, Szczypiński FT, Little MA, Santolini V, Jones CD, Evans R, Wilson C, Wu X, Thorne MF, Bennison MJ, Cui P, Cooper AI, Jelfs KE, Slater AG. Inducing Social Self‐Sorting in Organic Cages To Tune The Shape of The Internal Cavity. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Valentina Abet
- Department of Chemistry and Materials Innovation FactoryUniversity of Liverpool Crown Street Liverpool L69 7ZD UK
| | - Filip T. Szczypiński
- Department of ChemistryImperial College LondonMolecular Sciences Research Hub White City Campus London W12 0BZ UK
| | - Marc A. Little
- Department of Chemistry and Materials Innovation FactoryUniversity of Liverpool Crown Street Liverpool L69 7ZD UK
| | - Valentina Santolini
- Department of ChemistryImperial College LondonMolecular Sciences Research Hub White City Campus London W12 0BZ UK
| | - Christopher D. Jones
- Department of Chemistry and Materials Innovation FactoryUniversity of Liverpool Crown Street Liverpool L69 7ZD UK
| | - Robert Evans
- Aston Institute of Materials Research, School of Engineering and Applied ScienceAston University Birmingham B4 7ET UK
| | - Craig Wilson
- Department of Chemistry and Materials Innovation FactoryUniversity of Liverpool Crown Street Liverpool L69 7ZD UK
| | - Xiaofeng Wu
- Department of Chemistry and Materials Innovation FactoryUniversity of Liverpool Crown Street Liverpool L69 7ZD UK
| | - Michael F. Thorne
- Department of Chemistry and Materials Innovation FactoryUniversity of Liverpool Crown Street Liverpool L69 7ZD UK
| | - Michael J. Bennison
- Department of Chemistry and Materials Innovation FactoryUniversity of Liverpool Crown Street Liverpool L69 7ZD UK
| | - Peng Cui
- Department of Chemistry and Materials Innovation FactoryUniversity of Liverpool Crown Street Liverpool L69 7ZD UK
| | - Andrew I. Cooper
- Department of Chemistry and Materials Innovation FactoryUniversity of Liverpool Crown Street Liverpool L69 7ZD UK
| | - Kim E. Jelfs
- Department of ChemistryImperial College LondonMolecular Sciences Research Hub White City Campus London W12 0BZ UK
| | - Anna G. Slater
- Department of Chemistry and Materials Innovation FactoryUniversity of Liverpool Crown Street Liverpool L69 7ZD UK
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11
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Kunde T, Nieland E, Schröder HV, Schalley CA, Schmidt BM. A porous fluorinated organic [4+4] imine cage showing CO2 and H2 adsorption. Chem Commun (Camb) 2020; 56:4761-4764. [DOI: 10.1039/d0cc01872d] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We report the first POC, containing perfluorinated aromatic panels forming quickly and in high purity, despite low preorganization encoded in the starting materials.
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Affiliation(s)
- Tom Kunde
- Institut für Organische Chemie und Makromolekulare Chemie
- Heinrich-Heine-Universität Düsseldorf
- Universitätsstraße 1
- D-40225 Düsseldorf
- Germany
| | - Esther Nieland
- Institut für Organische Chemie und Makromolekulare Chemie
- Heinrich-Heine-Universität Düsseldorf
- Universitätsstraße 1
- D-40225 Düsseldorf
- Germany
| | - Hendrik V. Schröder
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- Arnimallee 20
- D-14195 Berlin
- Germany
| | - Christoph A. Schalley
- Institut für Chemie und Biochemie
- Freie Universität Berlin
- Arnimallee 20
- D-14195 Berlin
- Germany
| | - Bernd M. Schmidt
- Institut für Organische Chemie und Makromolekulare Chemie
- Heinrich-Heine-Universität Düsseldorf
- Universitätsstraße 1
- D-40225 Düsseldorf
- Germany
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