1
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Liu Y, Liu FZ, Li S, Liu H, Yan K. Biasing the Formation of Solution-Unstable Intermediates in Coordination Self-Assembly by Mechanochemistry. Chemistry 2023; 29:e202302563. [PMID: 37670119 DOI: 10.1002/chem.202302563] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/07/2023]
Abstract
Due to the reversible nature of coordination bonds and solvation effect, coordination self-assembly pathways are often difficult to elucidate experimentally in solution, as intermediates and products are in constant equilibration. The present study shows that some of these transient and high-energy self-assembly intermediates can be accessed by means of ball-milling approaches. Among them, highly aqueous-unstable Pd3 L11 and Pd6 L14 open-cage intermediates of the framed Fujita Pd6 L14 cage and Pd2 L22 , Pd3 L21 and Pd4 L22 intermediates of Mukherjee Pd6 L24 capsule are successfully trapped in solid-state, where Pd=tmedaPd2+ , L1=2,4,6-tris(4-pyridyl)-1,3,5-triazine and L2=1,3,5-tris(1-imidazolyl)benzene). Their structures are assigned by a combination of solution-based characterization tools such as standard NMR spectroscopy, DOSY NMR, ESI-MS and X-ray diffraction. Collectively, these results highlight the opportunity of using mechanochemistry to access unique chemical space with vastly different reactivity compared to conventional solution-based supramolecular self-assembly reactions.
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Affiliation(s)
- Yan Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Fang-Zi Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Shi Li
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Hua Liu
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - KaKing Yan
- School of Physical Science and Technology, ShanghaiTech University, Shanghai, 201210, China
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2
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Okazawa A, Sanada N, Takahashi S, Sato H, Hiraoka S. Pathway selection in the self-assembly of Rh 4L 4 coordination squares under kinetic control. Commun Chem 2023; 6:248. [PMID: 37968322 PMCID: PMC10651846 DOI: 10.1038/s42004-023-01053-7] [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: 06/07/2023] [Accepted: 11/06/2023] [Indexed: 11/17/2023] Open
Abstract
Pathway selection principles in reversible reaction networks such as molecular self-assembly have not been established yet, because achieving kinetic control in reversible reaction networks is more complicated than in irreversible ones. In this study, we discovered that coordination squares consisting of cis-protected dinuclear rhodium(II) corner complexes and linear ditopic ligands are assembled under kinetic control, perfectly preventing the corresponding triangles, by modulating their energy landscapes with a weak monotopic carboxylate ligand (2,6-dichlorobenzoate: dcb-) as the leaving ligand. Experimental and numerical approaches revealed the self-assembly pathway where the cyclization step to form the triangular complex is blocked by dcb-. It was also found that one of the molecular squares assembled into a dimeric structure owing to the solvophobic effect, which was characterized by nuclear magnetic resonance spectroscopy and single-crystal X-ray analysis.
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Affiliation(s)
- Atsushi Okazawa
- Department of Electrical Engineering and Bioscience, Waseda University, Tokyo, 169-8555, Japan
| | - Naoki Sanada
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| | - Satoshi Takahashi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Kyoto, 615-8510, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, 606-8103, Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan.
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3
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Takahashi S, Iuchi S, Hiraoka S, Sato H. Theoretical and computational methodologies for understanding coordination self-assembly complexes. Phys Chem Chem Phys 2023; 25:14659-14671. [PMID: 37051715 DOI: 10.1039/d3cp00082f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
This perspective highlights three theoretical and computational methods to capture the coordination self-assembly processes at the molecular level: quantum chemical modeling, molecular dynamics, and reaction network analysis. These methods cover the different scales from the metal-ligand bond to a more global aspect, and approaches that are best suited to understand the coordination self-assembly from different perspectives are introduced. Theoretical and numerical researches based on these methods are not merely ways of interpreting the experimental studies but complementary to them.
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Affiliation(s)
- Satoshi Takahashi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
| | - Satoru Iuchi
- Graduate School of Informatics, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Nishikyo-ku, Kyoto 615-8510, Japan.
- Fukui Institute for Fundamental Chemistry, Kyoto University, Sakyo-ku, Kyoto 606-8103, Japan
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4
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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: 68] [Impact Index Per Article: 34.0] [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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5
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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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6
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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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7
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Zhang X, Takahashi S, Aratsu K, Kikuchi I, Sato H, Hiraoka S. Cyclization or bridging: which occurs faster is the key to the self-assembly mechanism of Pd 6L 3 coordination prisms. Phys Chem Chem Phys 2022; 24:2997-3006. [PMID: 35037923 DOI: 10.1039/d1cp04448f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The self-assembly processes of Pd6L3 coordination prisms consisting of cis-protected Pd(II) complexes and porphyrin-based tetratopic ligands with four 3-pyridyl or 4-pyridyl groups (L) were investigated by experimental and numerical methods, QASAP (quantitative analysis of self-assembly process) and NASAP (numerical analysis of self-assembly process), respectively. It was found that contrary to common intuition macrocyclization takes place faster than the bridging reaction in the prism assembly and that the bridging reaction occurring before the macrocyclization tends to produce kinetically trapped species. A numerical simulation demonstrates that the relative magnitude of the rate constants between the macrocyclization and the bridging reaction is the key factor that determines whether the self-assembly leads to the thermodynamically most stable prism or to kinetically trapped species. Finding the key elementary reactions that largely affect the selection of the major assembly pathway is helpful to rationally control the products under kinetic control via modulation of the energy landscape.
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Affiliation(s)
- Xinman Zhang
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
| | - Satoshi Takahashi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
| | - Keisuke Aratsu
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
| | - Isamu Kikuchi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan.,Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto 615-8510, Japan.,Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan.
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8
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Tateishi T, Takahashi S, Kikuchi I, Aratsu K, Sato H, Hiraoka S. Unexpected Self-Assembly Pathway to a Pd(II) Coordination Square-Based Pyramid and Its Preferential Formation beyond the Boltzmann Distribution. Inorg Chem 2021; 60:16678-16685. [PMID: 34652136 DOI: 10.1021/acs.inorgchem.1c02570] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Experimental and theoretical investigations of the self-assembly process of a Pd(II) coordination M6L4 square-based pyramid (SP) were conducted. It was found that the probable self-assembly pathway, in which the dimerization of M2L2 with two M leads to SP, expected from the connectivity of the building blocks is not a major self-assembly pathway to the M6L4 SP. Whether the M6L4 SP is assembled or M2L2 is trapped is determined by an inter- or intramolecular reaction in a chain-like M2L2X, where X is a leaving ligand. The kinetically trapped state where the M6L4 SP is produced from M2L2 beyond the Boltzmann distribution was realized by a concentration-induced process and was kept for at least 2 months at 298 K.
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Affiliation(s)
- Tomoki Tateishi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Satoshi Takahashi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Isamu Kikuchi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Keisuke Aratsu
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan.,Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto 615-8510, Japan.,Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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9
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Schulte TR, Holstein JJ, Schneider L, Adam A, Haberhauer G, Clever GH. A New Mechanically-Interlocked [Pd 2 L 4 ] Cage Motif by Dimerization of two Peptide-based Lemniscates. Angew Chem Int Ed Engl 2020; 59:22489-22493. [PMID: 32845570 PMCID: PMC7756597 DOI: 10.1002/anie.202010995] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Indexed: 12/31/2022]
Abstract
Most metallo-supramolecular assemblies of low nuclearity adopt simple topologies, with bridging ligands spanning neighboring metal centers in a direct fashion. Here we contribute a new structural motif to the family of host compounds with low metal count (two) that consists of a pair of doubly-interlocked, Figure-eight-shaped subunits, also termed "lemniscates". Each metal is chelated by two chiral bidentate ligands, composed of a peptidic macrocycle that resembles a natural product with two pyridyl-terminated arms. DFT calculation results suggest that dimerization of the mononuclear halves is driven by a combination of 1) Coulomb interaction with a central anion, 2) π-stacking between intertwined ligand arms and 3) dispersive interactions between the structure's compact inner core bedded into an outer shell composed of the cavitand-type macrocycles. The resulting cage-like architecture was characterized by NMR, MS and X-ray structure analyses. This new mechanically bonded system highlights the scope of structural variety accessible in metal-mediated self-assemblies composed of only a few constituents.
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Affiliation(s)
- Thorben R. Schulte
- Faculty of Chemistry and Chemical BiologyTU Dortmund Univ.Otto-Hahn-Str. 644227DortmundGermany
| | - Julian J. Holstein
- Faculty of Chemistry and Chemical BiologyTU Dortmund Univ.Otto-Hahn-Str. 644227DortmundGermany
| | - Laura Schneider
- Faculty of Chemistry and Chemical BiologyTU Dortmund Univ.Otto-Hahn-Str. 644227DortmundGermany
| | - Abdulselam Adam
- Institute for Organic ChemistryUniv. Duisburg-EssenUniversitätsstr. 745117EssenGermany
| | - Gebhard Haberhauer
- Institute for Organic ChemistryUniv. Duisburg-EssenUniversitätsstr. 745117EssenGermany
| | - Guido H. Clever
- Faculty of Chemistry and Chemical BiologyTU Dortmund Univ.Otto-Hahn-Str. 644227DortmundGermany
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10
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Schulte TR, Holstein JJ, Schneider L, Adam A, Haberhauer G, Clever GH. Ein neues, mechanisch verzahntes [Pd
2
L
4
] Käfigmotiv durch Dimerisierung von zwei Peptid‐basierten Lemniskaten. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202010995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Thorben R. Schulte
- Fakultät für Chemie und Chemische Biologie TU Dortmund Otto-Hahn-Str. 6 44227 Dortmund Deutschland
| | - Julian J. Holstein
- Fakultät für Chemie und Chemische Biologie TU Dortmund Otto-Hahn-Str. 6 44227 Dortmund Deutschland
| | - Laura Schneider
- Fakultät für Chemie und Chemische Biologie TU Dortmund Otto-Hahn-Str. 6 44227 Dortmund Deutschland
| | - Abdulselam Adam
- Institut für Organische Chemie Univ. Duisburg-Essen Universitätsstr. 7 45117 Essen Deutschland
| | - Gebhard Haberhauer
- Institut für Organische Chemie Univ. Duisburg-Essen Universitätsstr. 7 45117 Essen Deutschland
| | - Guido H. Clever
- Fakultät für Chemie und Chemische Biologie TU Dortmund Otto-Hahn-Str. 6 44227 Dortmund Deutschland
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11
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Hiraoka S, Takahashi S, Sato H. Coordination Self-Assembly Processes Revealed by Collaboration of Experiment and Theory: Toward Kinetic Control of Molecular Self-Assembly. CHEM REC 2020; 21:443-459. [PMID: 33241912 DOI: 10.1002/tcr.202000124] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 12/16/2022]
Abstract
The importance of the collaboration of experiment and theory has been proven in many examples in science and technology. Here, such a new example is shown in the investigation of molecular self-assembly process, which is a complicated multi-step chemical reaction occurring in the reaction network composed of a huge number of intermediates. An experimental method, QASAP (quantitative analysis of self-assembly process), developed by us and a numerical approach, NASAP (numerical analysis of self-assembly process), that analyzes the experimental data obtained by QASAP to draw detail molecular self-assembly pathways, which was also developed by us, are introduced, and their application to the investigation of Pd(II)-mediated coordination assemblies are presented. Further, the possibility of the prediction of the outcomes of molecular self-assembly by varying the reaction conditions is also demonstrated. Finally, a future direction in the field of artificial molecular self-assembly based on pathway-dependent self-assembly, that is, kinetic control of molecular self-assembly is discussed.
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Affiliation(s)
- Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Satoshi Takahashi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Kyoto, 615-8510, Japan.,Elements Strategy Initiative for Catalyst and Batteries, Kyoto University, Kyoto, 615-8510, Japan.,Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto, 606-8103, Japan
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12
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Takahashi S, Tateishi T, Sasaki Y, Sato H, Hiraoka S. Towards kinetic control of coordination self-assembly: a case study of a Pd 3L 6 double-walled triangle to predict the outcomes by a reaction network model. Phys Chem Chem Phys 2020; 22:26614-26626. [PMID: 33201952 DOI: 10.1039/d0cp04623j] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Numerical analysis of self-assembly process (NASAP) was performed for a [Pd3L6]6+ double-walled triangle (DWT) complex. With a chemical reaction network and a parameter set of the reaction rate constants obtained from a numerical search in an eighteen-dimensional parameter space to obtain a good fit to the data from the experimental counterpart (quantitative analysis of self-assembly process, QASAP), a refined calculation resulted in a detailed time evolution of each molecular species. Analysis based on those clues revealed dominant self-assembly pathways and a balance between inter- and intramolecular reactions, and enabled prediction of the reaction outcomes depending on the initial stoichiometric ratio under kinetic control.
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Affiliation(s)
- Satoshi Takahashi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan.
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13
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Kumar A, Mukherjee PS. Multicomponent Self‐Assembly of Pd
II
/Pt
II
Interlocked Molecular Cages: Cage‐to‐Cage Conversion and Self‐Sorting in Aqueous Medium. Chemistry 2020; 26:4842-4849. [DOI: 10.1002/chem.202000122] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/05/2020] [Indexed: 12/31/2022]
Affiliation(s)
- Atul Kumar
- Inorganic and Physical Chemistry DepartmentIndian Institute of Science Bangalore 560012 India
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14
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Tateishi T, Takahashi S, Okazawa A, Martí-Centelles V, Wang J, Kojima T, Lusby PJ, Sato H, Hiraoka S. Navigated Self-Assembly of a Pd2L4 Cage by Modulation of an Energy Landscape under Kinetic Control. J Am Chem Soc 2019; 141:19669-19676. [DOI: 10.1021/jacs.9b07779] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Tomoki Tateishi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Satoshi Takahashi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Atsushi Okazawa
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Vicente Martí-Centelles
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, Scotland, United Kingdom
| | - Jianzhu Wang
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, Scotland, United Kingdom
| | - Tatsuo Kojima
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Paul J. Lusby
- EaStCHEM School of Chemistry, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, Scotland, United Kingdom
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto 615-8510, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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15
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Foianesi-Takeshige LH, Takahashi S, Tateishi T, Sekine R, Okazawa A, Zhu W, Kojima T, Harano K, Nakamura E, Sato H, Hiraoka S. Bifurcation of self-assembly pathways to sheet or cage controlled by kinetic template effect. Commun Chem 2019. [DOI: 10.1038/s42004-019-0232-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Abstract
The template effect is a key feature to control the arrangement of building blocks in assemblies, but its kinetic nature remains elusive compared to the thermodynamic aspects, with the exception of very simple reactions. Here we report a kinetic template effect in a self-assembled cage composed of flexible ditopic ligands and Pd(II) ions. Without template anion, a micrometer-sized sheet is kinetically trapped (off-pathway), which is converted into the thermodynamically most stable cage by the template anion. When the template anion is present from the start, the cage is selectively produced by the preferential cyclization of a dinuclear intermediate (on-pathway). Quantitative and numerical analyses of the self-assembly of the cage on the on-pathway revealed that the accelerating effect of the template is stronger for the early stage reactions of the self-assembly than for the final cage formation step itself, indicating the kinetic template effect.
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16
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Tateishi T, Yasutake Y, Kojima T, Takahashi S, Hiraoka S. Self-assembly process of a quadruply interlocked palladium cage. Commun Chem 2019. [DOI: 10.1038/s42004-019-0123-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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17
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Komine S, Takahashi S, Kojima T, Sato H, Hiraoka S. Self-Assembly Processes of Octahedron-Shaped Pd6L4 Cages. J Am Chem Soc 2019; 141:3178-3186. [DOI: 10.1021/jacs.8b12890] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Shohei Komine
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Satoshi Takahashi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Tatsuo Kojima
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Kyoto 615-8510, Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University, Kyoto 615-8510, Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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18
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Takahashi S, Sasaki Y, Hiraoka S, Sato H. A stochastic model study on the self-assembly process of a Pd2L4 cage consisting of rigid ditopic ligands. Phys Chem Chem Phys 2019; 21:6341-6347. [DOI: 10.1039/c8cp06102e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Numerical analysis considering explicit conformational difference revealed the self-assembly process of a Pd2L4 cage containing rigid ditopic ligands.
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Affiliation(s)
- Satoshi Takahashi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Yuya Sasaki
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University
- Kyoto 615-8510
- Japan
- Elements Strategy Initiative for Catalysts and Batteries, Kyoto University
- Kyoto 615-8510
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19
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Komine S, Tateishi T, Kojima T, Nakagawa H, Hayashi Y, Takahashi S, Hiraoka S. Self-assembly processes of octahedron-shaped Pd6L12 cages. Dalton Trans 2019; 48:4139-4148. [DOI: 10.1039/c8dt04931a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Self-assembly processes of three octahedron-shaped [Pd6L12]12+ cages were investigated by an NMR-based quantitative approach (QASAP).
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Affiliation(s)
- Shohei Komine
- Department of Basic Science
- Graduate School of Arts and Sciences
- The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Tomoki Tateishi
- Department of Basic Science
- Graduate School of Arts and Sciences
- The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Tatsuo Kojima
- Department of Basic Science
- Graduate School of Arts and Sciences
- The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Haruna Nakagawa
- Department of Basic Science
- Graduate School of Arts and Sciences
- The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Yasuhiro Hayashi
- Department of Basic Science
- Graduate School of Arts and Sciences
- The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Satoshi Takahashi
- Department of Basic Science
- Graduate School of Arts and Sciences
- The University of Tokyo
- Tokyo 153-8902
- Japan
| | - Shuichi Hiraoka
- Department of Basic Science
- Graduate School of Arts and Sciences
- The University of Tokyo
- Tokyo 153-8902
- Japan
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20
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Kai S, Tateishi T, Kojima T, Takahashi S, Hiraoka S. Self-Assembly of a Pd4L8 Double-Walled Square Takes Place through Two Kinds of Metastable Species. Inorg Chem 2018; 57:13083-13086. [DOI: 10.1021/acs.inorgchem.8b02470] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shumpei Kai
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Tomoki Tateishi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Tatsuo Kojima
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Satoshi Takahashi
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Shuichi Hiraoka
- Department of Basic Science, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo 153-8902, Japan
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