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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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2
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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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3
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Guerra JVS, Alves LFG, Bourissou D, Lopes-de-Oliveira PS, Szalóki G. Cavity Characterization in Supramolecular Cages. J Chem Inf Model 2023. [PMID: 37129917 DOI: 10.1021/acs.jcim.3c00328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Confining molecular guests within artificial hosts has provided a major driving force in the rational design of supramolecular cages with tailored properties. Over the last 30 years, a set of design strategies have been developed that enabled the controlled synthesis of a myriad of cages. Recently, there has been a growing interest in involving in silico methods in this toolbox. Cavity shape and size are important parameters that can be easily accessed by inexpensive geometric algorithms. Although these algorithms are well developed for the detection of nonartificial cavities (e.g., enzymes), they are not routinely used for the rational design of supramolecular cages. In order to test the capabilities of this tool, we have evaluated the performance and characteristics of seven different cavity characterization software in the context of 22 analogues of well-known supramolecular cages. Among the tested software, KVFinder project and Fpocket proved to be the most software to characterize supramolecular cavities. With the results of this work, we aim to popularize this underused technique within the supramolecular community.
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Affiliation(s)
- João V S Guerra
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), Rua Giuseppe Máximo Scolfaro, 10000, Bosque Das Palmeiras, Campinas, SP 13083-100, Brazil
| | - Luiz F G Alves
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), Rua Giuseppe Máximo Scolfaro, 10000, Bosque Das Palmeiras, Campinas, SP 13083-100, Brazil
| | - Didier Bourissou
- Laboratoire Hétérochimie Fondamentale et Appliquée (LHFA, UMR 5069), CNRS, Université Toulouse III─Paul Sabatier, 118 Route de Narbonne, Toulouse 31062, Cedex 09, France
| | - Paulo S Lopes-de-Oliveira
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), Rua Giuseppe Máximo Scolfaro, 10000, Bosque Das Palmeiras, Campinas, SP 13083-100, Brazil
| | - György Szalóki
- Laboratoire Hétérochimie Fondamentale et Appliquée (LHFA, UMR 5069), CNRS, Université Toulouse III─Paul Sabatier, 118 Route de Narbonne, Toulouse 31062, Cedex 09, France
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4
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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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5
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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] [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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Chauhan P, Javed S. Crystallographic capture of caged diamondoids: Camphor and adamantanes’ guests‐encapsulation on specific recognition‐sites of host MOF. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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] [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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8
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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: 8] [Impact Index Per Article: 4.0] [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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Delle Piane M, Pesce L, Cioni M, Pavan GM. Reconstructing Reactivity in Dynamic Host-Guest Systems at Atomistic Resolution: Amide Hydrolysis Under Confinement in the Cavity of a Coordination Cage. Chem Sci 2022; 13:11232-11245. [PMID: 36320487 PMCID: PMC9517058 DOI: 10.1039/d2sc02000a] [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: 04/06/2022] [Accepted: 08/28/2022] [Indexed: 11/21/2022] Open
Abstract
Spatial confinement is widely employed by nature to attain unique efficiency in controlling chemical reactions. Notable examples are enzymes, which selectively bind reactants and exquisitely regulate their conversion into products. In an attempt to mimic natural catalytic systems, supramolecular metal–organic cages capable of encapsulating guests in their cavity and of controlling/accelerating chemical reactions under confinement are attracting increasing interest. However, the complex nature of these systems, where reactants/products continuously exchange in-and-out of the host, makes it often difficult to elucidate the factors controlling the reactivity in dynamic regimes. As a case study, here we focus on a coordination cage that can encapsulate amide guests and enhance their hydrolysis by favoring their mechanical twisting towards reactive molecular configurations under confinement. We designed an advanced multiscale simulation approach that allows us to reconstruct the reactivity in such host–guest systems in dynamic regimes. In this way, we can characterize amide encapsulation/expulsion in/out of the cage cavity (thermodynamics and kinetics), coupling such host–guest dynamic equilibrium with characteristic hydrolysis reaction constants. All computed kinetic/thermodynamic data are then combined, obtaining a statistical estimation of reaction acceleration in the host–guest system that is found in optimal agreement with the available experimental trends. This shows how, to understand the key factors controlling accelerations/variations in the reaction under confinement, it is necessary to take into account all dynamic processes that occur as intimately entangled in such host–guest systems. This also provides us with a flexible computational framework, useful to build structure–dynamics–property relationships for a variety of reactive host–guest systems. Encapsulation of guests in metal–organic cages allows control over chemical reactivity. Focusing on the hydrolysis of amides, here we show an effective molecular simulation approach to reconstruct reactivity in host–guest systems in dynamic regimes.![]()
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Affiliation(s)
- Massimo Delle Piane
- Department of Applied Science and Technology, Politecnico di Torino Corso Duca degli Abruzzi 24 10129 Torino Italy
| | - Luca Pesce
- 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
| | - Matteo Cioni
- Department of Applied Science and Technology, Politecnico di Torino Corso Duca degli Abruzzi 24 10129 Torino Italy
| | - 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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Norjmaa G, Maréchal JD, 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] [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 Barcelona, 08193, Cerdanyola del Valles, Barcelona, Catalonia, Spain
| | - Jean-Didier Maréchal
- Departament de Química and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Universitat Autònoma de Barcelona, 08193, Cerdanyola del Valles, Barcelona, Catalonia, Spain
| | - Gregori Ujaque
- Departament de Química and Centro de Innovación en Química Avanzada (ORFEO-CINQA), Universitat Autònoma de Barcelona, 08193, Cerdanyola del Valles, Barcelona, Catalonia, Spain
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