Picking the lock of coordination cage catalysis

Piskorz, Tomasz K.; Martí-Centelles, Vicente; Spicer, Rebecca L.; Duarte, Fernanda; Lusby, Paul J.

doi:10.1039/d3sc02586a

Cited by 28 publications

(19 citation statements)

References 205 publications

(337 reference statements)

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“…Although binding of the DNP pair is, in principle, a reversible equilibrium, the strong binding under the conditions used effectively makes the inhibition irreversible, a rarely seen phenomenon. [15] This is in contrast to the work by Reek and co-workers, [16] and Bergman, Raymond and co-workers, [17] who both observed reversible product inhibition. In a follow-up report by Bergman, Raymond, Toste and co-workers, product inhibition was avoided by addition of maleimide, resulting in a follow-on reaction of the initiallygenerated product with the added maleimide to give a more weakly binding cycloadduct which vacated the active site, facilitating catalytic turnover.…”

Section: Catalysis Of the S N Ar Reaction Of Dnfbmentioning

confidence: 74%

A Study on Auto‐Catalysis and Product Inhibition: A Nucleophilic Aromatic Substitution Reaction Catalysed within the Cavity of an Octanuclear Coordination Cage

Dorrat,

Taylor,

Young

et al. 2024

Chemistry A European J

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The ability of an octanuclear cubic coordination cage to catalyse a nucleophilic aromatic substitution reaction on a cavity‐bound guest was studied with 2,4‐dinitrofluorobenzene (DNFB) as the guest/substrate. It was found that DNFB undergoes a catalysed reaction with hydroxide ions within the cavity of the cubic cage (in aqueous buffer solution, pH 8.6). The rate enhancement of kcat/kuncat was determined to be 23, with cavity binding of the guest being required for catalysis to occur. The product, 2,4‐dinitrophenolate (DNP), remained bound within the cavity due to electrostatic stabilisation and exerts two apparently contradictory effects: it initially auto‐catalyses the reaction when present at low concentrations, but at higher concentrations inhibits catalysis when a pair of DNP guests block the cavity. When encapsulated, the UV/Vis absorption spectrum of DNP is red‐shifted when compared to the spectrum of free DNP in aqueous solution. Further investigations using other aromatic guests determined that a similar red‐shift on cavity binding also occurred for 4‐nitrophenolate (4NP) at pH 8.6. The red‐shift was used to determine the stoichiometry of guest binding of DNP and 4NP within the cage cavity, which was confirmed by structural analysis with X‐ray crystallography; and also used to perform catalytic kinetic studies in the solution‐state.

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Section: Catalysis Of the S N Ar Reaction Of Dnfbmentioning

confidence: 74%

A Study on Auto‐Catalysis and Product Inhibition: A Nucleophilic Aromatic Substitution Reaction Catalysed within the Cavity of an Octanuclear Coordination Cage

Dorrat,

Taylor,

Young

et al. 2024

Chemistry A European J

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“…Moreover, the host–guest chemistry of heterometallic MSAs needs to be examined in more detail as the lower symmetry cavity environments that these systems offer should lead to greater guest selectivity, which in turn could result in better, more enzyme-like, catalysis. 199…”

Section: Discussionmentioning

confidence: 99%

Heterometallic cages: synthesis and applications

Moree,

Faulkner,

Crowley

2024

Chem. Soc. Rev.

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“…Discrete three-dimensional (3D) organic and metal-organic (porous) cages have emerged as promising biomimetic systems. [1,2,3] They offer synthetic modularity and tunability, enabling chemists to efficiently create structures with customized sizes and shapes from simple building blocks. [4,5,6,7] A critical factor contributing to their functional properties is the presence of a welldefined inner cavity capable of binding and even catalyzing chemical reactions, prompting chemists to draw parallels between these systems and enzymes.…”

Section: Introductionmentioning

confidence: 99%

CageCavityCalc (C3): A computational tool for calculating and visualizing cavities in Molecular Cages

Martí-Centelles,

Piskorz,

Duarte

2024

Preprint

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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 remain 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 Chimera. To enhance user accessibility, a PyMol plugin has been created, allowing non-specialists 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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Picking the lock of coordination cage catalysis

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...

Cited by 28 publications

References 205 publications

A Study on Auto‐Catalysis and Product Inhibition: A Nucleophilic Aromatic Substitution Reaction Catalysed within the Cavity of an Octanuclear Coordination Cage

A Study on Auto‐Catalysis and Product Inhibition: A Nucleophilic Aromatic Substitution Reaction Catalysed within the Cavity of an Octanuclear Coordination Cage

Heterometallic cages: synthesis and applications

CageCavityCalc (C3): A computational tool for calculating and visualizing cavities in Molecular Cages

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