Host-Guest Chemistry of Truncated Tetrahedral Imine Cages with Ammonium Ions

CageCavityCalc (C3): A Computational Tool for Calculating and Visualizing Cavities in Molecular Cages

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.

Isomerism of Cyclodextrin Tetramer Induced by Alkali Halide Cluster Ions Observed by Ion Mobility Spectrometry-Mass Spectrometry

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.

Purely Covalent Molecular Cages and Containers for Guest Encapsulation

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.

Solution NMR of synthetic cavity containing supramolecular systems: what have we learned on and from?

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.

A Giant [8+12] Boronic Ester Cage with 48 Terminal Alkene Units in the Periphery for Postsynthetic Alkene Metathesis

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.

Examination of the Dynamic Covalent Chemistry of [2 + 3]-Imine Cages

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.

Inducing Social Self-Sorting in Organic Cages To Tune The Shape of The Internal Cavity

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.

A porous fluorinated organic [4+4] imine cage showing CO2 and H2 adsorption

We report the first POC, containing perfluorinated aromatic panels forming quickly and in high purity, despite low preorganization encoded in the starting materials.