Large Self-Assembled Chiral Organic Cages: Synthesis, Structure, and Shape Persistence

Enantioselective Self-Assembly of a Homochiral Tetrahedral Cage Comprising Only Achiral Precursors

How Nature synthesizes enantiomerically pure substances from achiral or racemic resources remains a mystery. In this study, we aimed to emulate this natural phenomenon by constructing chiral tetrahedral cages through self-assembly, achieved by condensing two achiral compounds-a trisamine and a trisaldehyde. The occurrence of intercomponent CH⋅⋅⋅π interactions among the phenyl building blocks within the cage frameworks results in twisted conformations, imparting planar chirality to the tetrahedrons. In instances where the trisaldehyde precursor features electron-withdrawing ester side chains, we observed that the intermolecular CH⋅⋅⋅π forces are strong enough to prevent racemization. To attain enantioselective self-assembly, a chiral amine was introduced during the imine formation process. The addition of three equivalents of chiral amino mediator to one equivalent of the achiral trisaldehyde precursor formed a trisimino intermediate. This chiral compound was subsequently combined with the achiral trisamino precursor, leading to an imine exchange reaction that releasing the chiral amino mediator and formation of the tetrahedral cage with an enantiomeric excess (ee) of up to 75 %, exclusively composed of achiral building blocks. This experimental observation aligns with theoretical calculations based on the free energies of related cage structures. Moreover, since the chiral amine was not consumed during the imine exchange cycle, it enabled the enantioselective self-assembly of the tetrahedral cage for multiple cycles when new batches of the achiral trisaldehyde and trisamino precursors were successively added.

Functionalization of Magnetic UiO-66-NH2 with a Chiral Cu(l-proline)2 Complex as a Hybrid Asymmetric Catalyst for CO2 Conversion into Cyclic Carbonates

In this study, a chiral [Cu(l-proline)2] complex-modified Fe3O4@SiO2@UiO-66-NH2(Zr) metal-organic framework [Fe3O4@SiO2@UiO-66-NH-Cu(l-proline)2] via multifunctionalization strategies was designed and synthesized. One simple approach to chiralize an achiral MOF-structure that cannot be directly chiralized using a chiral secondary agent like 4-hydroxy-l-proline. Therefore, this chiral catalyst was synthesized with a simple and multistep method. Accordingly, Fe3O4@SiO2@UiO-66-NH2 has been synthesized via Fe3O4 modification with tetraethyl orthosilicate and subsequently with ZrCl4 and 2-aminoterephthalic acid. The presence of the silica layer helps to stabilize the Fe3O4 core, while the bonding between Zr4+ and the -OH groups in the silica layer promotes the development of Zr-MOFs on the Fe3O4 surface, and then the surfaces of the synthesized magnetic MOFs composite are functionalized with 1,2-dichloroethane and Cu(II) complex with 4-hydroxy-l-proline, [Cu(l-proline)2] to afford the magnetically chiral nanocatalyst. Multiple techniques were employed to characterize this magnetically chiral nanocatalyst such as Fourier transform infrared (FT-IR), X-ray photoelectron spectroscopy (XPS), field-emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), energy-dispersive X-ray spectrometry (EDX), powder X-ray diffraction (PXRD), circular dichroism (CD), inductively coupled plasma (ICP), thermogravimetric analysis (TGA), vibrating-sample magnetometry (VSM), and Brunauer-Emmett-Teller (BET) analyses. Moreover, a magnetically chiral nanocatalyst shows the asymmetric CO2 fixation reaction under solvent-free conditions at 80 °C and in ethanol under reflux conditions with up to 99 and 98% ee, respectively. Furthermore, the reaction mechanism was illustrated concerning the total energy of the reactant, intermediates and product, and the structural parameters were analyzed.

Deep generative design of porous organic cages via a variational autoencoder

Porous organic cages (POCs) are a class of porous molecular materials characterised by their tunable, intrinsic porosity; this functional property makes them candidates for applications including guest storage and separation. Typically formed via dynamic covalent chemistry reactions from multifunctionalised molecular precursors, there is an enormous potential chemical space for POCs due to the fact they can be formed by combining two relatively small organic molecules, which themselves have an enormous chemical space. However, identifying suitable molecular precursors for POC formation is challenging, as POCs often lack shape persistence (the cage collapses upon solvent removal with loss of its cavity), thus losing a key functional property (porosity). Generative machine learning models have potential for targeted computational design of large functional molecular systems such as POCs. Here, we present a deep-learning-enabled generative model, Cage-VAE, for the targeted generation of shape-persistent POCs. We demonstrate the capacity of Cage-VAE to propose novel, shape-persistent POCs, via integration with multiple efficient sampling methods, including Bayesian optimisation and spherical linear interpolation.

Regio- and Enantioselective Macrocyclization from Dynamic Imine Formation: Chemo- and Enantioselective Fluorescent Recognition of Lysine

The dynamic covalent chemistry of imines is utilized to conduct a regioselective as well as enantioselective synthesis of an unsymmetric (C1) chiral macrocycle from the reaction of an unsymmetric (C1) chiral dialdehyde, (S)-4, that contains a salicylaldehyde unit and a benzaldehyde unit, with lysine, an unsymmetric (C1) chiral diamine. The enantioselectivity is further enhanced in the presence of Zn2+. Compound (S)-4 in combination with Zn2+ is found to be a highly chemoselective as well as enantioselective fluorescent probe for lysine. It can be used to detect specific enantiomers of this amino acid.

The progress on porous organic materials for chiral separation

Chiral compounds have similar structures and properties, but their pharmacological action is very different or even opposite. Therefore, the separation of chiral compounds has great significance in pharmaceutical and agriculture. Porous organic materials are novel crystalline porous materials, which possess high surface area, controllable pore size, and favorable functionalization. Therefore, porous organic materials are considered to be an ideal material for chiral separation. In this review, we summarized the progress of chiral porous organic materials for chiral separation in recent years. Furthermore, the applications of chiral porous organic materials as chiral separation medias (chromatography stationary phases and membrane materials) in enantioseparation were highlighted. Finally, the remaining challenges and future directions for porous organic materials in chiral separation were also briefly outlined further to promote the development of porous organic materials in chiral separation.

Explainable graph neural networks for organic cages

The development of accurate and explicable machine learning models to predict the properties of topologically complex systems is a challenge in materials science. Porous organic cages, a class of polycyclic molecular materials, have potential application in molecular separations, catalysis and encapsulation. For most applications of porous organic cages, having a permanent internal cavity in the absence of solvent, a property termed “shape persistence” is critical. Here, we report the development of Graph Neural Networks (GNNs) to predict the shape persistence of organic cages. Graph neural networks are a class of neural networks where the data, in our case that of organic cages, are represented by graphs. The performance of the GNN models was measured against a previously reported computational database of organic cages formed through a range of [4 + 6] reactions with a variety of reaction chemistries. The reported GNNs have an improved prediction accuracy and transferability compared to random forest predictions. Apart from the improvement in predictive power, we explored the explicability of the GNNs by computing the integrated gradient of the GNN input. The contribution of monomers and molecular fragments to the shape persistence of the organic cages could be quantitatively evaluated with integrated gradients. With the added explicability of the GNNs, it was possible not only to accurately predict the property of organic materials, but also to interpret the predictions of the deep learning models and provide structural insights for the discovery of future materials.

We report the development of explainable Graph Neural Networks to predict shape persistence of organic cages. Integrated gradient analysis identifies collapse-inducing molecular fragments and helps chemists design more shape persistent structures.

Symmetrically Tetra-functionalized Pillar[6]arenes Prepared by Fragment Coupling

Due to the highly symmetrical structures generated from one-pot syntheses, the partial functionalization of macrocycles is usually beset with low yields and onerous purifications of the target multifunctional macrocycles. To improve this circumstance, taking pillar[6]arenes as an example, a two-step fragment coupling method is developed for synthesizing symmetrically tetra-functionalized pillar[6]arenes, namely X-pillar[6]arenes. This method is simple and versatile, which makes hetero-fragment coupling and pre-functionalization available. Nine new macrocycles and a pillar[6]arene-based cage are prepared. In addition, one of the newly synthesized macrocycles, COOEtEtXP[6] , exhibits a strong cyan luminescence in the solid state under irradiation by 365 nm UV light. This emission originates from intramolecular through-space conjugation. Meanwhile, formation of a supramolecular polymer by multiple non-covalent intra/intermolecular interactions help rigidify the structure and make COOEtEtXP[6] an efficient solid-state emitter. It is believed that this fragment coupling can also be used to realize the multi-functionalization of other macrocycles.

Dynamic Nucleophilic Aromatic Substitution of Tetrazines

A dynamic nucleophilic aromatic substitution of tetrazines (SN Tz) is presented herein. It combines all the advantages of dynamic covalent chemistry with the versatility of the tetrazine moiety. Indeed, libraries of compounds or sophisticated molecular structures can be easily obtained, which are susceptible to post-functionalization by inverse electron demand Diels-Alder (IEDDA) reaction, which also locks the exchange. Additionally, the structures obtained can be disassembled upon the application of the right stimulus, either UV irradiation or a suitable chemical reagent. Moreover, SN Tz is compatible with the imine chemistry of anilines. The high potential of this methodology has been proved by building two responsive supramolecular systems: A macrocycle that displays a light-induced release of acetylcholine; and a truncated [4+6] tetrahedral shape-persistent fluorescent cage, which is disassembled by thiols unless it is post-stabilized by IEDDA.

Soluble Congeners of Prior Insoluble Shape-Persistent Imine Cages

One of the most applied reaction types to synthesize shape‐persistent organic cage compounds is the imine condensation reaction and it is assumed that the formed cages are thermodynamically controlled products due to the reversibility of the imine condensation. However, most of the synthesized imine cages reported are formed as precipitate from the reaction mixture and therefore rather may be kinetically controlled products. There are even examples in literature, where resulting cages are not soluble at all in common organic solvents to characterize or study their formation by NMR spectroscopy in solution. Here, a triptycene triamine containing three solubilizing n‐hexyloxy chains has been used to synthesize soluble congeners of prior insoluble cages. This allowed us to study the formation as well as the reversibility of cage formation in solution by investigating exchange of building blocks between the cages and deuterated derivatives thereof.

Chiral Self-sorting of Giant Cubic [8+12] Salicylimine Cage Compounds

Chiral self-sorting is intricately connected to the complicated chiral processes observed in nature and no artificial systems of comparably complexity have been generated by chemists. However, only a few examples of purely organic molecules have been reported so far, where the self-sorting process could be controlled. Herein, we describe the chiral self-sorting of large cubic [8+12] salicylimine cage compounds based on a chiral TBTQ precursor. Out of 23 possible cage isomers only the enantiopure and a meso cage were observed to be formed, which have been unambiguously characterized by single crystal X-ray diffraction. Furthermore, by careful choice of solvent the formation of meso cage could be controlled. With internal diameters of din =3.3-3.5 nm these cages are among the largest organic cage compounds characterized and show very high specific surface areas up to approx. 1500 m2  g-1 after desolvation.

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.

A Robust Porous Quinoline Cage: Transformation of a [4+6] Salicylimine Cage by Povarov Cyclization

Porous shape-persistent organic cages have become the object of interest in recent years because they are soluble and thus processable from solution. A variety of cages can be achieved by applying dynamic covalent chemistry (DCC), but they are less chemically stable. Here the transformation of a salicylimine cage into a quinoline cage by a twelve-fold Povarov reaction as the key step is described. Besides the chemical stability of the cage over a broad pH regime, it shows a unique absorption and emission depending on acid concentration. Furthermore, thin films for the vapor detection of acids were investigated, showing color switches from pale-yellow to red, and characteristic emission profiles.

High-Throughput Approaches for the Discovery of Supramolecular Organic Cages

The assembly of complex molecules, such as organic cages, can be achieved through supramolecular and dynamic covalent strategies. Their use in a range of applications has been demonstrated, including gas uptake, molecular separations, and in catalysis. However, the targeted design and synthesis of new species for particular applications is challenging, particularly as the systems become more complex. High-throughput computation-only and experiment-only approaches have been developed to streamline the discovery process, although are still not widely implemented. Additionally, combined hybrid workflows can dramatically accelerate the discovery process and lead to the serendipitous discovery and rationalisation of new supramolecular assemblies that would not have been designed based on intuition alone. This Minireview focuses on the advances in high-throughput approaches that have been developed and applied in the discovery of supramolecular organic cages.

A Robotics-Inspired Screening Algorithm for Molecular Caging Prediction

We define a molecular caging complex as a pair of molecules in which one molecule (the “host” or “cage”) possesses a cavity that can encapsulate the other molecule (the “guest”) and prevent it from escaping. Molecular caging complexes can be useful in applications such as molecular shape sorting, drug delivery, and molecular immobilization in materials science, to name just a few. However, the design and computational discovery of new caging complexes is a challenging task, as it is hard to predict whether one molecule can encapsulate another because their shapes can be quite complex. In this paper, we propose a computational screening method that predicts whether a given pair of molecules form a caging complex. Our method is based on a caging verification algorithm that was designed by our group for applications in robotic manipulation. We tested our algorithm on three pairs of molecules that were previously described in a pioneering work on molecular caging complexes and found that our results are fully consistent with the previously reported ones. Furthermore, we performed a screening experiment on a data set consisting of 46 hosts and four guests and used our algorithm to predict which pairs are likely to form caging complexes. Our method is computationally efficient and can be integrated into a screening pipeline to complement experimental techniques.

Organic Imine Cages: Molecular Marriage and Applications

Imine condensation has been known to chemists for more than a century and is used extensively to synthesize large organic cages of defined shapes and sizes. Surprisingly, in the context of the synthetic methods for organic imine cages (OICs), a self-sorting/self-selection (molecular marriage) process has been overlooked over the years. Such processes are omnipresent in nature, from the creation of galaxies to the formation of the smallest building blocks of life (the cell). Such processes have the incredible ability to guide a system toward the formation of a specific product or products out of a collection of equally probable multiple possibilities. This Minireview sheds light on new opportunities in cage design offered by the self-sorting/self-selection protocol in OICs. Recent efforts to explore organic cages for various exciting new applications are discussed; for example, for detection of harmful small organic molecules, as templates for nucleation of metal nanoparticles (MNPs), and as proton-conducting materials.

Computational modelling of solvent effects in a prolific solvatomorphic porous organic cage

Crystal structure prediction methods can enable the in silico design of functional molecular crystals, but solvent effects can have a major influence on relative lattice energies, sometimes thwarting predictions. This is particularly true for porous solids, where solvent included in the pores can have an important energetic contribution. We present a Monte Carlo solvent insertion procedure for predicting the solvent filling of porous structures from crystal structure prediction landscapes, tested using a highly solvatomorphic porous organic cage molecule, CC1. Using this method, we can understand why the predicted global energy minimum structure for CC1 is never observed from solvent crystallisation. We also explain the formation of three different solvatomorphs of CC1 from three structurally-similar chlorinated solvents. Calculated solvent stabilisation energies are found to correlate with experimental results from thermogravimetric analysis, suggesting a future computational framework for a priori materials design that factors in solvation effects.

One-step Access to Resorcinsalens-Solvent-Dependent Synthesis, Tautomerism, Self-sorting and Supramolecular Architectures of Chiral Polyimine Analogues of Resorcinarene

Substituted 2,4- and 4,6-dihydroxyisophthalaldehydes were condensed with optically pure and racemic trans-1,2-diaminocyclohexane to form resorcinarene-like polyimine macrocycles (resorcinsalens), the structure and stoichiometry of which were controlled by the choice of the reaction medium. Particularly, the cyclocondensation reactions were driven by the solubility, tautomerization, or by social self-sorting. The resorcinsalens crystallized as inclusion compounds, in which the guest molecules were situated either in channels or in voids. In the highly hydrated crystals of one of the [2+2] macrocycles and chloroform-solvated crystals of a [4+4] product the channels were interconnected, as in zeolites, enabling possible migration of loosely bound solvent molecules in three dimensions. The association mode depended on the structural modification of the host molecule and the type of included solvent molecule(s).

Quantification of Stereochemical Communication in Metal-Organic Assemblies

The derivation and application of a statistical mechanical model to quantify stereochemical communication in metal-organic assemblies is reported. The factors affecting the stereochemical communication within and between the metal stereocenters of the assemblies were experimentally studied by optical spectroscopy and analyzed in terms of a free energy penalty per "incorrect" amine enantiomer incorporated, and a free energy of coupling between stereocenters. These intra- and inter-vertex coupling constants are used to track the degree of stereochemical communication across a range of metal-organic assemblies (employing different ligands, peripheral amines, and metals); temperature-dependent equilibria between diastereomeric cages are also quantified. The model thus provides a unified understanding of the factors that shape the chirotopic void spaces enclosed by metal-organic container molecules.

Quantification of Stereochemical Communication in Metal-Organic Assemblies

The derivation and application of a statistical mechanical model to quantify stereochemical communication in metal-organic assemblies is reported. The factors affecting the stereochemical communication within and between the metal stereocenters of the assemblies were experimentally studied by optical spectroscopy and analyzed in terms of a free energy penalty per "incorrect" amine enantiomer incorporated, and a free energy of coupling between stereocenters. These intra- and inter-vertex coupling constants are used to track the degree of stereochemical communication across a range of metal-organic assemblies (employing different ligands, peripheral amines, and metals); temperature-dependent equilibria between diastereomeric cages are also quantified. The model thus provides a unified understanding of the factors that shape the chirotopic void spaces enclosed by metal-organic container molecules.

Synthesis of a rigid C3v -symmetric tris-salicylaldehyde as a precursor for a highly porous molecular cube

The development of a synthetic approach to a C3v -symmetric tris-salicylaldehyde based on triptycene is presented. The tris-salicylaldehyde is a versatile precursor for porous molecular materials, as demonstrated in the [4+4] condensation reaction with a triptycene triamine to form a molecular shape-persistent porous cube. The amorphous material of the molecular porous cube shows a very high surface area of 1014 m(2)  g(-1) (BET model) and a high uptake of CO2 (18.2 wt % at 273 K and 1 bar). Furthermore, during the multistep synthesis of the tris-salicylaldehyde precursor, a relatively rare (twofold) addition of the aryne to the anthracene in the 1,4- and 1,4,5,8-positions have been found during a Diels-Alder reaction, as proven by X-ray structure analysis.