Understanding static, dynamic and cooperative porosity in molecular materials

Design and assembly of porous organic cages

Porous organic cages (POCs) represent a notable category of porous materials, showing remarkable material properties due to their inherent porosity. Unlike extended frameworks which are constructed by strong covalent or coordination bonds, POCs are composed of discrete molecular units held together by weak intermolecular forces. Their structure and chemical traits can be systematically tailored, making them suitable for a range of applications including gas storage and separation, molecular separation and recognition, catalysis, and proton and ion conduction. This review provides a comprehensive overview of POCs, covering their synthesis methods, structure and properties, computational approaches, and applications, serving as a primer for those who are new to the domain. A special emphasis is placed on the growing role of computational methods, highlighting how advanced data-driven techniques and automation are increasingly aiding the rapid exploration and understanding of POCs. We conclude by addressing the prevailing challenges and future prospects in the field.

Metal cation substitution can tune CO2, H2O and CH4 switching pressure in transiently porous coordination networks

Compared to rigid physisorbents, switching coordination networks that reversibly transform between closed (non-porous) and open (porous) phases offer promise for gas/vapour storage and separation owing to their improved working capacity and desirable thermal management properties. We recently introduced a coordination network, X-dmp-1-Co, which exhibits switching enabled by transient porosity. The resulting "open" phases are generated at threshold pressures even though they are conventionally non-porous. Herein, we report that X-dmp-1-Co is the parent member of a family of transiently porous coordination networks [X-dmp-1-M] (M = Co, Zn and Cd) and that each exhibits transient porosity but switching events occur at different threshold pressures for CO2 (0.8, 2.1 and 15 mbar, for Co, Zn and Cd, respectively, at 195 K), H2O (10, 70 and 75% RH, for Co, Zn and Cd, respectively, at 300 K) and CH4 (<2, 10 and 25 bar, for Co, Zn and Cd, respectively, at 298 K). Insight into the phase changes is provided through in situ SCXRD and in situ PXRD. We attribute the tuning of gate-opening pressure to differences and changes in the metal coordination spheres and how they impact dpt ligand rotation. X-dmp-1-Zn and X-dmp-1-Cd join a small number of coordination networks (<10) that exhibit reversible switching for CH4 between 5 and 35 bar, a key requirement for adsorbed natural gas storage.

Porous Organic Cages

Porous organic cages (POCs) are a relatively new class of low-density crystalline materials that have emerged as a versatile platform for investigating molecular recognition, gas storage and separation, and proton conduction, with potential applications in the fields of porous liquids, highly permeable membranes, heterogeneous catalysis, and microreactors. In common with highly extended porous structures, such as metal-organic frameworks (MOFs), covalent organic frameworks (COFs), and porous organic polymers (POPs), POCs possess all of the advantages of highly specific surface areas, porosities, open pore channels, and tunable structures. In addition, they have discrete molecular structures and exhibit good to excellent solubilities in common solvents, enabling their solution dispersibility and processability─properties that are not readily available in the case of the well-established, insoluble, extended porous frameworks. Here, we present a critical review summarizing in detail recent progress and breakthroughs─especially during the past five years─of all the POCs while taking a close look at their strategic design, precise synthesis, including both irreversible bond-forming chemistry and dynamic covalent chemistry, advanced characterization, and diverse applications. We highlight representative POC examples in an attempt to gain some understanding of their structure-function relationships. We also discuss future challenges and opportunities in the design, synthesis, characterization, and application of POCs. We anticipate that this review will be useful to researchers working in this field when it comes to designing and developing new POCs with desired functions.

Reversible transformations between the non-porous phases of a flexible coordination network enabled by transient porosity

Flexible metal-organic materials that exhibit stimulus-responsive switching between closed (non-porous) and open (porous) structures induced by gas molecules are of potential utility in gas storage and separation. Such behaviour is currently limited to a few dozen physisorbents that typically switch through a breathing mechanism requiring structural contortions. Here we show a clathrate (non-porous) coordination network that undergoes gas-induced switching between multiple non-porous phases through transient porosity, which involves the diffusion of guests between discrete voids through intra-network distortions. This material is synthesized as a clathrate phase with solvent-filled cavities; evacuation affords a single-crystal to single-crystal transformation to a phase with smaller cavities. At 298 K, carbon dioxide, acetylene, ethylene and ethane induce reversible switching between guest-free and gas-loaded clathrate phases. For carbon dioxide and acetylene at cryogenic temperatures, phases showing progressively higher loadings were observed and characterized using in situ X-ray diffraction, and the mechanism of diffusion was computationally elucidated.

Selective and Reversible Solvent Uptake in Tetra-4-(4-pyridyl)phenylmethane-based Supramolecular Organic Frameworks

The dynamic behavior of supramolecular organic frameworks (SOFs) based on the rigid tetra-4-(4-pyridyl)phenylmethane (TPPM) organic tecton has been elucidated through 3D electron diffraction, X-ray powder diffraction and differential scanning calorimetry (DSC) analysis. The SOF undergoes a reversible single-crystal-to-single-crystal transformation when exposed to vapours of selected organic solvents, moving from a closed structure with isolated small voids to an expanded structure with solvated channels along the b axis. The observed selectivity is dictated by the fitting of the guest in the expanded SOF, following the degree of packing coefficient. The effect of solvent uptake on TPPM solid-state fluorescence was investigated, evidencing a significant variation in the emission profile only in the presence of chloroform.

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.

Facile synthesis of covalent organic frameworks functionalized with graphene hydrogel for effectively extracting organophosphorus pesticides from vegetables

A novel covalent organic framework material (3DGA@COFs), for use as a solid-phase dispersion sorbent, has been synthesized for extracting organophosphorus pesticides (OPs) from vegetables. The prepared 3DGA@COFs material exhibited many advantageous features, including a large specific surface area (127.95 m²/g) and high pore volume (0.0344 cm³/g), which made it an ideal sorbent for sample pretreatment. The experimental conditions affecting extraction performance (adsorbent type, adsorbent amount, reaction time, pH, ionic concentration, and eluent) were optimized systematically. The extracted analytes were detected by HPLC-MS/MS. Under optimized conditions, the proposed method exhibited a wide linear range (0.5-100 μg/L) and low limits of detection (0.01-0.14 μg/L). The recoveries (75.40%-102.13%) satisfied the requirements for a precise detection method. The proposed method was successfully used for determining malathion, triazophos, quinalphos in lettuce, tomato and cucumber samples, thus indicating the potential of using 3DGA@COFs materials for pretreating vegetable samples.

Exploring cooperative porosity in organic cage crystals using in situ diffraction and molecular simulations

A porous organic cage crystal, α-CC2, shows unexpected adsorption of sulphur hexafluoride (SF₆) in its cage cavities: analysis of the static crystal structure indicates that SF₆ is occluded, as even the smallest diatomic gas, H₂, is larger than the window of the cage pore. Herein, we use in situ powder X-ray diffraction (PXRD) experiments to provide unequivocal evidence for the presence of SF₆ inside the 'occluded' cage voids, pointing to a mechanism of dynamic flexibility of the system. By combining PXRD results with molecular dynamics simulations, we build a molecular level picture of the cooperative porosity in α-CC2 that facilitates the passage of SF₆ into the cage voids.

An imine linked fluorescent covalent organic cage: the sensing of chloroform vapour and metal ions, and the detection of nitroaromatics

Fluorescent covalent organic cage molecule (F-COC) showed enhanced emission intensity in chloroform solution and polymer matrix film form in presence of chloroform vapours.

Adsorption and sequential thermal release of F2 , Cl2 , and Br2 molecules by a porous organic cage material (CC3-R): Molecular dynamics and grand-canonical Monte Carlo simulations

The adsorption-desorption behavior of fluorine, chlorine, and bromine molecules onto a crystalline porous organic cage, namely CC3-R was calculated at different temperatures using molecular dynamics (MD) and grand-canonical Monte Carlo (GCMC) simulations. Self-diffusion coefficients, radial distribution functions (RDF), and adsorption isotherms were calculated for this purpose. The results show that CC3-R has varied capacities to capture these halogens at ambient and high temperatures, so that the thermal release of fluorine is completed with increasing temperature up to around 70°C and chlorine molecules remain at the CC3-R surface up to 100°C and all bromine molecules are removed from the CC3-R surface at 200°C. We found that bromine self-diffusion was almost independent of temperature between 0 and 100°C in contrast to fluorine and chlorine. Among different diffusion regimes, Knudsen diffusion appears to have an important role in the adsorption of heavy halogens at higher temperatures.

Twist and sliding dynamics between interpenetrated frames in Ti-MOF revealing high proton conductivity

We report the design and synthesis of a titanium catecholate framework, MOF-217, comprised of 2,4,6-tri(3,4-dihydroxyphenyl)-1,3,5-triazine (TDHT) and isolated TiO6 clusters, with 2-fold interpenetrated srs topology. The dynamics of the organic linker, breaking the C 3h symmetry, allowed for reversible twist and sliding between interpenetrated frames upon temperature change and the inclusion of small molecules. Introduction of 28 wt% imidazole into the pores of MOF-217, 28% Im-in-MOF-217, resulted in four orders of magnitude increase in proton conductivity, due to the appropriate accommodation of imidazole molecules and their proton transfer facilitated by the H-bond to the MOF structure across the pores. This MOF-based proton conductor can be operated at 100 °C with a proton conductivity of 1.1 × 10-3 S cm-1, standing among the best performing anhydrous MOF proton conductors at elevated temperature. The interframe dynamics represents a unique feature of MOFs that can be accessed in the future design of proton conductors.

Hysteresis in the gas sorption isotherms of metal–organic cages accompanied by subtle changes in molecular packing

Cooperative gas uptake in metal–organic cages is tuned using supramolecular chemistry.

Understanding the effect of host flexibility on the adsorption of CH4, CO2 and SF6 in porous organic cages

Molecular simulations for gas adsorption in microporous materials with flexible host structures is challenging and, hence, relatively rare. To date, most gas adsorption simulations have been carried out using the grand-canonical Monte Carlo (GCMC) method, which fundamentally does not allow the structural flexibility of the host to be accounted for. As a result, GCMC simulations preclude investigation into the effect of host flexibility on gas adsorption. On the other hand, approaches such as molecular dynamics (MD) that simulate the dynamic evolution of a system almost always require a fixed number of particles in the simulation box. Here we use a hybrid GCMC/MD scheme to include host flexibility in gas adsorption simulations. We study the adsorption of three gases – CH4, CO2 and SF6 – in the crystal of a porous organic cage (POC) molecule, CC3-R, whose structural flexibility is known by experiment to play an important role in adsorption of large guest molecules [L. Chen, P. S. Reiss, S. Y. Chong, D. Holden, K. E. Jelfs, T. Hasell, M. A. Little, A. Kewley, M. E. Briggs, A. Stephenson, K. Mark Thomas, J. A. Armstrong, J. Bell, J. Busto, R. Noel, J. Liu, D. M. Strachan, P. K. Thallapally, A. I. Cooper, Separation of rare gases and chiral molecules by selective binding in porous organic cages. Nat. Mater. 2014, 13, 954, D. Holden, S. Y. Chong, L. Chen, K. E. Jelfs, T. Hasell, A. I. Cooper, Understanding static, dynamic and cooperative porosity in molecular materials. Chem. Sci. 2016, 7, 4875]. The results suggest that hybrid GCMC/MD simulations can reproduce experimental adsorption results, without the need to adjust the host–guest interactions in an ad hoc way. Negligible errors in adsorption capacity and isosteric heat are observed with the rigid-host assumption for small gas molecules such as CH4 and CO2 in CC3-R, but the adsorption capacity of the larger SF6 molecule in CC3-R is hugely underestimated if flexibility is ignored. By contrast, hybrid GCMC/MD adsorption simulations of SF6 in CC3-R can accurately reproduce experiment. This work also provides a molecular level understanding of the cooperative adsorption mechanism of SF6 in the CC3-R molecular crystal.

Eigencages: Learning a Latent Space of Porous Cage Molecules

Porous organic cage molecules harbor nanosized cavities that can selectively adsorb gas molecules, lending them applications in separations and sensing. The geometry of the cavity strongly influences their adsorptive selectivity. For comparing cages and predicting their adsorption properties, we embed/encode a set of 74 porous organic cage molecules into a low-dimensional, latent "cage space" on the basis of their intrinsic porosity. We first computationally scan each cage to generate a three-dimensional (3D) image of its porosity. Leveraging the singular value decomposition, in an unsupervised manner, we then learn across all cages an approximate, lower-dimensional subspace in which the 3D porosity images congregate. The "eigencages" are the set of orthogonal, characteristic 3D porosity images that span this lower-dimensional subspace, ordered in terms of importance. A latent representation/encoding of each cage follows by approximately expressing it as a combination of the eigencages. We show that the learned encoding captures salient features of the cavities of porous cages and is predictive of properties of the cages that arise from cavity shape. Our methods could be applied to learn latent representations of cavities within other classes of porous materials and of shapes of molecules in general.

Computationally-inspired discovery of an unsymmetrical porous organic cage

A completely unsymmetrical porous organic cage was synthesised from a C_2v symmetrical building block that was identified by a computational screen. The cage was formed through a 12-fold imine condensation of a tritopic C_2v symmetric trialdehyde with a ditopic C₂ symmetric diamine in a [4 + 6] reaction. The cage was rigid and microporous, as predicted by the simulations, with an apparent Brunauer-Emmett-Teller surface area of 578 m² g^-1. The reduced symmetry of the tritopic building block relative to its topicity meant there were 36 possible structural isomers of the cage. Experimental characterisation suggests a single isomer with 12 unique imine environments, but techniques such as NMR could not conclusively identify the isomer. Computational structural and electronic analysis of the possible isomers was used to identify the most likely candidates, and hence to construct a 3-dimensional model of the amorphous solid. The rational design of unsymmetrical cages using building blocks with reduced symmetry offers new possibilities in controlling the degree of crystallinity, porosity, and solubility, of self-assembled materials.

An evolutionary algorithm for the discovery of porous organic cages

The chemical and structural space of possible molecular materials is enormous, as they can, in principle, be built from any combination of organic building blocks. Here we have developed an evolutionary algorithm (EA) that can assist in the efficient exploration of chemical space for molecular materials, helping to guide synthesis to materials with promising applications. We demonstrate the utility of our EA to porous organic cages, predicting both promising targets and identifying the chemical features that emerge as important for a cage to be shape persistent or to adopt a particular cavity size. We identify that shape persistent cages require a low percentage of rotatable bonds in their precursors (<20%) and that the higher topicity building block in particular should use double bonds for rigidity. We can use the EA to explore what size ranges for precursors are required for achieving a given pore size in a cage and show that 16 Å pores, which are absent in the literature, should be synthetically achievable. Our EA implementation is adaptable and easily extendable, not only to target specific properties of porous organic cages, such as optimal encapsulants or molecular separation materials, but also to any easily calculable property of other molecular materials.

Oriented Two-Dimensional Porous Organic Cage Crystals

The formation of two-dimensional (2D) oriented porous organic cage crystals (consisting of imine-based tetrahedral molecules) on various substrates (such as silicon wafers and glass) by solution-processing is reported. Insight into the crystallinity, preferred orientation, and cage crystal growth was obtained by experimental and computational techniques. For the first time, structural defects in porous molecular materials were observed directly and the defect concentration could be correlated with crystal growth rate. These oriented crystals suggest potential for future applications, such as solution-processable molecular crystalline 2D membranes for molecular separations.

Computationally-Guided Synthetic Control over Pore Size in Isostructural Porous Organic Cages

The physical properties of 3-D porous solids are defined by their molecular geometry. Hence, precise control of pore size, pore shape, and pore connectivity are needed to tailor them for specific applications. However, for porous molecular crystals, the modification of pore size by adding pore-blocking groups can also affect crystal packing in an unpredictable way. This precludes strategies adopted for isoreticular metal-organic frameworks, where addition of a small group, such as a methyl group, does not affect the basic framework topology. Here, we narrow the pore size of a cage molecule, CC3, in a systematic way by introducing methyl groups into the cage windows. Computational crystal structure prediction was used to anticipate the packing preferences of two homochiral methylated cages, CC14-R and CC15-R, and to assess the structure-energy landscape of a CC15-R/CC3-S cocrystal, designed such that both component cages could be directed to pack with a 3-D, interconnected pore structure. The experimental gas sorption properties of these three cage systems agree well with physical properties predicted by computational energy-structure-function maps.

Constructing two dimensional amide porous polymer to promote selective oxidation reactions

Rare example of carboxamide linked 2D COF has been synthesized and applied as robust organic catalyst for selective oxidation reactions with no metal add-ons. The reaction undergoes free radical mechanism aided by the conjugated π-cloud and amide functionality present in the COF.

Application of computational methods to the design and characterisation of porous molecular materials

Composed from discrete units, porous molecular materials (PMMs) possess properties not observed for conventional, extended solids. Molecular simulations provide crucial understanding for the design and characterisation of these unique materials.

Shape-persistent fluorescent tetraphenylmethane dendrimers

We report the first examples of a new class of rigid dendrimers made of three-dimensional tetraphenylmethane units connected by ethynylene linkers.