Unlocking the computational design of metal-organic cages

Cage-Based Metal-Organic Framework Featuring a Double-Yolk Core-Shell U6L3@U18L14 Structure for Iodine Capture

Cage-based MOFs, with their customizable chemical environments and precisely controllable nanospaces, show great potential for the selective adsorption of guest molecules with specific structures. In this work, we have constructed a novel cage-based MOF [(CH3)2NH2]2[(UO2)2(TMTTA)]·11.5DMF·2H2O (IHEP-51), utilizing a triazine derivative poly(carboxylic acid), 4,4',4″-(((1,3,5-triazine-2,4,6-triyl)tris(((4-carboxycyclohexyl)methyl)azanediyl))tris(methylene))tribenzoic acid (H6TMTTA), as an organic ligand and uranyl as a metal node. The 2-fold interpenetrated (3,6,6)-connected framework of IHEP-51 features two types of supramolecular cage structures: the Pyrgos[2]cage U6L3 and the huge cage U18L14. They are further assembled into a double-yolk core-shell U6L3@U18L14 structure, making it suitable for I2 capture. The maximum adsorption capacities of IHEP-51 for iodine in solution and gaseous iodine are 420.4 and 1561.2 mg·g-1, respectively. XPS, Raman spectra, single-crystal X-ray diffraction, and DFT calculations reveal that the adsorbed iodine is located inside the U6L3 Pyrgos[2]cage in the form of I3-, thus resulting in the formation of a (I3)2@U6L3@U18L14 ternary core-shell structure.

Topological control in paddlewheel metal-organic cages via ligand length variation

Varying the length of phenanthrene-derived ligands switches the selective assembly of MIInLn metal-organic cages (MOCs, n = 6 or 8) between tetrahedral, square, or triangular architectures. The limit of this approach is explored for both Cu2 and Rh2 paddlewheel MOCs, and supported by solution, solid-state and computational analysis.

Supramolecular and molecular capsules, cages and containers

Stemming from early seminal notions of molecular recognition and encapsulation, three-dimensional, cavity-containing capsular compounds and assemblies have attracted intense interest due to the ability to modulate chemical and physical properties of species encapsulated within these confined spaces compared to bulk environments. With such a diverse range of covalent motifs and non-covalent (supramolecular) interactions available to assemble building blocks, an incredibly wide-range of capsular-type architectures have been developed. Furthermore, synthetic tunability of the internal environments gives chemists the opportunity to engineer systems for uses in sensing, sequestration, catalysis and transport of molecules, just to name a few. In this tutorial review, an overview is provided into the design principles, synthesis, characterisation, structural facets and properties of coordination cages, porous organic cages, supramolecular capsules, foldamers and mechanically interlocked molecules. Using seminal and recent examples, the advantages and limitations of each system are explored, highlighting their application in various tasks and functions.

A Combined Experimental and Computational Exploration of Heteroleptic cis-Pd2L2L'2 Coordination Cages through Geometric Complementarity

Heteroleptic (mixed-ligand) coordination cages are of interest as host systems with more structurally and functionally complex cavities than homoleptic architectures. The design of heteroleptic cages, however, is far from trivial. In this work, we experimentally probed the self-assembly of Pd(II) ions with binary ligand combinations in a combinatorial fashion to search for new cis-Pd2L2L'2 heteroleptic cages. A hierarchy of computational analyses was then applied to these systems with the aim of elucidating key factors for rationalising self-assembly outcomes. Simple and inexpensive geometric analyses were shown to be effective in identifying complementary ligand pairs. Preliminary results demonstrated the viability of relatively rapid semi-empirical calculations for predicting the topology of thermodynamically favoured assemblies with rigid ligands, whilst more flexible systems proved challenging. Stemming from this, key challenges were identified for future work developing effective computational forecasting tools for self-assembled metallo-supramolecular systems.

Metallicious: Automated Force-Field Parameterization of Covalently Bound Metals for Supramolecular Structures

Metal ions play a central, functional, and structural role in many molecular structures, from small catalysts to metal-organic frameworks (MOFs) and proteins. Computational studies of these systems typically employ classical or quantum mechanical approaches or a combination of both. Among classical models, only the covalent metal model reproduces both geometries and charge transfer effects but requires time-consuming parameterization, especially for supramolecular systems containing repetitive units. To streamline this process, we introduce metallicious, a Python tool designed for efficient force-field parameterization of supramolecular structures. Metallicious has been tested on diverse systems including supramolecular cages, knots, and MOFs. Our benchmarks demonstrate that parameters accurately reproduce the reference properties obtained from quantum calculations and crystal structures. Molecular dynamics simulations of the generated structures consistently yield stable simulations in explicit solvent, in contrast to similar simulations performed with nonbonded and cationic dummy models. Overall, metallicious facilitates the atomistic modeling of supramolecular systems, key for understanding their dynamic properties and host-guest interactions. The tool is freely available on GitHub (https://github.com/duartegroup/metallicious).

Structural Transformations of Metal-Organic Cages through Tetrazine-Alkene Reactivity

The assembly of metal-organic cages is governed by metal ion coordination preferences and the geometries of the typically rigid and planar precursor ligands. PdnL2n cages are among the most structurally diverse, with subtle differences in the metal-ligand coordination vectors resulting in drastically different assemblies, however almost all rely on rigid aromatic linkers to avoid the formation of intractable mixtures. Here we exploit the inverse electron-demand Diels-Alder (IEDDA) reaction between tetrazine linker groups and alkene reagents to trigger structural changes induced by post-assembly modification. The structure of the 1,4-dihydropyridazine produced by IEDDA (often an afterthought in click chemistry) is crucial; its two sp3 centers increase flexibility and nonplanarity, drastically changing the range of accessible coordination vectors. This triggers an initial Pd4L8 tetrahedral cage to transform into different Pd2L4 lantern cages, with both the transformation extent (thermodynamics) and rate (kinetics) dependent on the alkene dienophile selected. With cyclopentene, the unsymmetrical 1,4-dihydropyridazine ligands undergo integrative sorting in the solid state, with both head-to-tail orientation and enantiomer selection, leading to a single isomer from the 39 possible. This preference is rationalized through entropy, symmetry, and hydrogen bonding. Subsequent oxidation of the 1,4-dihydropyridazine to the aromatic pyridazine rigidifies the ligands, restoring planarity. The oxidized ligands no longer fit in the lantern structure, inducing further structural transformations into Pd4L8 tetrahedra and Pd3L6 double-walled triangles. The concept of controllable addition of limited additional flexibility and then its removal through well-defined reactivity we envisage being of great interest for structural transformations of any class of supramolecular architecture.

Design and Synthesis of Red-Absorbing Fluoran Leuco Dyes Supported by Computational Screening

We report here on the design and synthesis of red-absorbing fluoran leuco dyes (LD). An essential part of the present dye development process is a computational screening of the candidate molecules, which allows for both time-efficient and accurate in silico characterization of the dyes. We focus our study here on the robust benzo[a]fluoran scaffold frequently used in leuco dyes. For the computational screening of LD candidates, an automated DFT-based simulation protocol has been developed and applied. The protocol consists of a combinatorial generation of the molecular structures of possible LD candidates, followed by simulations of their optimized molecular geometries, with their UV-Vis spectra as the main figure of merit. In the present application of the simulation protocol, more than 1600 structures of possible LD candidates have been evaluated. Finally, two structures, LD01 and LD02, have been chosen from the list of the best computed LD candidates to be synthesized and characterized. Our study demonstrates how the synergy between experiment and simulation can facilitate the design of novel leuco dyes.

Computational Screening of Putative Catalyst Transition Metal Complexes as Guests in a Ga4L612- Nanocage

Metal-organic cages form well-defined microenvironments that can enhance the catalytic proficiency of encapsulated transition metal complexes (TMCs). We introduce a screening protocol to efficiently identify TMCs that are promising candidates for encapsulation in the Ga4L612- nanocage. We obtain TMCs from the Cambridge Structural Database with geometric and electronic characteristics amenable to encapsulation and mine the text of associated manuscripts to curate TMCs with documented catalytic functionality. By docking candidate TMCs inside the nanocage cavity and carrying out electronic structure calculations, we identify a subset of successfully optimized candidates (TMC-34) and observe that encapsulated guests occupy an average of 60% of the cavity volume, in line with previous observations. Notably, some guests occupy as much as 72% of the cavity as a result of linker rotation. Encapsulation has a universal effect on the electrostatic potential (ESP), systematically decreasing the ESP at the metal center of each TMC in the TMC-34 data set, while minimally altering TMC metal partial charges. Collectively these observations support geometry-based screening of potential guests and suggest that encapsulation in Ga4L612- cages could electrostatically stabilize diverse cationic or electropositive intermediates. We highlight candidate guests with associated known reactivity and solubility most amenable for encapsulation in experimental follow-up studies.

A pair of conjoined trinuclear sub-frameworks in a pentanuclear double-cavity discrete coordination cage

Combination of Pd(ii) with selected bis-monodentate ligands produces the familiar multinuclear Pd m L2m type self-assembled "single-cavity discrete coordination cages" (SCDCC). If the ligand provides parallel coordination vectors, then it forms a binuclear Pd2L4 type cage, whereas utilization of ligands having appropriately divergent coordination vectors results in specific higher nuclear complexes. In contrast, preparation of emergent "multi-cavity discrete coordination cages" (MCDCC) using Pd(ii) and designer ligands is quite captivating where the neighboring cavities of the framework are conjoined with each other through a common metal center. A pair of conjoined binuclear Pd2L4 type sub-frameworks are present in a trinuclear Pd3L4 type double-cavity cage prepared from Pd(ii) and a tris-monodentate ligand having parallel coordination vectors. The present work envisioned a design to make double-cavity coordination cages having a pair of conjoined trinuclear Pd3L6 type sub-frameworks. To fulfill the objective we combined Pd(ii) with a mixture of designer bis-monodentate ligand (L) and tris-monodentate ligand (L') in a 5 : 4 : 4 ratio in one pot to afford the targeted pentanuclear type cage. The choice of bis-monodentate ligand L is based on the divergent nature of the coordination vectors suitable to produce a Pd3L6 type SCDCC. The tris-monodentate ligand L' having two arms is designed in such a manner that each of the arms reasonably resembles L. Study of the complexation behavior of Pd(ii) with L' provided additional guiding factors essential for the successful making of type MCDCC by integrative self-sorting. A few other MCDCC including lower symmetry versions were also prepared in the course of the work.

Encapsulation engineering of porous crystalline frameworks for delayed luminescence and circularly polarized luminescence

Delayed luminescence (DF), including phosphorescence and thermally activated delayed fluorescence (TADF), and circularly polarized luminescence (CPL) exhibit common and broad application prospects in optoelectronic displays, biological imaging, and encryption. Thus, the combination of delayed luminescence and circularly polarized luminescence is attracting increasing attention. The encapsulation of guest emitters in various host matrices to form host-guest systems has been demonstrated to be an appealing strategy to further enhance and/or modulate their delayed luminescence and circularly polarized luminescence. Compared with conventional liquid crystals, polymers, and supramolecular matrices, porous crystalline frameworks (PCFs) including metal-organic frameworks (MOFs), covalent-organic frameworks (COFs), zeolites and hydrogen-bonded organic frameworks (HOFs) can not only overcome shortcomings such as flexibility and disorder but also achieve the ordered encapsulation of guests and long-term stability of chiral structures, providing new promising host platforms for the development of DF and CPL. In this review, we provide a comprehensive and critical summary of the recent progress in host-guest photochemistry via the encapsulation engineering of guest emitters in PCFs, particularly focusing on delayed luminescence and circularly polarized luminescence. Initially, the general principle of phosphorescence, TADF and CPL, the combination of DF and CPL, and energy transfer processes between host and guests are introduced. Subsequently, we comprehensively discuss the critical factors affecting the encapsulation engineering of guest emitters in PCFs, such as pore structures, the confinement effect, charge and energy transfer between the host and guest, conformational dynamics, and aggregation model of guest emitters. Thereafter, we summarize the effective methods for the preparation of host-guest systems, especially single-crystal-to-single-crystal (SC-SC) transformation and epitaxial growth, which are distinct from conventional methods based on amorphous materials. Then, the recent advancements in host-guest systems based on PCFs for delayed luminescence and circularly polarized luminescence are highlighted. Finally, we present our personal insights into the challenges and future opportunities in this promising field.

Water-Soluble Molecular Cages for Biological Applications

The field of molecular cages has attracted increasing interest in relation to the development of biological applications, as evidenced by the remarkable examples published in recent years. Two key factors have contributed to this achievement: First, the remarkable and adjustable host-guest chemical properties of molecular cages make them highly suitable for biological applications. This allows encapsulating therapeutic molecules to improve their properties. Second, significant advances have been made in synthetic methods to create water-soluble molecular cages. Achieving the necessary water solubility is a significant challenge, which in most cases requires specific chemical groups to overcome the inherent hydrophobic nature of the molecular cages which feature the organic components of the cage. This can be achieved by either incorporating water-solubilizing groups with negative/positive charges, polyethylene glycol chains, etc.; or by introducing charges directly into the cage structure itself. These synthetic strategies allow preparing water-soluble molecular cages for diverse biological applications, including cages' anticancer activity, anticancer drug delivery, photodynamic therapy, and molecular recognition of biological molecules. In the review we describe selected examples that show the main concepts to achieve water solubility in molecular cages and some selected recent biological applications.

MACE: Automated Assessment of Stereochemistry of Transition Metal Complexes and Its Applications in Computational Catalysis

Computational chemistry pipelines typically commence with geometry generation, well-established for organic compounds but presenting a considerable challenge for transition metal complexes. This paper introduces MACE, an automated computational workflow for converting chemist SMILES/MOL representations of the ligands and the metal center to 3D coordinates for all feasible stereochemical configurations for mononuclear octahedral and square planar complexes directly suitable for quantum chemical computations and implementation in high-throughput computational chemistry workflows. The workflow is validated through a structural screening of a data set of transition metal complexes extracted from the Cambridge Structural Database. To further illustrate the power and capabilities of MACE, we present the results of a model DFT study on the hemilability of pincer ligands in Ru, Fe, and Mn complexes, which highlights the utility of the workflow for both focused mechanistic studies and larger-scale high-throughput pipelines.

Systematic exploration of accessible topologies of cage molecules via minimalistic models

Cages are macrocyclic structures with an intrinsic internal cavity that support applications in separations, sensing and catalysis. These materials can be synthesised via self-assembly of organic or metal-organic building blocks. Their bottom-up synthesis and the diversity in building block chemistry allows for fine-tuning of their shape and properties towards a target property. However, it is not straightforward to predict the outcome of self-assembly, and, thus, the structures that are practically accessible during synthesis. Indeed, such a prediction becomes more difficult as problems related to the flexibility of the building blocks or increased combinatorics lead to a higher level of complexity and increased computational costs. Molecular models, and their coarse-graining into simplified representations, may be very useful to this end. Here, we develop a minimalistic toy model of cage-like molecules to explore the stable space of different cage topologies based on a few fundamental geometric building block parameters. Our results capture, despite the simplifications of the model, known geometrical design rules in synthetic cage molecules and uncover the role of building block coordination number and flexibility on the stability of cage topologies. This leads to a large-scale and systematic exploration of design principles, generating data that we expect could be analysed through expandable approaches towards the rational design of self-assembled porous architectures.

Dynamics of organophosphate guest encapsulation in heteroleptic coordination cages

Heteroleptic coordination cages allow the design of different host structures that can bind guest molecules within their cavities. In a previous work, the energetics of organophosphate encapsulation in palladium(II)-based heteroleptic coordination cages that differ in terms of their ability to form hydrogen bonds have been investigated [Platzek et al., Endohedrally Functionalized Heteroleptic Coordination Cages for Phosphate Ester Binding, Angew. Chem., Int. Ed. 2022, 61, e2022093]. The present work focuses on the dynamics of this system. Dynamic information is obtained through the application of a Markov state model (MSM) to unbiased multi-microsecond atomistic molecular dynamics simulations of guest binding and release. The MSM reveals that both the bound state and the binding/unbinding pathways are highly dynamic, with different types of interactions mediating the binding of the diphenylphosphate guest. Thus, the simulations highlight the dynamic nature of the nanoconfinement in the host-guest systems, with possible implications for the use of such coordination cages as catalysts.

Guest Encapsulation Alters the Thermodynamic Landscape of a Coordination Host

The architecture of self-assembled host molecules can profoundly affect the properties of the encapsulated guests. For example, a rigid cage with small windows can efficiently protect its contents from the environment; in contrast, tube-shaped, flexible hosts with large openings and an easily accessible cavity are ideally suited for catalysis. Here, we report a "Janus" nature of a Pd6L4 coordination host previously reported to exist exclusively as a tube isomer (T). We show that upon encapsulating various tetrahedrally shaped guests, T can reconfigure into a cage-shaped host (C) in quantitative yield. Extracting the guest affords empty C, which is metastable and spontaneously relaxes to T, and the T⇄C interconversion can be repeated for multiple cycles. Reversible toggling between two vastly different isomers paves the way toward controlling functional properties of coordination hosts "on demand".

Dynamic Cages-Towards Nanostructured Smart Materials

The interest in capsular assemblies such as dynamic organic and coordination cages has blossomed over the last decade. Given their chemical and structural variability, these systems have found applications in diverse fields of research, including energy conversion and storage, catalysis, separation, molecular recognition, and live-cell imaging. In the exploration of the potential of these discrete architectures, they are increasingly being employed in the formation of more complex systems and smart materials. This Review highlights the most promising pathways to overcome common drawbacks of cage systems (stability, recovery) and discusses the most promising strategies for their hybridization with systems featuring various dimensionalities. Following the description of the most recent advances in the fabrication of zero to three-dimensional cage-based systems, this Review will provide the reader with the structure-dependent relationship between the employed cages and the properties of the materials.

Theoretical and computational methodologies for understanding coordination self-assembly complexes

This perspective highlights three theoretical and computational methods to capture the coordination self-assembly processes at the molecular level: quantum chemical modeling, molecular dynamics, and reaction network analysis. These methods cover the different scales from the metal-ligand bond to a more global aspect, and approaches that are best suited to understand the coordination self-assembly from different perspectives are introduced. Theoretical and numerical researches based on these methods are not merely ways of interpreting the experimental studies but complementary to them.

Role of Counterions in the Structural Stabilisation of Redox-Active Metal-Organic Frameworks

The crystal structures of metal-organic frameworks (MOFs) are typically determined by the strong chemical bonds formed between the organic and inorganic building units. However, the latest generation of redox-active frameworks often rely on counterions in the pores to access specific charge states of the components. Here, we model the crystal structures of three layered MOFs based on the redox-active ligand 2,5-dihydroxybenzoquinone (dhbq): Ti2 (Cl2 dhbq)3 , V2 (Cl2 dhbq)3 and Fe2 (Cl2 dhbq)3 with implicit and explicit counterions. Our full-potential first-principles calculations indicate that while the reported hexagonal structure is readily obtained for Ti and V, the Fe framework is stabilised only by the presence of explicit counterions. For high counterion concentrations, we observe the formation of an electride-like pocket in the pore center. An outlook is provided on the implications of solvent and counterion control for engineering the structures and properties of porous solids.

Enantioselective fullerene functionalization through stereochemical information transfer from a self-assembled cage

The regioselective functionalization of C₆₀ remains challenging, while the enantioselective functionalization of C₆₀ is difficult to explore due to the need for complex chiral tethers or arduous chromatography. Metal-organic cages have served as masks to effect the regioselective functionalization of C₆₀. However, it is difficult to control the stereochemistry of the resulting fullerene adducts through this method. Here we report a means of defining up to six stereocentres on C₆₀, achieving enantioselective fullerene functionalization. This method involves the use of a metal-organic cage built from a chiral formylpyridine. Fullerenes hosted within the cavity of the cage can be converted into a series of C₆₀ adducts through chemo-, regio- and stereo-selective Diels-Alder reactions with the edges of the cage. The chiral formylpyridine ultimately dictates the stereochemistry of these chiral fullerene adducts without being incorporated into them. Such chiral fullerene adducts may become useful in devices requiring circularly polarized light manipulation.

Computational modeling to assist in the discovery of supramolecular materials

Computational modeling is increasingly used to assist in the discovery of supramolecular materials. Supramolecular materials are typically primarily built from organic components that are self-assembled through noncovalent bonding and have potential applications, including in selective binding, sorption, molecular separations, catalysis, optoelectronics, sensing, and as molecular machines. In this review, the key areas where computational prediction can assist in the discovery of supramolecular materials, including in structure prediction, property prediction, and the prediction of how to synthesize a hypothetical material are discussed, before exploring the potential impact of artificial intelligence techniques on the field. Throughout, the importance of close integration with experimental materials discovery programs will be highlighted. A series of case studies from the author's work across some different supramolecular material classes will be discussed, before finishing with a discussion of the outlook for the field.

Catalysis by [Ga4 L6 ]12- Metallocage on the Nazarov Cyclization: The Basicity of Complexed Alcohol is Key

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.

Helicate versus Mesocate in Quadruple-Stranded Lanthanide Cages: A Computational Insight

To drive the synthesis of metallo-supramolecular assemblies (MSAs) and to fully exploit their functional properties, robust computational tools are crucial. The capability to model and to rationalize different parameters that can influence the outcome is mandatory. Here, we report a computational insight on the factors that can determine the relative stability of the supramolecular isomers helicate and mesocate in lanthanide-based quadruple-stranded assemblies. The considered MSAs have the general formula [Ln₂L₄]²⁻ and possess a cavity suitable to allocate guests. The analysis was focused on three different factors: the ligand rigidity and the steric hindrance, the presence of a guest inside the cavity, and the guest dimension. Three different quantum mechanical calculation set-ups (in vacuum, with the solvent, and with the solvent and the dispersion correction) were considered. Comparison between theoretical and experimental outcomes suggests that all calculations correctly estimated the most stable isomer, while the inclusion of the dispersion correction is mandatory to reproduce the geometrical parameters. General guidelines can be drawn: less rigid and less bulky is the ligand and less stable is the helicate, and the presence of a guest can strongly affect the isomerism leading to an inversion of the stability by increasing the guest size when the ligand is flexible.

Advances in the Structural Strategies of the Self-Assembly of Photoresponsive Supramolecular Systems

Photosensitive supramolecular systems have garnered attention due to their potential to catalyze highly specific tasks through structural changes triggered by a light stimulus. The tunability of their chemical structure and charge transfer properties provides opportunities for designing and developing smart materials for multidisciplinary applications. This review focuses on the approaches reported in the literature for tailoring properties of the photosensitive supramolecular systems, including MOFs, MOPs, and HOFs. We discuss relevant aspects regarding their chemical structure, action mechanisms, design principles, applications, and future perspectives.

Assembling metal-organic cages as porous materials

There is growing interest in metal-organic cages (MOCs) as porous materials owing to their processability in solution. The discrete molecular character and surface features of MOCs have a direct impact on the interactions between cages, enabling the final physical state of the materials to be tuned. In this tutorial review, we discuss how to use MOCs as core building units, highlighting the role played by surface functionalisation of MOCs in leading to porous materials in a range of states covering crystalline solids, soft matter, liquids and composites. We finish by providing an outlook on the opportunities for this work to serve as a foundation for the development of increasingly complex functional porous materials structured over various length scales.