Complete Dynamic Reconstruction of C60, C70, and (C59N)2 Encapsulation into an Adaptable Supramolecular Nanocapsule

A Conjugated Phenylene Nanocage with a Guest-Adaptive Deformable Cavity

The highly strained, phenylene-derived organic cages are typically regarded as very rigid entities, yet their deformation potential and supramolecular properties remain underexplored. Herein, we report a pliable conjugated phenylene nanocage by synergistically merging rigid and flexible building blocks. The anisotropic cage molecule contains branched phenylene chains capped by a calix[6]arene moiety, the delicate conformational changes of which endow the cage with a remarkably deformable cavity. When complexing with fullerene guests, the cage showcases excellent guest-adaptivity, with its cavity volume capable of swelling by as much as 85 %.

The use of collective variables and enhanced sampling in the simulations of existing and emerging microporous materials

Microporous materials, including zeolites, metal-organic frameworks, and cage compounds, offer diverse functionalities due to their unique dynamics and guest confinement properties. These materials play a significant role in separation, catalysis, and sensing, but their complexity hinders exploration using traditional atomistic simulations. This review explores collective variables (CVs) paired with enhanced sampling as a powerful approach to enable efficient investigation of key features in microporous materials. We highlight successful applications of CVs in studying adsorption, diffusion, phase transitions, and mechanical properties, demonstrating their crucial role in guiding material design and optimisation. The future of CVs lies in integration with techniques like machine learning, allowing for enhanced efficiency and accuracy. By tailoring CVs to specific materials and developing multi-scale approaches we can further unlock the intricacies of these fascinating materials. Simulations are a cornerstone in unravelling the complexities of microporous materials and are crucial for our future understanding.

Regioswitchable Bingel Bis-Functionalization of Fullerene C70 via Supramolecular Masks

Isomer-pure functionalized fullerenes are required to boost the development of fullerene chemistry in any field, but their multiple functionalization renders a mixture of regioisomers that are very difficult to purify by chromatography. For the specific case of C70, its nonspherical geometry makes its regioselective functionalization more challenging than that of spherical C60. In this work, the supramolecular mask approach is applied for the first time to C70, which is encapsulated in two different nanocapsules to achieve the Bingel bis-cyclopropanation at α-bonds of opposite poles. Based on the tetragonal prismatic geometry imposed by the smaller supramolecular mask tested, the obtained major bis-adduct is completely reversed (major 5 o'clock) compared to bare C70 functionalization (major 2 o'clock). Moreover, by further restricting the accessibility of C70 using a three-shell Matryoshka mask and dibenzyl-bromomalonate, a single regiospecific 2 o'clock bis-isomer is obtained, owing to the perfect complementarity of the mask and the addend steric properties. The outcome of the reactions is fully explained at the molecular level by means of a thorough molecular dynamics (MD) study of the accessibility of the α-bonds to produce the different bis-adducts.

Recent advances in supramolecular fullerene chemistry

Fullerene chemistry has come a long way since 1990, when the first bulk production of C60 was reported. In the past decade, progress in supramolecular chemistry has opened some remarkable and previously unexpected opportunities regarding the selective (multiple) functionalization of fullerenes and their (self)assembly into larger structures and frameworks. The purpose of this review article is to provide a comprehensive overview of these recent developments. We describe how macrocycles and cages that bind strongly to C60 can be used to block undesired addition patterns and thus allow the selective preparation of single-isomer addition products. We also discuss how the emergence of highly shape-persistent macrocycles has opened opportunities for the study of photoactive fullerene dyads and triads as well as the preparation of mechanically interlocked compounds. The preparation of two- or three-dimensional fullerene materials is another research area that has seen remarkable progress over the past few years. Due to the rapidly decreasing price of C60 and C70, we believe that these achievements will translate into all fields where fullerenes have traditionally (third-generation solar cells) and more recently been applied (catalysis, spintronics).

Picking the lock of coordination cage catalysis

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 hosting a guest, pictorially mimicking the action of a substrate binding to the active site of an enzyme. While there are now a growing collection of coordination cages that show highly proficient catalysis, exhibiting both excellent activity and efficient turnover, this number is still small compared to the vast library of metal-organic structures that are known. In this review, we will attempt to unpick and discuss the key features that make an effective coordination cage catalyst, linking structure to activity (and selectivity) using lessons learnt from both experimental and computational analysis of the most notable exemplars. We will also provide an outlook for this area, reasoning why coordination cages have the potential to become the gold-standard in (synthetic) non-covalent catalysis.

Synthesis of C60 /[10]CPP-Catenanes by Regioselective, Nanocapsule-Templated Bingel Bis-Addition

The addition of two unsymmetric malonate esters to the Buckminster fullerene C60 can lead to 22 spectroscopically distinguishable isomeric products and therefore represents a formidable synthesis challenge. In this work, we achieve 87 % selectivity for the formation of a single (in,out-trans-3) isomer by combining three approaches: (i) we use a starting material, in which the two malonates are covalently connected (tether approach); (ii) we form the strong supramolecular complex of C60 with the shape-persistent [10]CPP macrocycle (template approach) and (iii) we embed this complex further within a self-assembled nanocapsule (shadow mask approach). Variation of the spacer chain shed light on the limitations of the approach and the ring dynamics in the unusual [2]catenanes were studied in silico with atomistic resolution. This work significantly widens the scope of mechanically interlocked architectures comprising cycloparaphenylenes (CPP).

Akaike's Information Criterion for Stoichiometry Inference of Supramolecular Complexes

"How do we decide the stoichiometry of host-guest complexes?" This question has long been answered by the Job plot since its first report in 1928. However, as the Job plot was claimed to be misleading in 2016, the question became an open question again and called for renewed investigations. An information-theoretic approach, called Akaike's information criterion, is introduced in this study to select the best model of host-guest complexes, which can rank the models with weight of evidence. A few test cases with unique cylindrical hosts were examined to demonstrate the applicability of the information-theoretic method. Consequently, reasonable views over the thermodynamic behaviors of dumbbell-and-cylinder complexes were obtained. Akaike's information criterion can be a useful and superior alternative to statistical null hypothesis testing, which was proposed as a remedy in place of the Job plot.

An Organic Molecular Nanobarrel that Hosts and Solubilizes C60

Organic cages have gained increasing attention in recent years as molecular hosts and porous materials. Among these, barrel-shaped cages or molecular nanobarrels are promising systems to encapsulate large hosts as they possess windows of the same size as their internal cavity. However, these systems have received little attention and remain practically unexplored despite their potential. Herein, we report the design and synthesis of a new trigonal prismatic organic nanobarrel with two large triangular windows with a diameter of 12.7 Å optimal for the encapsulation of C₆₀ . Remarkably, this organic nanobarrel shows a high affinity for C₆₀ in solvents in which C₆₀ is virtually insoluble, providing stable solutions of C₆₀ .

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.

Supramolecular nanocapsules as two-fold stabilizers of outer-cavity sub-nanometric Ru NPs and inner-cavity ultra-small Ru clusters

The synthesis of metallic nanoparticles (MNP) with high surface area and controlled shape is of paramount importance to increase their catalytic performance. The detailed growing process of NP is mostly unknown and understanding the specific steps would pave the way for a rational synthesis of the desired MNP. Here we take advantage of the stabilization properties exerted by the tetragonal prismatic supramolecular nanocapsule 8·(BArF)₈ to develop a synthetic methodology for sub-nanometric RuNP (0.6-0.7 nm). The catalytic properties of these sub-nanometric nanoparticles were tested on the hydrogenation of styrene, obtaining excellent selectivity for the hydrogenation of the alkene moiety. In addition, the encapsulation of [Ru₅] clusters inside the nanocapsule is strikingly observed in most of the experimental conditions, as ascertained by HR-MS. Moreover, a thorough DFT study enlightens the nature of the [Ru₅] clusters as tb-Ru₅H₂(η⁶-PhH)₂(η⁶-pyz)₃ (2) trapped by two arene moieties of the clip, or as tb-Ru₅H₂(η¹-pyz)₆(η⁶-pyz)₃ (3) trapped between the two Zn-porphyrin units of the nanocapsule. Both options fulfill the Wade-Mingos counting rules, i.e. 72 CVEs for the closotb. The trapped [Ru₅] metallic clusters are proposed to be the first-grown seeds of subsequent formation of the subnanometric RuNP. Moreover, the double role of the nanocapsule in stabilising ∼0.7 nm NPs and also in hosting ultra-small Ru clusters, is unprecedented and may pave the way towards the synthesis of ultra-small metallic clusters for catalytic purposes.

Computational Modeling of Supramolecular Metallo-organic Cages-Challenges and Opportunities

Self-assembled metallo-organic cages have emerged as promising biomimetic platforms that can encapsulate whole substrates akin to an enzyme active site. Extensive experimental work has enabled access to a variety of structures, with a few notable examples showing catalytic behavior. However, computational investigations of metallo-organic cages are scarce, not least due to the challenges associated with their modeling and the lack of accurate and efficient protocols to evaluate these systems. In this review, we discuss key molecular principles governing the design of functional metallo-organic cages, from the assembly of building blocks through binding and catalysis. For each of these processes, computational protocols will be reviewed, considering their inherent strengths and weaknesses. We will demonstrate that while each approach may have its own specific pitfalls, they can be a powerful tool for rationalizing experimental observables and to guide synthetic efforts. To illustrate this point, we present several examples where modeling has helped to elucidate fundamental principles behind molecular recognition and reactivity. We highlight the importance of combining computational and experimental efforts to speed up supramolecular catalyst design while reducing time and resources.

An Adaptable Water-Soluble Molecular Boat for Selective Separation of Phenanthrene from Isomeric Anthracene

Anthracene crude oil is a common source of phenanthrene for its industrial use. The isolation of phenanthrene from this source is a challenging task due to very similar physical properties to its isomer anthracene. We report here a water-soluble Pd(II) molecular boat (MB1) with unusual structural topology that was obtained by assembling a flexible tetrapyridyl donor (L) with a cis-Pd(II) acceptor. The flexible backbone of the boat enabled it to breathe in the presence of a guest optimizing the fit within the cavity. The boat binds phenanthrene more strongly than anthracene, which enabled separation of phenanthrene with an >98% purity from an equimolar mixture of the two isomers using MB1 as an extracting agent. MB1 represents a unique example of a coordination receptor suitable for selective aqueous extraction of phenanthrene from anthracene with reusability of several cycles.

Unlocking the computational design of metal-organic cages

Metal-organic cages are macrocyclic structures that can possess an intrinsic void that can hold molecules for encapsulation, adsorption, sensing, and catalysis applications. As metal-organic cages may be comprised from nearly any combination of organic and metal-containing components, cages can form with diverse shapes and sizes, allowing for tuning toward targeted properties. Therefore, their near-infinite design space is almost impossible to explore through experimentation alone and computational design can play a crucial role in exploring new systems. Although high-throughput computational design and screening workflows have long been known as powerful tools in drug and materials discovery, their application in exploring metal-organic cages is more recent. We show examples of structure prediction and host-guest/catalytic property evaluation of metal-organic cages. These examples are facilitated by advances in methods that handle metal-containing systems with improved accuracy and are the beginning of the development of automated cage design workflows. We finally outline a scope for how high-throughput computational methods can assist and drive experimental decisions as the field pushes toward functional and complex metal-organic cages. In particular, we highlight the importance of considering realistic, flexible systems.

Guest-Driven Self-Assembly and Chiral Induction of Photofunctional Lanthanide Tetrahedral Cages

Chiral luminescent lanthanide-organic cages have many potential applications in enantioselective recognition, sensing, and asymmetric catalysis. However, due to the paucity of structures and their limited cavities, host-guest chemistry with lanthanide-organic cages has remained elusive so far. Herein, we report a guest-driven self-assembly and chiral induction approach for the construction of otherwise inaccessible Ln₄L₄-type (Ln = lanthanide ions, i.e., Eu^III, Tb^III; L = ligand) tetrahedral hosts. Single crystal analyses on a series of host-guest complexes reveal remarkable guest-adaptive cavity breathing on the tetrahedral cages, reflecting the advantage of the variation tolerance on coordination geometry of the f-elements. Meanwhile, noncovalent confinement of pyrene within the lanthanide cage not only leads to diminishment of its excimer emission but also facilitates guest to host energy transfer, opening up a new sensitization window for the lanthanide luminescence on the cage. Moreover, stereoselective self-assembly of either Λ₄- or Δ₄- type Eu₄L₄ cages has been realized via chiral induction with R/S-BINOL or R/S-SPOL templates, as confirmed by NMR, circular dichroism (CD), and circularly polarized luminescence (CPL) with high dissymmetry factors (g_lum) up to ±0.125.

Cooperativity of steric bulk and H-bonding in coordination sphere engineering: heteroleptic PdII cages and bowls by design

Recently developed self-assembly strategies allow to rationally reduce the symmetry of metallosupramolecular architectures. In addition, the combination of multiple ligand types without creating compound mixtures has become possible. Among several approaches to realize non-statistical heteroleptic assembly, Coordination Sphere Engineering (CSE) makes use of secondary repulsive or attractive interactions in direct vicinity of the metal nodes. Previously, we used steric congestion to turn dinuclear [Pd₂L₄] cages with fourfold symmetry into [Pd₂L₃X₂] (X = solvent, halide) bowl structures. Here, we introduce a new subtype of this strategy based on balancing hydrogen bonding and repulsive interactions between ligands carrying quinoline (L^Qu) and 1,8-naphthyridine (L^Na) donors to generate trans-[Pd₂L₂] and [Pd₂L₃L′] cages, assisted by templation of encapsulated fullerenes. Combined with steric congestion caused by acridine (L^Ac) donors, we further report the first example of a heteroleptic [Pd₂L₂L′X₂] bowl. Formation, structure and fullerene binding ability of these metallo-supramolecular hosts were studied by NMR, mass spectrometry and single crystal X-ray diffraction.

Coordination Sphere Engineering (CSE) allows non-statistical assembly of heteroleptic supramolecular architectures by fine adjustment of steric and electronic features around square-planar Pd(ii) cations with naphthyridine donors.

Graphitic supramolecular architectures based on corannulene, fullerene, and beyond

In this Feature Article, we survey the advances made in the field of fulleretic materials over the last five years. Merging the intriguing characteristics of fulleretic molecules with hierarchical materials can lead to enhanced properties of the latter for applications in optoelectronic, biomaterial, and heterogeneous catalysis sectors. As there has been significant growth in the development of fullerene- and corannulene-containing materials, this article will focus on studies performed during the last five years exclusively, and highlight the recent trends in designing fulleretic compounds and understanding their properties, that has enriched the repertoire of carbon-rich functional materials.

Modeling Kinetics and Thermodynamics of Guest Encapsulation into the [M4L6]12- Supramolecular Organometallic Cage

The encapsulation of molecular guests into supramolecular hosts is a complex molecular recognition process in which the guest displaces the solvent from the host cavity, while the host deforms to let the guest in. An atomistic description of the association would provide valuable insights on the physicochemical properties that guide it. This understanding may be used to design novel host assemblies with improved properties (i.e., affinities) toward a given class of guests. Molecular simulations may be conveniently used to model the association processes. It is thus of interest to establish efficient protocols to trace the encapsulation process and to predict the associated magnitudes ΔG_bind and ΔG_bind^⧧. Here, we report the calculation of the Gibbs energy barrier and Gibbs binding energy by means of explicit solvent molecular simulations for the [Ga₄L₆]^12– metallocage encapsulating a series of cationic molecules. The ΔG_bind^⧧ for encapsulation was estimated by means of umbrella sampling simulations. The steps involved were identified, including ion-pair formation and naphthalene rotation (from L ligands of the metallocage) during the guest’s entrance. The ΔG_bind values were computed using the attach–pull–release method. The results reveal the sensitivity of the estimates on the force field parameters, in particular on atomic charges, showing that higher accuracy is obtained when charges are derived from implicit solvent quantum chemical calculations. Correlation analysis identified some indicators for the binding affinity trends. All computed magnitudes are in very good agreement with experimental observations. This work provides, on one side, a benchmarked way to computationally model a highly charged metallocage encapsulation process. This includes a nonstandard parameterization and charge derivation procedure. On the other hand, it gives specific mechanistic information on the binding processes of [Ga₄L₆]^12– at the molecular level where key motions are depicted. Taken together, the study provides an interesting option for the future design of metal–organic cages.

First Synthesis of the Inherently Chiral Trans-4' Bisadduct of C59 N Azafullerene by Using Cyclo-[2]-dodecylmalonate as a Tether

The multiaddition chemistry of azafullerene C₅₉ N has been scarcely explored, and the isolation of pure bisadducts is in its infancy. Encouraged by the recent regioselective synthesis of the inherently chiral equatorial_face bisadduct of C₅₉ N, we focused on the isolation of the first trans-4 bisadduct in a simple two-step approach. The first regioselective synthesis of the trans-4 bisadduct of C₅₉ N by using cyclo-[2]-dodecylmalonate as a tether is now reported. The newly synthesized bisadduct has C₁ symmetry, as evidenced by ¹³ C NMR, while X-ray crystallography validated the trans-4' addition pattern. Furthermore, the inherently chiral trans-4' C₅₉ N bisadduct was enantiomerically resolved, and the mirror-image relation of the two enantiomers was probed by circular dichroism spectroscopy. Finally, UV-Vis and redox assays suggested that the addition pattern has a reflection in the light-harvesting and redox properties of the bisadduct.

Structural Flexibility in Metal-Organic Cages

Metal-organic cages (MOCs) have emerged as a diverse class of molecular hosts with potential utility across a vast spectrum of applications. With advances in single-crystal X-ray diffraction and economic methods of computational structure optimisation, cavity sizes can be readily determined. In combination with a chemist's intuition, educated guesses about the likelihood of particular guests being bound within these porous structures can be made. Whilst practically very useful, simple rules-of-thumb, such as Rebek's 55% rule, fail to take into account structural flexibility inherent to MOCs that can allow hosts to significantly adapt their internal cavity. An often unappreciated facet of MOC structures is that, even though relatively rigid building blocks may be employed, conformational freedom can enable large structural changes. If it could be exploited, this flexibility might lead to behavior analogous to the induced-fit of substrates within the active sites of enzymes. To this end, in-roads have already been made to prepare MOCs incorporating ligands with large degrees of conformational freedom. Whilst this may make the constitution of MOCs harder to predict, it has the potential to lead to highly sophisticated and functional synthetic hosts.

Comprehensive Characterization of the Self-Folding Cavitand Dynamics

The conformational equilibria and guest exchange process of a resorcin[4]arene derived self-folding cavitand receptor have been characterized in detail by molecular dynamics simulations (MD) and ¹ H EXSY NMR experiments. A multi-timescale strategy for exploring the fluxional behaviour of this system has been constructed, exploiting conventional MD and accelerated MD (aMD) techniques. The use of aMD allows the reconstruction of the folding/unfolding process of the receptor by sampling high-energy barrier processes unattainable by conventional MD simulations. We obtained MD trajectories sampling events occurring at different timescales from ns to s: 1) rearrangement of the directional hydrogen bond seam stabilizing the receptor, 2) folding/unfolding of the structure transiting partially open intermediates, and 3) guest departure from different folding stages. Most remarkably, reweighing of the biased aMD simulations provided kinetic barriers that are in very good agreement with those determined experimentally by ¹ H NMR. These results constitute the first comprehensive characterization of the complex dynamic features of cavitand receptors. Our approach emerges as a valuable rational design tool for synthetic host-guest systems.

A Self-Assembled Palladium(II) Barrel for Binding of Fullerenes and Photosensitization Ability of the Fullerene-Encapsulated Barrel

Fullerene extracts obtained from fullerene soot lack their real application due to their poor solubility in common solvents and difficulty in purification. Encapsulation of these extracts in a suitable host is an important approach to address these issues. We present a new Pd₆ barrel (1), which is composed of three 1,4-dihydropyrrolo[3,2-b]pyrrole panels, clipped through six cis-Pd^II acceptors. Large open windows and cavity make it an efficient host for a large guest. Favorable interactions between the ligand and fullerene (C₆₀ and C₇₀ ) allows the barrel to encapsulate fullerene efficiently. Thorough investigation reveals that barrel 1 has a stronger binding affinity towards C₇₀ over C₆₀ , resulting in the predominant extraction of C₇₀ from a mixture of the two. Finally, the fullerene encapsulated barrels C₆₀ ⊂1 and C₇₀ ⊂1 were found to be efficient for visible-light-induced singlet oxygen generation. Such preferential binding of C₇₀ and photosensitizing ability of C₆₀ ⊂1 and C₇₀ ⊂1 are noteworthy.

A three-shell supramolecular complex enables the symmetry-mismatched chemo- and regioselective bis-functionalization of C60

Molecular Russian dolls (matryoshkas) have proven useful for testing the limits of preparative supramolecular chemistry but applications of these architectures to problems in other fields are elusive. Here we report a three-shell, matryoshka-like complex-in which C₆₀ sits inside a cycloparaphenylene nanohoop, which in turn is encapsulated inside a self-assembled nanocapsule-that can be used to address a long-standing challenge in fullerene chemistry, namely the selective formation of a particular fullerene bis-adduct. Spectroscopic evidence indicates that the ternary complex is sufficiently stable in solution for the two outer shells to affect the addition chemistry of the fullerene guest. When the complex is subjected to Bingel cyclopropanation conditions, the exclusive formation of a single trans-3 fullerene bis-adduct was observed in a reaction that typically yields more than a dozen products. The selectivity facilitated by this matryoshka-like approach appears to be a general phenomenon and could be useful for applications where regioisomerically pure C₆₀ bis-adducts have been shown to have superior properties compared with isomer mixtures.

Rationalization of chirality transfer and fast conformational changes in a tris(2-pyridylmethyl)amine-based cage

The key features that govern the chirality transfer in a structurally contracted covalent cage, consisting of a northern chiral cyclotriveratrylene (CTV) connected to a southern tris(2-pyridyl-methyl)amine (TPA) unit by three methyl bridges, are described. The preferential orientation of the propeller arrangement of TPA is dictated by its compact structure, with an arm of the TPA unit pointing inside the cage, together with the relative positioning of the three pyridines regarding the chiral CTV cap. The diastereomers with P/P (or M/M) configurations for the CTV and TPA units adopt eclipsed structures and were found to be more stable by 40 kJ mol-1 than the P/M (or M/P) diastereomer which displays a staggered arrangement. The existence of isomerization pathways between isomers of the cage with low energy barriers (38 kJ mol-1) accounts for the 1H-NMR signal, which is consistent with an averaged C 3 structure.

Effective Encapsulation of C60 by Metal-Organic Frameworks with Polyamide Macrocyclic Linkers

A flexible benzylic amide macrocycle, functionalized with two carboxylic acid groups, was employed as the organic ligand for the preparation of robust copper(II)- and zinc(II)-based metal-organic frameworks. These polymers crystallized in the C2/m space group of the monoclinic crystal system, creating non-interpenetrated channels in one direction with an extraordinary solvent-accessible volume of 46 %. Unlike metal-organic rotaxane frameworks having benzylic amide macrocycles as linkers, the absence of the thread in these novel reticular materials causes a decrease of dimensionality and an improvement of pore size and dynamic guest adaptability. We studied the incorporation of fullerene C₆₀ inside the adjustable pocket generated between two macrocycles connected to the same dinuclear clusters, occupying a remarkable 98 % of the cavities inside the network. The use of these materials as hosts for the selective recognition of different fullerenes was evaluated, mainly encapsulating the smaller size fullerene derivative in several mixtures of C₆₀ and C₇₀ .

Straightforward supramolecular purification of C84 from a fullerene extract

An efficient, one-step protocol for the enrichment of C₈₄ (up to 86%) directly from a fullerene extract is reported, by utilizing a tetragonal prismatic nanocapsule with a suitable size and shape for selective encapsulation.