Host Cage Research Articles

Water Molecules Confined in Cryptophane Nanocages: Structures and Dynamics Driven by Hydrogen Bonding and Water Chains.

Cryptophanes (Crs) are roughly spherical organic nanocages used as vehicles for hosting xenon atoms in 129Xe NMR biosensor (XBS) structures. Crs also bind other guests, importantly water, which is abundant in biological systems. In other host cages, it has been found that the release of "high-energy" water from confinement constitutes an important contribution to the binding affinity of nonwater guests. Despite that, the role of water has received little attention in the XBS field. Based on molecular dynamics simulations in explicit water solvent, we here study the properties of confined water in three different CrA cages that have an identical interior but are functionalized with 0, 3, or 6 water solubility-enhancing, hydrophilic CH2COOH moieties. The number of the solubility groups is found to be a decisive factor for the structures and dynamics of the confined water. Formation of stable water-molecule chains is predicted within the cage with six hydrophilic groups, starting with the anchoring of one water molecule at the portal between the cage and the bulk solution. We find that the experimentally measured differences in the Xe-binding affinities of the cages can be related to the average number of hydrogen bonds per confined water molecule. The rotational dynamics of the confined water is significantly slower than that in the bulk, suggesting NMR relaxation measurements to study the intracavity water. The present findings reveal new details about the microscopic cryptophane-H2O host-guest chemistry, which will become important in the design of improved XBS devices.

Endohedral metallofullerene molecular nanomagnets.

Magnetic lanthanide (Ln) metal complexes exhibiting magnetic bistability can behave as molecular nanomagnets, also known as single-molecule magnets (SMMs), suitable for storing magnetic information at the molecular level, thus attracting extensive interest in the quest for high-density information storage and quantum information technologies. Upon encapsulating Ln ion(s) into fullerene cages, endohedral metallofullerenes (EMFs) have been proven as a promising and versatile platform to realize chemically robust SMMs, in which the magnetic properties are able to be readily tailored by altering the configurations of the encapsulated species and the host cages. In this review, we present critical discussions on the molecular structures and magnetic characterizations of EMF-SMMs, with the focus on their peculiar molecular and electronic structures and on the intriguing molecular magnetism arising from such structural uniqueness. In this context, different families of magnetic EMFs are summarized, including mononuclear EMF-SMMs wherein single-ion anisotropy is decisive, dinuclear clusterfullerenes whose magnetism is governed by intramolecular magnetic interaction, and radical-bridged dimetallic EMFs with high-spin ground states that arise from the strong ferromagnetic coupling. We then discuss how molecular assemblies of SMMs can be constructed, in a way that the original SMM behavior is either retained or altered in a controlled manner, thanks to the chemical robustness of EMFs. Finally, on the basis of understanding the structure-magnetic property correlation, we propose design strategies for high-performance EMF-SMMs by engineering ligand fields, electronic structures, magnetic interactions, and molecular vibrations that can couple to the spin states.

Coordination-cage binding and catalysed hydrolysis of organophosphorus chemical warfare agent simulants.

The use of organophosphorus chemical warfare agents still remains an ongoing global threat. Here we investigate the binding of small-molecule organic guests including phosphate esters, sulfonate esters, carbonate esters and a sulfite ester - some of which act as simulants for organophosphorus chemical warfare agents - in the cavity of a water-soluble coordination cage. For several of these guest species, binding constants in the range 102 to 103 M-1 were determined in water/DMSO (98 : 2 v/v) solution, through a combination of fluorescence and 1H NMR spectroscopy, and subsequent fitting of titration data to a 1 : 1 binding isotherm model. For three cage/guest complexes crystallographic structure determinations were possible: in two cases (with guests phenyl methanesulfonate and phenyl propyl carbonate) the guest lies inside the cavity, forming a range of CH⋯O hydrogen-bonding interactions with the cage interior surface involving CH groups on the cationic cage surface that act as H-bond donors and O atoms on the guests that act as H-bond acceptors. In a third case, with the guest 4-nitrophenyl-methanesulfonate, the guest lies in the spaces outside a cage cavity between cages and forms weak CH⋯O interactions with the cage exterior surface: the cavity is occupied by a network of H-bonded water molecules, though this guest does show cavity binding in solution. For the isomeric guests 4-nitrophenyl-methanesulfonate and 4-nitrophenyl methyl sulfite, hydrolysis in water/DMSO (98 : 2 v/v) could be monitored colorimetrically via appearance of the 4-nitrophenolate anion; both showed accelerated hydrolysis rates in the presence of the host cage with second-order rate constants for the catalysed reactions in the range 10-3 to 10-2 M-1 s-1 at pH 9. The typical rate dependence on external pH and the increased reaction rates when chloride ions are present (which can bind inside the cavity and displace other cavity-bound guests) imply that the catalysed reaction actually occurs at the external surface of the cage rather than inside the cavity.

Structure, stability, reactivity and bonding in noble gas compounds.

Noble gases (Ngs) are recognized as the least reactive elements due to their fully filled valence electronic configuration. Their reluctance to engage in chemical bond formation necessitates extreme conditions such as low temperatures, high pressures, and reagents with high reactivity. In this Perspective, we discuss our endeavours in the theoretical prediction of viable Ng complexes, emphasizing the pursuit of synthesizing them under nearly ambient conditions. Our research encompasses various bonding categories of Ng complexes and our primary aim is to comprehend the bonding mechanisms within these complexes, utilizing state-of-the-art theoretical tools such as natural bond orbital, energy decomposition, and electron density analyses. These complex types manifest distinct bonding scenarios. In the non-insertion type, the donor-acceptor interaction strength hinges on the polarizing ability of the binding atom, drawing the electron density of the Ng towards itself. In certain instances, especially with heavier Ng elements, this interaction reaches a magnitude where it can be considered a covalent bond. Conversely, in most insertion cases, the Ng prefers to share electrons to form a covalent bond on one side while interacting electrostatically on the other side. In rare cases, both bonds may be portrayed as electron-shared covalent bonds. Furthermore, a host cage serves as an excellent platform to explore the limits of achieving Ng-Ng bonds (even for helium), under high pressure.

Enrichment of Chlorine in Porous Organic Nanocages for High-Performance Rechargeable Lithium-Chlorine Batteries.

Rechargeable Li-Cl2 batteries are recognized as promising candidates for energy storage due to their ultrahigh energy densities and superior safety features. However, Li-Cl2 batteries suffer from a short cycle life and low Coulombic efficiency (CE) at a high specific cycling capacity due to a sluggish and insufficient Cl2 supply during the redox reaction. To achieve Li-Cl2 batteries with high discharge capacity and CE, herein, we propose and design an imine-functionalized porous organic nanocage (POC) to enrich Cl2 molecules. Based on density functional theory (DFT) calculations, the imine group sites in host cages strongly interact with Cl2 molecules, facilitating the rapid capture of Cl2. As a result, the output capacity of the Li-Cl2 battery using POC (Li-Cl2@POC) is significantly boosted, achieving an ultrahigh discharge capacity of 4000 mAh/g at ∼100% CE. Benefiting from the designed POC, the highest utilization ratio of deposited LiCl at the first cycle in the Li-Cl2@POC battery reaches as high as 85%, superior to all reported values. The Li-Cl2@POC battery exhibits excellent electrochemical performance even at low temperatures, delivering stable cycling over 200 cycles under a capacity of 2000 mAh/g at -20 °C with a voltage plateau of 3.5 V and an average CE of 99.7%. We also demonstrate that the Li-Cl2@POC cells can be assembled and well-operated in a dry room, showing advantages for mass production. Our designed POC promotes the practical deployment of rechargeable Li-Cl2 batteries.

An exponential-potential description for the guest–host interactions in rattler-containing cage materials

Anomalous low-energy excitations (ALEs) associated with the vibrations of atoms accommodated in a space with large freedom of motion are frequently observed in cage materials. Such ALEs have been of great interest for their important roles in large electron–phonon coupling targeting high-TC superconductivity as well as phonon–phonon scattering giving rise to low thermal conductivity to achieve high thermoelectric performance. In our previous work, we showed that van der Waals-like repulsive interactions between the atoms forming the host cage and the atoms accommodated inside the cage (rattler) play a crucial role in giving small force constants and consequently nearly dispersionless low-energy phonons. In the present work, we show that the exponential law derived from the revised Morse potential model that we used previously could provide a universal trend for the ALEs of three typical cage materials: clathrates, skutterudites, and pyrochlores. This not only confirms the effectiveness of the potential model but also provides a clear description for different types of rattler vibrational modes based on the deduced parameters from the potential model. In addition to the free space in which a rattler can move and the mass of the rattler, which we considered in our previous work, structural anisotropy, electronegativity of the component cage atoms, and the coordination number of the rattler are shown to be important factors for description of an ALE.

Bader's Topological Bond Path Does Not Necessarily Indicate Stabilizing Interaction-Proof Studies Based on the Ng@[3n]cyclophane Endohedral Complexes.

According to Bader's quantum theory of atoms in molecules (QTAIM), the simultaneous presence of a bond path and the corresponding bond critical point between any two atoms is both a necessary and sufficient condition for the atoms to be bonded to one another. In principle, this means that this pair of atoms should make a stabilizing contribution to the molecular system. However, the multitude of so-called counterintuitive bond paths strongly suggests that this statement is not necessarily true. Particularly 'troublesome' are endohedral complexes, in which encapsulation-enforced proximity between the trapped guest (e.g., an atom) and the host's cage system usually 'produces' many counterintuitive bond paths. In the author's opinion, the best evidence to demonstrate the repulsive nature of the intra-cage guest⋯host interaction is the use of some trapping systems containing small escape channels and then showing that the initially trapped entity spontaneously escapes outside the host's cage during geometry optimization of the initially built guest@host endohedral complex. For this purpose, a group of 24 Ng@[3n]cyclophane (3≤n≤6) endohedral complexes is used. As a result, arguments are presented showing that Bader's topological bond path does not necessarily indicate a stabilizing interaction.

Selective Noble Gas Inclusion in Pentagon-Dodecahedral X20-Cages.

Using DFT-based computational chemistry calculations (ωB97XD/def2-tzvp//ωB97XD/def2-svp/svpfit + ZPE(ωB97XD/def2-svp/svpfit)), binding energies of noble gases encapsulated in a series of dodecahedrane molecules (general formula: X20H20 where X = C, Si, Ge, Sn and Pb, and X20 where X = N, P, As, Sb and Bi) were calculated to learn about the noble gas selectivity. Based on calculated binding energies, the Sn20H20 cage can best accommodate noble gases with a medium size radius (Ar and Kr), while the Pb20H20 dodecahedrane cage is best suited for noble gases with the larger radii (Xe and Rn). On the other hand, from the elements of the V main group of the periodic table, the Bi20 cage has shown the best results to selectively encapsulate Ar and Kr, with the amounts of energy being released being -5.24 kcal/mol and -6.13 kcal/mol, respectively. By monitoring the geometric changes of all here-reported host cages upon encapsulating the noble gas guest, the host has shown minor to no flexibility, testifying to the high rigidity of the dodecahedrane structure which was further reflected in very high encapsulating energies.

Tetradehydro-Diels-Alder Reactions of Flexible Arylalkynes via Folding Inside a Molecular Cage.

The tetradehydro-Diels-Alder (TDDA) reaction is a useful transformation for the rapid assembly of polycyclic scaffolds from simple linear precursors in a single synthetic step. However, the reaction requires careful substrate design and harsh reaction conditions to overcome the inherent entropic cost for this transformation. Herein we report an efficient site-selective TDDA transformation within a self-assembled Pd6L4 cage. Despite the large size, the flexibility of the employed substrates allows for efficient encapsulation within the host cavity. The rate of thermal cyclization of the encapsulated guest was found to be greatly enhanced, and high product selectivity for an unsymmetrical substrate was observed. The efficiency of this system relies on the precise conformational control of the substrate within the confined space of the host cage.

Cover Picture

The cover picture depicts two oxide cluster, Lu2O and Er2O, nested in the robust Cs(6)‐C82 fullerene cage, respectively. Their crystallographic structures display a large variation in the angles of the clusters within the cage (146.74° vs. 116.51°), suggesting flexible configurations of the oxide clusters heavily dependent on the radius of encapsulated metal ions. This work discloses the role of metal species in adjusting cluster conformation, and facilitates the understanding of interplay between the encapsulated cluster and host cage. More details are discussed in the article by Lu et al. on page 1915—1920.image

Molecular Barrels as Potential Hosts: From Synthesis to Applications

Self-assembled discrete molecular architectures that show selective molecular recognition within their internal cavities are highly desirable. Such hosts often show guest recognition through several noncovalent interactions. This emulates the activity of naturally occurring enzymes and proteins. Research in the formation of 3D cages of different shapes and sizes has progressed rapidly since the development of coordination-driven self-assembly and dynamic covalent chemistry. Such molecular cages find applications in catalysis, stabilization of metastable molecules, purification of isomeric mixtures via selective encapsulation, and even in biomedical applications. Most of these applications stem from the ability of the host cages to bind guests strongly in a selective fashion, providing a suitable environment for the guests to perform their functions. Molecular cages having closed architectures with small windows either show poor encapsulation or inhibit easy guest release while those with wide open structures fail to form stable host-guest complexes. In this context, molecular barrels obtained by dynamic metal-ligand/covalent bond formation techniques possess optimized architectures. With a hollow-walled cavity and two large openings, molecular barrels satisfy the structural requirements for many applications. In this perspective, we will discuss in detail the synthetic strategies for obtaining barrels or barrel-like architectures employing dynamic coordination and covalent interactions, their structure-based classification, and their applications in catalysis, storing transient molecules, separation of chemicals, and photoinduced antibacterial activity. We aim to highlight the structural advantages of molecular barrels over other architectures for efficiently carrying out several functions and for the development of new applications.

Atomistic-geometric simulations to investigate the mechanical stability of monocrystalline sI methane hydrates under pressure

Gas hydrate mechanical stability under pressure is critically important in energy supply, global warming, and carbon-neutral technologies. The stability of these polyhedral guest–host crystals under increasing pressure is affected by host cage type and face connectivity as well as guest gas occupancy. The geometry-imposed cage connectivity generates crystal lattices that include inclusion-matrix material composite structures. In this paper, we integrate Density Functional Theory simulations with a polyhedral-inspired composite material model that quantifies stability limits, failure modes, and the impact of the type of cage occupancy. DFT reveals the existence of two failure mechanisms under increasing pressure: (i) a multistep lattice breakdown under total occupancy and under only large cage occupancy and (ii) a single-step breakdown under zero occupancy as well as with only small cage occupancy. The DFT-composite model predicts optimal occupancy pathways to generate strength and critical occupancy pathways to promote decomposition.

The preservation of sarin and O,O'-diisopropyl fluorophosphate inside coordination cage hosts.

The host-guest chemistry of O,O'-diisopropyl fluorophosphate (DFP), a phosphonofluoridate G-series chemical warfare agent simulant, was investigated in the presence of a number of octanuclear cubic coordination cage hosts. The aim was to demonstrate cage-catalysed hydrolysis of DFP at near neutral pH: however, two octanuclear coordination cages, HPEG (containing water-solubilising PEG groups) and HW (containing water-solubilising hydroxymethyl groups), were actually found to increase the lifetime of DFP in aqueous buffer solution (pH 8.7). Crystallographic analysis of DFP with a structurally related host cage revealed that DFP binds to windows in the cage surface, not in the internal cavity. The phosphorus-fluorine bond is directed into the cavity rather than towards the external environment, with the cage/DFP association protecting DFP from hydrolysis. Initial studies with the chemical warfare agent (CWA) sarin (GB) with HPEG cage in a buffered solution also showed a drastically reduced rate of hydrolysis for sarin when bound in the host cage. The ability of these cages to inhibit hydrolysis of these P-F bond containing organophosphorus guests, by encapsulation, may have applications in forensic sample preservation and analysis.

Can the Fluxionality in Borospherene Influence the Confinement-Induced Bonding between Two Noble Gas Atoms?

A density functional theory study is performed to determine the stability and bonding in the neon dimer inside the B30N30 fullerene cage, the fluxional B40 cage, and within non-fluxional cages such as B12N12 and C60. The nature of bonding in the Ne2 encapsulated B40 is compared with the that in other cages in an attempt to determine whether any possible alterations are brought about by the dynamical nature of the host cage apart from the associated confinement effects. The bonding analysis includes the natural bond order (NBO), Bader's Atoms-in-Molecules electron density analysis (AIM), and energy decomposition analysis (EDA), revealing the non-covalent nature of the interactions between the Ne atoms and that between the Ne and the cage atoms. The formation of all the Ne2@cage systems is thermochemically unfavourable, the least being that for the B30N30 cage, which can easily be made favourable at lower temperatures. The Ne-Ne distance is lowest in the smallest cage and increases as the cage size increase due to steric relaxation experienced by the dimer. The dynamical picture of the systems is investigated by performing ab initio molecular dynamics simulations using the atom-centred density matrix propagation (ADMP) technique, which shows the nature of the movement of the dimer inside the cages, and by the fact that since it moves as a single entity, a weak bonding force holds them together, apart from their proven kinetic stability.

Infrared spectroscopy as a tool for the analysis of framework topology and extra-framework components in microporous cancrinite- and sodalite-related aluminosilicates

The identification of the framework type in multilayer cancrinite- and sodalite-group minerals and synthetic compounds is predominantly based on the unit-cell dimensions determined from powder or single-crystal X-ray diffraction data, by analogy with previously characterized samples with known crystal structures. However, topological type of the framework cannot be reliably determined in this way because of the different possible ABC staking sequences and different sets of cages with the same number of layers in the repeat unit. To solve this problem, additional criteria are required. The use of infrared (IR) spectroscopy makes it possible to distinguish topologically different types with the same unit-cell parameters. The most important diagnostic range in the IR spectrum (the “finger-print region”, from 510 to 760 cm−1) corresponds to the O–T–O bending vibrations (T = Si, Al). The spectral bands at 705 ± 8, 528 ± 5, 547 ± 4, and 555 ± 3 cm−1 indicate the presence of the sodalite, Losod, liottite, and giuseppettite cages, respectively. The band at 528 ± 5 cm−1 shifts towards ∼518 cm−1 in the case when Losod cage hosts carbonate group. The IR spectrum in the “finger-print region” can be also used to identify a mineral species belonging to two-layer or three-layer minerals with different extra-framework compositions. The wavenumber of the antisymmetric stretching mode of the 12CO2 molecule, which is a common admixed extra-framework constituent in minerals belonging to the cancrinite and sodalite groups, depends on the kind of the host cage or channel: 2340–2343 cm−1 for the sodalite cage, 2338 cm−1 for the Losod cage, and 2351–2353 cm−1 for the liottite cage and wide channel in the cancrinite-type framework.

Improved Estimates of Host-Guest Interaction Energies for Endohedral Fullerenes Containing Rare Gas Atoms, Small Molecules, and Cations.

Endohedral fullerenes have evinced much interest from the fundamental and applications points of view. However, given the nature of the weak interaction between the guest species and the host cage in these confined systems, the interaction energy values obtained using various theoretical methods, and different basis sets vary over a wide range. For example, the reported interaction energy for the HF@C60 system ranges from -2.5 kcal/mol to -14.9 kcal/mol. In the present manuscript, we report reliable interaction energy values for different endohedral fullerenes (He@C60 , Ne@C60 , Ar@C60 , Kr@C60 , H2 @C60 , HF@C60 , H2 O@C60 , NH3 @C60 , CH4 @C60 , Li+ @C60 , Na+ @C60 , and K+ @C60 ) obtained using the domain-based local pair natural orbital coupled-cluster singles, doubles, and perturbative triples (DLPNO-CCSD(T)) method and the def2-TZVP basis set. We believe that these energy values could be considered as benchmark values, and the performance of other quantum chemical methods could be assessed accordingly. Local energy decomposition analysis within the DLPNO-CCSD(T) framework is used to estimate the electrostatic, exchange, and dispersion components of the interaction energy for some of the endohedral fullerenes.

Use of Bayes factors to evaluate the effects of host genetics, litter and cage on the rabbit cecal microbiota

BackgroundThe rabbit cecum hosts and interacts with a complex microbial ecosystem that contributes to the variation of traits of economic interest. Although the influence of host genetics on microbial diversity and specific microbial taxa has been studied in several species (e.g., humans, pigs, or cattle), it has not been investigated in rabbits. Using a Bayes factor approach, the aim of this study was to dissect the effects of host genetics, litter and cage on 984 microbial traits that are representative of the rabbit microbiota.ResultsAnalysis of 16S rDNA sequences of cecal microbiota from 425 rabbits resulted in the relative abundances of 29 genera, 951 operational taxonomic units (OTU), and four microbial alpha-diversity indices. Each of these microbial traits was adjusted with mixed linear and zero-inflated Poisson (ZIP) models, which all included additive genetic, litter and cage effects, and body weight at weaning and batch as systematic factors. The marginal posterior distributions of the model parameters were estimated using MCMC Bayesian procedures. The deviance information criterion (DIC) was used for model comparison regarding the statistical distribution of the data (normal or ZIP), and the Bayes factor was computed as a measure of the strength of evidence in favor of the host genetics, litter, and cage effects on microbial traits. According to DIC, all microbial traits were better adjusted with the linear model except for the OTU present in less than 10% of the animals, and for 25 of the 43 OTU with a frequency between 10 and 25%. On a global scale, the Bayes factor revealed substantial evidence in favor of the genetic control of the number of observed OTU and Shannon indices. At the taxon-specific level, significant proportions of the OTU and relative abundances of genera were influenced by additive genetic, litter, and cage effects. Several members of the genera Bacteroides and Parabacteroides were strongly influenced by the host genetics and nursing environment, whereas the family S24-7 and the genus Ruminococcus were strongly influenced by cage effects.ConclusionsThis study demonstrates that host genetics shapes the overall rabbit cecal microbial diversity and that a significant proportion of the taxa is influenced either by host genetics or environmental factors, such as litter and/or cage.

Exploring Guest–Host Interactions in Gas Hydrates: Insights from Quantum Mechanics

Gas hydrates are comprised of guest molecules and host cages. The stability of a gas hydrate is determined by the host–guest interactions. In this work, the relationship between the characteristics...

Disruptive influence of the host cage C60 on the guest He–H+ bond and bonding in H3+

Although a helium atom prefers to stay at the centre of a fullerene (C60) cage and a proton binds with one of the carbon atoms from inside, DFT(MN15)/cc-pVTZ and DLPNO-MP2/def2-TZVP calculations show that the helium atom and the proton in HeH+ prefer to stay away from the centre of the cage, weakening the He–H+ covalent bond considerably. Both the helium atom and the proton exhibit noncovalent interactions with the carbon atoms of two pentagons at the opposite ends of the fullerene cage. Our calculations also show that a linear arrangement of H3+ (inside C60), pointing towards the centres of two pentagons opposite to each other, with the proton breaking away from H2, is energetically more favored over the equilateral triangle geometry of free H3+.

Direct identification of HMX via guest-induced fluorescence turn-on of molecular cage

Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) is one of the most widely used powerful explosives. The direct and selective detection of HMX, without the requirement of specialized equipment, remains a great challenge due to its extremely low volatility, unfavorable reduction potential and lack of aromatic rings. Here, we report the first chemical probe of direct identification of HMX at ppb sensitivity based on a designed metal-organic cage (MOC). The cage features two unsaturated dicopper units and four electron donating amino groups inside the cavity, providing multiple binding sites to selectively enhance host-guest events. It was found that compared to other explosive molecules the capture of HMX inside the cavity would strongly modulate the emissive behavior of the host cage, resulting in highly induced fluorescence “turn-on” (160 folds). Based on the density functional theory (DFT) simulation, the mutual fit of both size and binding sites between host and guest leads to the synergistic effects that perturb the ligand-to-metal charge-transfer (LMCT) process, which is probably the origin of such selective HMX-induced turn-on behavior.