Molecular Factors Controlling the Isomerization of Azobenzenes in the Cavity of a Flexible Coordination Cage

Revisiting the Origins of Reactivity and Selectivity in the Pd6L4-Cage-Catalyzed Diels-Alder Reactions: A Combined Computational and Experimental Study

Supramolecular metal-organic cages (MOCs) have gained attention as versatile catalytic platforms due to their self-assembled architectures and well-defined cavities, which mimic enzyme active sites and enable spatial confinement. This confinement modulates the reaction pathways and enhances the catalytic performance. Recent studies highlight their catalytic potential in various organic transformations, but the factors governing the MOC-catalyzed reactions remain incompletely understood. This work builds on prior computational studies of Diels-Alder reactions catalyzed by palladium-based MOCs, showing that the common view of transition-state stabilization via π-π interactions is not valid. Instead, we find that π-π interactions between the substrate and the ligands destabilize the transition state. Additionally, theoretical studies of regioselectivity, validated experimentally, suggest that substrate encapsulation efficiency is key to determining reaction selectivity. These findings provide new insights into the mechanisms of MOC-catalyzed reactions.

Diazocines as Guests of Cucurbituril Macrocycles: Light-Responsive Binding and Supramolecular Catalysis of Thermal Isomerization

The photoswitching of supramolecular host-guest complexes is the basis of numerous molecularly controlled macroscopic functions, such as sol-gel transition, photopharmacology, the active transport of ions or molecules, light-powered molecular machines, and much more. The most commonly used systems employ photoactive azobenzene guests and synthetic host molecules, which bind as the stable E isomers and dissociate as the Z forms after exposure to UV light. We present a new, extraordinarily efficient cucurbit[7]uril (CB7)/diazocine host/guest complex with inverted stability that self-assembles under UV irradiation and dissociates in the dark. The association constants of the Z and E isomers in water differ by more than 104-fold. We also show that the thermally activated E → Z isomerization is significantly accelerated by CB7, which is a rare case of enzyme-like catalysis by transition state stabilization without product inhibition. In contrast to CB7, cucurbit[8]uril (CB8) binds both isomers with high affinity, showing good selectivity (∼1000-fold) toward the Z isomer. Notably, this isomer preferentially binds CB8 relative to CB7 by a factor greater than 1 × 106. We also use the system to introduce a supramolecular photoacid that builds on the increased basicity of a guest bound to CB7 and on the extremely high affinity of the E isomer, which is utilized to displace the acid from CB7, thereby switching the pH of the solution.

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).

Synthesis, Characterization, and Photochemistry of a Ga2L3 Coordination Cage with Dithienylethene-Catecholate Ligands

Two new photoswitchable dithienylethene (DTE)-catechol ligands, specifically designed for group 13 metal coordination, were synthesized via Suzuki coupling reactions from a dichloro-DTE building block, each with varying longitudinal extensions. The shorter DTE-catechol ligand did not efficiently assemble with Ga3+ metal ions; however, elongation with a phenylene-amide spacer group enabled the successful formation of a novel triply DTE-functionalized coordination [Ga2L3]6- cage. This cage represents a unique example of integrating DTE photoswitches with main group metals in a supramolecular coordination framework. The [Ga2L3]6- cage was thoroughly characterized by NMR spectroscopy, including DOSY hydrodynamic volumetric analyses, high-resolution mass spectrometry, computational DFT, and photochemical analyses. The DFT studies highlighted the structural integrity and dynamic interplay within the helicate and mesocate isomeric forms of the [Ga2L3]6- cage upon photoswitching. While the free ligands exhibited all-photonic reversible switching at up to mM concentrations upon alternating irradiation at 365 and >495 nm, the [Ga2L3]6- cage demonstrated these capabilities under dilute μM conditions, albeit with lower efficiency and fatigue resistance. This behavior highlights the intricate relationship between rigid coordination with main group metals and the flexibility of the photoswitchable DTE ligands within the [Ga2L3]6- cage.

In vivo photopharmacological inhibition of hippocampal activity via multimodal probes - perspective and opening steps on experimental and computational challenges

Neurological conditions such as epilepsy can have a significant impact on people's lives. Here, we discuss a new perspective for the study/treatment of these conditions using photopharmacology. A multimodal, intracranial implant that incorporates fluidic channels for localised drug delivery, electrodes for recording and stimulation, and a light source for photoswitching is used for in vivo administration and deactivation of a photoresponsive AMPA antagonist. We review current advancements in the relevant disciplines and show experimentally that the inhibition of seizure-like events induced in the hippocampus by electrical stimulation can be altered upon switching the drug with light. We discuss the interconnection of the drug's photopharmacological properties with the design of the device by modelling light penetration into the rat brain with Monte Carlo simulations. This work delivers a new perspective, including initial experimental and computational efforts on in vivo photopharmacology to understand and eventually treat neurological conditions.

Deuteration as a General Strategy to Enhance Azobenzene-Based Photopharmacology

Chemical photoswitches have become a widely used approach for the remote control of biological functions with spatiotemporal precision. Several molecular scaffolds have been implemented to improve photoswitch characteristics, ranging from the nature of the photoswitch itself (e.g. azobenzenes, dithienylethenes, hemithioindigo) to fine-tuning of aromatic units and substituents. Herein, we present deuterated azobenzene photoswitches as a general means of enhancing the performance of photopharmacological molecules. Deuteration can improve azobenzene performance in terms of light sensitivity (higher molar extinction coefficient), photoswitch efficiency (higher photoisomerization quantum yield), and photoswitch kinetics (faster macroscopic rate of photoisomerization) with minimal alteration to the underlying structure of the photopharmacological ligand. We report synthesized deuterated azobenzene-based ligands for the optimized optical control of ion channel and G protein-coupled receptor (GPCR) function in live cells, setting the stage for the straightforward, widespread adoption of this approach.

The photochemical trans → cis and thermal cis → trans isomerization pathways of azobenzo-13-crown ether: A computational study on a strained cyclic azobenzene system

The isomerization of azobenzo-13-crown ether can be expected to be hindered due to the polyoxyethylene linkage connecting the 2,2'-positions of azobenzene. The mixed reference spin-flip time-dependent density functional theory results reveal that the planar and rotational minima of the first photo-excited singlet state (S1) of the trans-isomer pass through a barrier (2.5-5.0 kcal/mol) as it goes toward the torsional conical intersection (S0/S1) geometry ( Collapse

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Dilawar Singh Sisodiya Department of Chemistry, Birla Institute of Technology and Science (BITS), Pilani, K. K. Birla Goa Campus, Zuarinagar, India
Anjan Chattopadhyay Department of Chemistry, Birla Institute of Technology and Science (BITS), Pilani, K. K. Birla Goa Campus, Zuarinagar, India

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Photoinduced dual bond rotation of a nitrogen-containing system realized by chalcogen substitution

Photoinduced concerted multiple-bond rotation has been proposed in some biological systems. However, the observation of such phenomena in synthetic systems, in other words, the synthesis of molecules that undergo photoinduced multiple-bond rotation upon photoirradiation, has been a challenge in the photochemistry field. Here we describe a chalcogen-substituted benzamide system that exhibits photoinduced dual bond rotation in heteroatom-containing bonds. Introduction of the chalcogen substituent into a sterically hindered benzamide system provides sufficient kinetic stability and photosensitivity to enable the photoinduced concerted rotation. The presence of two different substituents on the phenyl ring in the thioamide derivative enables the generation of a pair of enantiomers and E/Z isomers. Using these four stereoisomers as indicators of which bonds are rotated, we monitor the photoinduced C-N/C-C concerted bond rotation in the thioamide derivative depending on external stimuli such as temperature and photoirradiation. Theoretical calculations provide insight on the mechanism of this selective photoinduced C-N/C-C concerted rotation.

Amplifying dual-visible-light photoswitching in aqueous media via confinement promoted triplet-triplet energy transfer

Achieving visible-light photochromism is a long-term goal of chemists keen to exploit the opportunities of molecular photoswitches in multi-disciplinary research studies. Triplet-sensitization offers a flexible approach to building diverse visible-light photoswitches using existing photochromic scaffolds, circumventing the need for sophisticated molecular design and synthesis. Unfortunately, distance-dependence and environment-sensitivity of triplet-excited species remain as key challenges that severely impair sensitization efficiency and limit their practical availability. We present herein a nature-inspired nanoconfinement strategy in which a triplet-sensitized visible-light photoswitch/sensitizer system is assembled into nanoconfined micelles (d ∼ 40 nm). A ca. 10-fold efficiency increase of triplet-triplet energy transfer for photochromism as well as an amplified fluorescence on/off contrast upon bi-directional visible-light excitation (470/560 nm) was achieved in full aqueous media. By virtue of this, the hybrid photoswitchable system is successfully applied for both flash information encryption and multiple dynamic cell imaging assays, further proving its versatility in materials and life science.

A CuI6L4 Cage Dynamically Reconfigures to Form Suit[4]anes and Selectively Bind Fluorinated Steroids

Simple organic ligands can self-assemble with metal ions to generate metal-organic cages, whose cavities bind guests selectively. This binding may enable new methods of chemical separation or sensing, among other useful functions. Here we report the preparation of a CuI6L4 pseudo-octahedral metal-organic cage, the ligands of which self-assemble from simple organic building blocks. Temperature, solvent, and the presence of different guests governed which structure predominated from a dynamic mixture of cage diastereomers with different arrangements of right- or left-handed metal vertices. Dissolution in dimethyl sulfoxide or the binding of tetrahedral guests led to a chiral tetrahedral T-symmetric framework, whereas low temperatures favored the achiral S4-symmetric diastereomer. Tetrahedral guests with long arms were encapsulated to form mechanically bonded suit[4]anes, with guest arms protruding out through host windows. The cage was also observed to bind fluorinated steroids, an important class of drug molecules, but not non-fluorinated steroids, providing the basis for new separation processes.

Light-Triggered Disassembly of Molecular Motor-based Supramolecular Polymers Revealed by High-Speed AFM

Photoresponsive supramolecular polymers have a major potential for applications in responsive materials that are externally triggered by light with spatio-temporal control of their polymerisation state. While changes in macroscopic properties revealed the adaptive nature of these materials, it remains challenging to capture the dynamic depolymerisation process at the molecular level, which requires fast observation techniques combined with in situ irradiation. By implementing in situ UV illumination into a High-Speed Atomic Force Microscope (HS-AFM) setup, we have been able to capture the disassembly of a light-driven molecular motor-based supramolecular polymer. The real-time visualisation of the light-triggered disassembly process not only reveals cooperative depolymerisation, it also shows that this process continues after illumination is halted. Combining the data with cryo-electron microscopy and spectroscopy approaches, we obtain a molecular-level description of the motor-based polymer dynamics reminiscent of actin chain-end depolymerisation. Our detailed understanding of supramolecular depolymerisation will drive the development of future responsive polymer systems.

Dual-controlled guest release from coordination cages

Despite having significant applications in the construction of controlled delivery systems with high anti-interference capability, to our knowledge dual-controlled molecular release has not yet been achieved based on small molecular/supramolecular entities. Herein, we report a dual-controlled release system based on coordination cages, for which releasing the guest from the cage demands synchronously altering the coordinative metal cations and the solvent. The cages, Hg5L2 and Ag5L2, are constructed via coordination-driven self-assembly of a corannulene-based ligand. While Hg5L2 shows a solvent-independent guest encapsulation in all the studied solvents, Ag5L2 is able to encapsulate the guests in only some of the solvents, such as acetone-d6, but will liberate the encapsulated guests in 1,1,2,2-tetrachloroethane-d2. Hg5L2 and Ag5L2 are interconvertible. Thus, the release of guests from Hg5L2 in acetone-d6 can be achieved, but requires two separate operations, including metal substitutions and a change of the solvent. Dual-controlled systems as such could be useful in complicated molecular release process to avoid those undesired stimulus-responses.

Photoresponsive Supramolecular Cages and Macrocycles

The utilisation of light to achieve precise manipulation and control over the structure and function of supramolecular assemblies has emerged as a highly promising approach in the development of complex, configurable, or multifunctional systems and nanoscopic machine-like entities. In this minireview, we highlight recent examples of self-assembled and covalently bound cages and macrocycles with a focus on the external and internal functionalisation of a structure with a photoswitchable unit or the embedment of a photoswitch into the framework of a structure. Functionalising the interior or exterior of a supramolecular cage or macrocycle with a photoresponsive group enables control over different properties, such as guest binding or assembly in the solid-state, while the overall shape of the assembly often undergoes no significant change. By directly integrating a photoswitchable unit into the framework of a supramolecular structure, the isomerisation can either induce a geometry change, the disassembly, or the disassembly and reassembly of the structure. Historical and recent examples covered in this review are based on azobenzene, diarylethene, stilbene photoswitches, or alkene motors that were incorporated into macrocycles and cages constructed by metal-organic, dynamic covalent, or covalent bonds.

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.

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".

Emergence of Photomodulated Protometabolism by Short Peptide-Based Assemblies

In the early Earth, rudimentary enzymes must have utilized the available light energy source to modulate protometabolic processes. Herein, we report the light-responsive C-C bond manipulation via short peptide-based assemblies bound to the photosensitive molecular cofactor (azo-based photoswitch) where the energy of the light source regulated the binding sites which subsequently modulated the retro-aldolase activity. In the presence of a continual source of high-energy photons, temporal realization of a catalytically more proficient state could be achieved under nonequilibrium conditions. Further, the hydrophobic surface of peptide assemblies facilitated the binding of an orthogonal molecular catalyst that showed augmented activity (promiscuous hydrolytic activity) upon binding. This latent activity was utilized for the in situ generation of light-sensitive cofactor that subsequently modulated the retro-aldolase activity, thus creating a reaction network.

Disequilibrating azobenzenes by visible-light sensitization under confinement

Photoisomerization of azobenzenes from their stable E isomer to the metastable Z state is the basis of numerous applications of these molecules. However, this reaction typically requires ultraviolet light, which limits applicability. In this study, we introduce disequilibration by sensitization under confinement (DESC), a supramolecular approach to induce the E-to-Z isomerization by using light of a desired color, including red. DESC relies on a combination of a macrocyclic host and a photosensitizer, which act together to selectively bind and sensitize E-azobenzenes for isomerization. The Z isomer lacks strong affinity for and is expelled from the host, which can then convert additional E-azobenzenes to the Z state. In this way, the host-photosensitizer complex converts photon energy into chemical energy in the form of out-of-equilibrium photostationary states, including ones that cannot be accessed through direct photoexcitation.

Unexplored Isomerization Pathways of Azobis(benzo-15-crown-5): Computational Studies on a Butterfly Crown Ether

Computational studies on trans → cis and cis → trans isomerizations of photoresponsive azobis(benzo-15-crown-5) have been reported in this work. The photoexcited ππ* state (S2) of the trans isomer relaxes through the planar S2 minimum and the planar S2/S1 conical intersection (both situated around 9 kcal/mol below the vertically excited S2 state) arising along the N═N stretching coordinate. The nπ* state (S1) of this isomer has both planar and rotated (clockwise and anticlockwise) minima, which may lead to a torsional conical intersection (S0/S1) geometry having a Collapse

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Affiliation(s)

Dilawar Singh Sisodiya Department of Chemistry, Birla Institute of Technology and Science (BITS), Pilani, K.K. Birla Goa Campus, Zuarinagar 403726, India
Sk Musharaf Ali Chemical Engineering Division, Bhabha Atomic Research Centre (BARC), Mumbai 400085, India
Anjan Chattopadhyay Department of Chemistry, Birla Institute of Technology and Science (BITS), Pilani, K.K. Birla Goa Campus, Zuarinagar 403726, India

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Into the dynamics of rotaxanes at atomistic resolution

Mechanically-interlocked molecules (MIMs) are at the basis of artificial molecular machines and are attracting increasing interest for various applications, from catalysis to drug delivery and nanoelectronics. MIMs are composed of mechanically-interconnected molecular sub-parts that can move with respect to each other, imparting these systems innately dynamical behaviors and interesting stimuli-responsive properties. The rational design of MIMs with desired functionalities requires studying their dynamics at sub-molecular resolution and on relevant timescales, which is challenging experimentally and computationally. Here, we combine molecular dynamics and metadynamics simulations to reconstruct the thermodynamics and kinetics of different types of MIMs at atomistic resolution under different conditions. As representative case studies, we use rotaxanes and molecular shuttles substantially differing in structure, architecture, and dynamical behavior. Our computational approach provides results in agreement with the available experimental evidence and a direct demonstration of the critical effect of the solvent on the dynamics of the MIMs. At the same time, our simulations unveil key factors controlling the dynamics of these systems, providing submolecular-level insights into the mechanisms and kinetics of shuttling. Reconstruction of the free-energy profiles from the simulations reveals details of the conformations of macrocycles on the binding site that are difficult to access via routine experiments and precious for understanding the MIMs' behavior, while their decomposition in enthalpic and entropic contributions unveils the mechanisms and key transitions ruling the intermolecular movements between metastable states within them. The computational framework presented herein is flexible and can be used, in principle, to study a variety of mechanically-interlocked systems.

Bistable Aryl Azopyrazolium Ionic Photoswitches in Water

We report a new class of arylazopyrazolium-based ionic photoswitches (AAPIPs). These AAPIPs with different counter ions have been accessed through a modular synthetic approach in high yields. More importantly, the AAPIPs exhibit excellent reversible photoswitching and exceptional thermal stability in water. The effects of solvents, counter ions, substitutions, concentration, pH, and glutathione (GSH) have been evaluated using spectroscopic investigations. The results revealed that the bistability of studied AAPIPs is robust and near quantitative. The thermal half-life of Z isomers is extremely high in water (up to years), and it can be lowered electronically by the electron-withdrawing groups or highly basic pH.

Photo- and Temperature-Induced Reversible Structural Transformation between Dodecanuclear and Pentadecanuclear Gold(I) Sulfido Complexes

Stimuli-responsive structural transformation has attracted much attention for its potential to mimic the behavior of biological transformations and functions. Here, two unprecedented dodecanuclear and pentadecanuclear gold(I) sulfido clusters (denoted trans-Au₁₂ and trans-Au₁₅, respectively) with impressive stimuli-responsive interconversion have been obtained by taking advantage of the judiciously designed tridentate phosphine ligand L_trans as the building block. Both UV light and temperature can be applied to trigger the structural conversions between trans-Au₁₂ and trans-Au₁₅. In addition, NMR, high-resolution electrospray ionization mass spectrometry, and UV-vis absorption spectroscopy have been employed to monitor the transformation process and decipher the mechanism of structural conversion. This work not only provides a paradigm to investigate photo-induced cluster-to-cluster transformation based on polydentate phosphine ligands but also offers a new direction for the construction of the stimuli-responsive materials.

Reactivity and Selectivity of the Diels-Alder Reaction of Anthracene in [Pd6L4]12+ Supramolecular Cages: A Computational Study

The field of supramolecular metal-organic cage catalysis has grown rapidly in recent years. However, theoretical studies regarding the reaction mechanism and reactivity and selectivity controlling factors for supramolecular catalysis are still underdeveloped. Herein, we demonstrate a detailed density functional theory study on the mechanism, catalytic efficiency, and regioselectivity of the Diels-Alder reaction in bulk solution and within two [Pd₆L₄]¹²⁺ supramolecular cages. Our calculations are consistent with experiments. The origins of the catalytic efficiency of the bowl-shaped cage 1 have been elucidated to be the host-guest stabilization of the transition states and the favorable entropy effect. The reasons for the switch of the regioselectivity from 9,10-addition to 1,4-addition within the octahedral cage 2 were attributed to the confinement effect and the noncovalent interactions. This work would shed light on the understanding of [Pd₆L₄]¹²⁺ metallocage-catalyzed reactions and provide a detailed mechanistic profile otherwise difficult to obtain from experiments. The findings of this study could also aid to the improvement and development of more efficient and selective supramolecular catalysis.

Subtle Stereochemical Effects Influence Binding and Purification Abilities of an FeII4L4 Cage

A tetrahedral Fe^II₄L₄ cage assembled from the coordination of triangular chiral, face-capping ligands to iron(II). This cage exists as two diastereomers in solution, which differ in the stereochemistry of their metal vertices, but share the same point chirality of the ligand. The equilibrium between these cage diastereomers was subtly perturbed by guest binding. This perturbation from equilibrium correlated with the size and shape fit of the guest within the host; insight as to the interplay between stereochemistry and fit was provided by atomistic well-tempered metadynamics simulations. The understanding thus gained as to the stereochemical impact on guest binding enabled the design of a straightforward process for the resolution of the enantiomers of a racemic guest.

Photoresponsive Supramolecular Polymers: From Light-Controlled Small Molecules to Smart Materials

Photoresponsive supramolecular polymers are well-organized assemblies based on highly oriented and reversible noncovalent interactions containing photosensitive molecules as (co-)monomers. They have attracted increasing interest in smart materials and dynamic systems with precisely controllable functions, such as light-driven soft actuators, photoresponsive fluorescent anticounterfeiting and light-triggered electronic devices. The present review discusses light-activated molecules used in photoresponsive supramolecular polymers with their main photo-induced changes, e.g., geometry, dipole moment, and chirality. Based on these distinct changes, supramolecular polymers formed by light-activated molecules exhibit photoresponsive disassembly and reassembly. As a consequence, photo-induced supramolecular polymerization, "depolymerization," and regulation of the lengths and topologies are observed. Moreover, the light-controlled functions of supramolecular polymers, such as actuation, emission, and chirality transfer along length scales, are highlighted. Furthermore, a perspective on challenges and future opportunities is presented. Besides the challenge of moving from harmful UV light to visible/near IR light avoiding fatigue, and enabling biomedical applications, future opportunities include light-controlled supramolecular actuators with helical motion, light-modulated information transmission, optically recyclable materials, and multi-stimuli-responsive supramolecular systems.

Homochiral Porous Metal-Organic Polyhedra with Multiple Kinds of Vertices

Metal-organic polyhedra featuring non-Archimedean/Platonic architectures with multiple kinds of vertices have aroused great attention for their fascinating structures and properties but are yet challenging to achieve. Here, we report a combinatorial strategy to make such nonclassic polyhedral cages by combining kinetically labile metal ions with non-planar organic linkers instead of the usual only inert metal centers and planar ligands. This facilitates the synthesis of an enantiopure twisted tetra(3-pyridyl)-based TADDOL (TADDOL = tetraaryl-1,3-dioxolane-4,5-dimethanol) ligand (L) capable of binding Ni(II) ions to produce a regular convex cage, Ni₆L₈, with two mixed metal/organic vertices and three rarely reported concave cages Ni₁₄L₈, Ni₁₈L₁₂, and Ni₂₄L₁₆ with three or four mixed vertices. Each of the cages has an amphiphilic cavity decorated with chiral dihydroxyl functionalities and packs into a three-dimensional structure. The enantioselective adsorption and separation performances of the cages are strongly dependent on their pore structure features. Particularly, Ni₁₄L₈ and Ni₁₈L₁₂ with wide openings can be solid adsorbents for the adsorptive and solid-phase extractive separation of a variety of racemic spirodiols with up to 98% ee, whereas Ni₆L₈ and Ni₂₄L₁₆ with smaller pore apertures cannot adsorb the racemates. The combination of single-crystal X-ray diffraction analysis of the host-guest adduct and GCMC simulation indicates that the enantiospecific recognition capabilities originate from the well-organized chiral inner sphere as well as multiple interactions within the chiral microenvironment. This work therefore provides an attractive strategy for the rational design of polyhedral cages, showing geometrically fascinating structures with properties different from those of classic assemblies.

Mechanoresponsive Metal-Organic Cage-Crosslinked Polymer Hydrogels

We report the formation of metal-organic cage-crosslinked polymer hydrogels. To enable crosslinking of the cages and subsequent network formation, we used homodifunctionalized poly(ethylene glycol) (PEG) chains terminally substituted with bipyridines as ligands for the Pd₆ L₄ corners. The encapsulation of guest molecules into supramolecular self-assembled metal-organic cage-crosslinked hydrogels, as well as ultrasound-induced disassembly of the cages with release of their cargo, is presented in addition to their characterization by nuclear magnetic resonance (NMR) techniques, rheology, and comprehensive small-angle X-ray scattering (SAXS) experiments. The constrained geometries simulating external force (CoGEF) method and barriers using a force-modified potential energy surface (FMPES) suggest that the cage-opening mechanism starts with the dissociation of one pyridine ligand at around 0.5 nN. We show the efficient sonochemical activation of the hydrogels HG_{3 -6} , increasing the non-covalent guest-loading of completely unmodified drugs available for release by a factor of ten in comparison to non-crosslinked, star-shaped assemblies in solution.

Light-Controlled Destruction and Assembly: Switching between Two Differently Composed Cage-Type Complexes

We report on two regioisomeric, diazocine ligands 1 and 2 that can both be photoswitched between the E- and Z-configurations with violet and green light. The self-assembly of the four species (1-Z, 1-E, 2-Z, 2-E) with Co^II ions was investigated upon changing the coordination vectors as a function of the ligand configuration (E vs Z) and regioisomer (1 vs 2). With 1-Z, Co₂ (1-Z)₃ was self-assembled, while a mixture of ill-defined species (oligomers) was observed with 2-Z. Upon photoswitching with 385 nm to the E configurations, the opposite was observed with 1-E forming oligomers and 2-E forming Co₂ (2-E)₃ . Light-controlled dis/assembly was demonstrated in a ligand competition experiment with sub-stoichiometric amounts of Co^II ions; alternating irradiation with violet and green light resulted in the reversible transformation between Co₂ (1-Z)₃ and Co₂ (2-E)₃ over multiple cycles without significant fatigue by photoswitching.

Multiple Effects of an Anionic Cyclodextrin Macrocycle on the Reversible Isomerization of a Photoactive Guest Dye

Understanding and controlling the reversible isomerization of photoactive molecules in order to obtain a tunable optical response is desirable for many photofunctional applications. This study describes the interesting effects of an anionic cyclodextrin host (sulfated-βCD, SCD) on the photoisomerization and protonation equilibrium of an important hemicyanine dye (trans-4-[4-(dimethylamino)styryl]-1-methylpyridinium iodide, DSP). The SCD host assists in unlocking the photoisomerization potential of DSP by promoting protonation of the dye. It also assists in stabilizing the cis isomer of the protonated dye, thereby significantly delaying the reverse cis to trans isomerization of DSPH⁺. Furthermore, the interplay of both hydrophobic and electrostatic interactions in the complex formation of SCD with DSPH⁺ makes the reverse cis to trans isomerization of DSPH⁺ amenable to influence by the added salt. The stimuli-responsive reversible isomerization of SCD-DSPH⁺ is an interesting case from the perspective of chemical sensing or light operated functional materials with host-guest systems.

Density-tunable pathway complexity in a minimalistic self-assembly model

An open challenge in self-assembly is learning how to design systems that can be conditionally guided towards different target structures depending on externally-controlled conditions. Using a theoretical and numerical approach, here we discuss a minimalistic self-assembly model that can be steered towards different types of ordered constructs at the equilibrium by solely tuning a facile selection parameter, namely the density of building blocks. Metadynamics and Langevin dynamics simulations allow us to explore the behavior of the system in and out of equilibrium conditions. We show that the density-driven tunability is encoded in the pathway complexity of the system, and specifically in the competition between two different main self-assembly routes. A comprehensive set of simulations provides insight into key factors allowing to make one self-assembling pathway prevailing on the other (or vice versa), determining the selection of the final self-assembled products. We formulate and validate a practical criterion for checking whether a specific molecular design is predisposed for such density-driven tunability of the products, thus offering a new, broader perspective to realize and harness this facile extrinsic control of conditional self-assembly.

Unraveling the timescale of the structural photo-response within oriented metal-organic framework films

Fundamental knowledge on the intrinsic timescale of structural transformations in photo-switchable metal-organic framework films is crucial to tune their switching performance and to facilitate their applicability as stimuli-responsive materials. In this work, for the first time, an integrated approach to study and quantify the temporal evolution of structural transformations is demonstrated on an epitaxially oriented DMOF-1-on-MOF film system comprising azobenzene in the DMOF-1 pores (DMOF-1/AB). We employed time-resolved Grazing Incidence Wide-Angle X-Ray Scattering measurements to track the structural response of the DMOF-1/AB film upon altering the length of the azobenzene molecule by photo-isomerization (trans-to-cis, 343 nm; cis-to-trans, 450 nm). Within seconds, the DMOF-1/AB response occurred fully reversible and over several switching cycles by cooperative photo-switching of the oriented DMOF-1/AB crystallites as confirmed further by infrared measurements. Our work thereby suggests a new avenue to elucidate the timescales and photo-switching characteristics in structurally responsive MOF film systems.

Reconstructing reactivity in dynamic host-guest systems at atomistic resolution: amide hydrolysis under confinement in the cavity of a coordination cage

Spatial confinement is widely employed by nature to attain unique efficiency in controlling chemical reactions. Notable examples are enzymes, which selectively bind reactants and exquisitely regulate their conversion into products. In an attempt to mimic natural catalytic systems, supramolecular metal-organic cages capable of encapsulating guests in their cavity and of controlling/accelerating chemical reactions under confinement are attracting increasing interest. However, the complex nature of these systems, where reactants/products continuously exchange in-and-out of the host, makes it often difficult to elucidate the factors controlling the reactivity in dynamic regimes. As a case study, here we focus on a coordination cage that can encapsulate amide guests and enhance their hydrolysis by favoring their mechanical twisting towards reactive molecular configurations under confinement. We designed an advanced multiscale simulation approach that allows us to reconstruct the reactivity in such host-guest systems in dynamic regimes. In this way, we can characterize amide encapsulation/expulsion in/out of the cage cavity (thermodynamics and kinetics), coupling such host-guest dynamic equilibrium with characteristic hydrolysis reaction constants. All computed kinetic/thermodynamic data are then combined, obtaining a statistical estimation of reaction acceleration in the host-guest system that is found in optimal agreement with the available experimental trends. This shows how, to understand the key factors controlling accelerations/variations in the reaction under confinement, it is necessary to take into account all dynamic processes that occur as intimately entangled in such host-guest systems. This also provides us with a flexible computational framework, useful to build structure-dynamics-property relationships for a variety of reactive host-guest systems.

Visible-Light-Responsive Self-Assembled Complexes: Improved Photoswitching Properties by Metal Ion Coordination

A photoswitchable ligand based on azobenzene is self-assembled with palladium(II) ions to form a [Pd2 (E-L)4 ]4+ cage. Irradiation with 470 nm light results in the near-quantitative switching to a monomeric species [Pd(Z-L)2 ]2+ , which can be reversed by irradiation with 405 nm light, or heat. The photoswitching selectivity towards the metastable isomer is significantly improved upon self-assembly, and the thermal half-life is extended from 40 days to 850 days, a promising approach for tuning photoswitching properties.

Ternary host-guest complexes with rapid exchange kinetics and photoswitchable fluorescence

Confinement within molecular cages can dramatically modify the physicochemical properties of the encapsulated guest molecules, but such host-guest complexes have mainly been studied in a static context. Combining confinement effects with fast guest exchange kinetics could pave the way toward stimuli-responsive supramolecular systems-and ultimately materials-whose desired properties could be tailored "on demand" rapidly and reversibly. Here, we demonstrate rapid guest exchange between inclusion complexes of an open-window coordination cage that can simultaneously accommodate two guest molecules. Working with two types of guests, anthracene derivatives and BODIPY dyes, we show that the former can substantially modify the optical properties of the latter upon noncovalent heterodimer formation. We also studied the light-induced covalent dimerization of encapsulated anthracenes and found large effects of confinement on reaction rates. By coupling the photodimerization with the rapid guest exchange, we developed a new way to modulate fluorescence using external irradiation.

Beyond Platonic: How to Build Metal-Organic Polyhedra Capable of Binding Low-Symmetry, Information-Rich Molecular Cargoes

The field of metallosupramolecular chemistry has advanced rapidly in recent years. Much work in this area has focused on the formation of hollow self-assembled metal-organic architectures and exploration of the applications of their confined nanospaces. These discrete, soluble structures incorporate metal ions as 'glue' to link organic ligands together into polyhedra.Most of the architectures employed thus far have been highly symmetrical, as these have been the easiest to prepare. Such high-symmetry structures contain pseudospherical cavities, and so typically bind roughly spherical guests. Biomolecules and high-value synthetic compounds are rarely isotropic, highly-symmetrical species. To bind, sense, separate, and transform such substrates, new, lower-symmetry, metal-organic cages are needed. Herein we summarize recent approaches, which taken together form the first draft of a handbook for the design of higher-complexity, lower-symmetry, self-assembled metal-organic architectures.

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.

Encapsulation within a coordination cage modulates the reactivity of redox-active dyes

Confining molecules within well-defined nanosized spaces can profoundly alter their physicochemical characteristics. For example, the controlled aggregation of chromophores into discrete oligomers has been shown to tune their optical properties whereas encapsulation of reactive species within molecular hosts can increase their stability. The resazurin/resorufin pair has been widely used for detecting redox processes in biological settings; yet, how tight confinement affects the properties of these two dyes remains to be explored. Here, we show that a flexible Pd^II₆L₄ coordination cage can efficiently encapsulate both resorufin and resazurin in the form of dimers, dramatically modulating their optical properties. Furthermore, binding within the cage significantly decreases the reduction rate of resazurin to resorufin, and the rate of the subsequent reduction of resorufin to dihydroresorufin. During our studies, we also found that upon dilution, the Pd^II₆L₄ cage disassembles to afford Pd^II₂L₂ species, which lacks the ability to form inclusion complexes - a process that can be reversed upon the addition of the strongly binding resorufin/resazurin guests. We expect that the herein disclosed ability of a water-soluble cage to reversibly modulate the optical and chemical properties of a molecular redox probe will expand the versatility of synthetic fluorescent probes in biologically relevant environments.

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.

Visible-Light Switching of Metallosupramolecular Assemblies

A photoswitchable ligand and palladium(II) ions form a dynamic mixture of self-assembled metallosupramolecular structures. The photoswitching ligand is an ortho-fluoroazobenzene with appended pyridyl groups. Combining the E-isomer with palladium(II) salts affords a double-walled triangle with composition [Pd3 L6 ]6+ and a distorted tetrahedron [Pd4 L8 ]8+ (1 : 2 ratio at 298 K). Irradiation with 410 nm light generates a photostationary state with approximately 80 % of the E-isomer of the ligand and results in the selective disassembly of the tetrahedron, the more thermodynamically stable structure, and the formation of the triangle, the more kinetically inert product. The triangle is then slowly transformed back into the tetrahedron over 2 days at 333 K. The Z-isomer of the ligand does not form any well-defined structures and has a thermal half-life of 25 days at 298 K. This approach shows how a thermodynamically preferred self-assembled structure can be reversibly pumped to a kinetic trap by small perturbations of the isomer distribution using non-destructive visible light.

Selective Encapsulation and Unusual Stabilization of cis-Isomers by a Spherical Polyaromatic Cavity

To explore new cavity functions, we herein employed  cis-trans   stereoisomers   with a N=N, C=C, or C=N unit as guest indicators for a polyaromatic capsule. Thanks to the rigid, spherical cavity with a diameter of ~1 nm, azobenzene and stilbene derivatives are quantitatively encapsulated by the capsule with 100%  cis -selectivity in water. The isomerization of the  cis -azo compound is suppressed against heat and light in the cavity, due to the confinement effect. Furthermore,  C,N -diphenyl imine derivatives are quantitatively encapsulated by the capsule in water and adopt an otherwise unstable  cis -form. The polyaromatic cavity suppresses the hydrolysis of the imines in water, even at elevated temperature, due to the shielding effect. Accordingly, the properties of the  cis-trans   isomers  could be largely altered through supramolecular manipulation.

A computational study of competing conformational selection and induced fit in an abiotic system

Host-guest complexations can be described by two competing mechanisms, conformational selection (CS) and induced fit (IF). In this work, we used a combination of nudged elastic band (NEB), adaptive steered molecular dynamics (ASMD), and density functional theory (DFT, with a correction for dispersion) to study the dynamics of the pathways (IF/CS) by which two conformers of basket B(+) and B(-) interconvert and trap CX₄ guests (X = Cl and Br). While the results from NEB/DFT studies disclosed host-guest noncovalent contacts reducing the basket's conformational dynamics, ASMD methodology suggested an associative mechanism for the guest complexation. With theory in excellent agreement with experiments, NEB and ASMD emerge as the methods of choice for studying dynamics of supramolecular systems.

Non-uniform Photoinduced Unfolding of Supramolecular Polymers Leading to Topological Block Nanofibers

Synthesis of one-dimensional nanofibers with distinct topological (higher-order structural) domains in the same main chain is one of the challenging topics in modern supramolecular polymer chemistry. Non-uniform structural transformation of supramolecular polymer chains by external stimuli may enable preparation of such nanofibers. To demonstrate feasibility of this post-polymerization strategy, we prepared a photoresponsive helically folded supramolecular polymers from a barbiturate monomer containing an azobenzene-embedded rigid π-conjugated scaffold. In contrast to previous helically folded supramolecular polymers composed of a more flexible azobenzene monomer, UV-light induced unfolding of the newly prepared helically folded supramolecular polymers occurred nonuniformly, affording topological block copolymers consisting of folded and unfolded domains. The formation of such blocky copolymers indicates that the photoinduced unfolding of the helically folded structures initiates from relatively flexible parts such as termini or defects. Spontaneous refolding of the unfolded domains was observed after visible-light irradiation followed by aging to restore fully folded structures.