Beyond Single-Cycle Autonomous Molecular Machines: Light-Powered Shuttling in a Multi-Cycle Reaction Network

Biomolecular machines autonomously convert energy into functions, driving systems away from thermodynamic equilibrium. This energy conversion is achieved by leveraging complex, kinetically asymmetric chemical reaction networks that are challenging to characterize precisely. In contrast, all known synthetic molecular systems in which kinetic asymmetry has been quantified are well described by simple single-cycle networks. Here, we report on a unique light-driven [2]rotaxane that enables the autonomous operation of a synthetic molecular machine with a multi-cycle chemical reaction network. Unlike all prior systems, the present one exploits a photoactive macrocycle, which features a different photoreactivity depending on the binding sites at which it resides. Furthermore, E to Z isomerization reverses the relative affinity of the macrocycle for two binding sites on the axle, resulting in a multi-cycle network. Building on the most recent theoretical advancements, this work quantifies kinetic asymmetry in a multi-cycle network for the first time. Our findings represent the simplest rotaxane capable of autonomous shuttling developed so far and offer a general strategy to generate and quantify kinetic asymmetry beyond single-cycle systems.

Macrocyclic receptors for anion recognition

Macrocyclic receptors have emerged as versatile and efficient molecular tools for the recognition and sensing of anions, playing a pivotal role in molecular recognition and supramolecular chemistry. The following review provides an overview of the recent advances in the design, synthesis, and applications of macrocyclic receptors specifically tailored for anion recognition. The unique structural features of macrocycles, such as their well-defined structures and pre-organised binding sites, contribute to their exceptional anion-binding capabilities that have led to their application across a broad range of the chemical and biological sciences.

Solvent effects in anion recognition

Anion recognition is pertinent to a range of environmental, medicinal and industrial applications. Recent progress in the field has relied on advances in synthetic host design to afford a broad range of potent recognition motifs and novel supramolecular structures capable of effective binding both in solution and at derived molecular films. However, performance in aqueous media remains a critical challenge. Understanding the effects of bulk and local solvent on anion recognition by host scaffolds is imperative if effective and selective detection in real-world media is to be viable. This Review seeks to provide a framework within which these effects can be considered both experimentally and theoretically. We highlight proposed models for solvation effects on anion binding and discuss approaches to retain strong anion binding in highly competitive (polar) solvents. The synthetic design principles for exploiting the aforementioned solvent effects are explored.

Tuning CH Hydrogen Bond-Based Receptors toward Picomolar Anion Affinity via the Inductive Effect of Distant Substituents

Inspired by nature, artificial hydrogen bond-based anion receptors have been developed to achieve high anion selectivity; however, their binding affinity is usually low. The potency of these receptors is usually increased by the introduction of aryl substituents, which withdraw electrons from their binding site through the resonance effect. Here, we show that the polarization of the C(sp3 )-H binding site of bambusuril receptors, and thus their potency to bind anions, can be modulated by the inductive effect. The presence of electron-withdrawing groups on benzyl substituents of bambusurils significantly increases their binding affinities to halides, resulting in the strongest iodide receptor reported to date with an association constant greater than 1013  M-1 in acetonitrile. A Hammett plot showed that while the bambusuril affinity toward halides linearly increases with the electron-withdrawing power of their substituents, their binding selectivity remains essentially unchanged.

Solvent Acts as the Referee in a Match-Up Between Charged and Preorganized Receptors

The prevalence of anion-cation contacts in biomolecular recognition under aqueous conditions suggests that ionic interactions should dominate the binding of anions in solvents across both high and low polarities. Investigations of this idea using titrations in low polarity solvents are impaired by interferences from ion pairing that prevent a clear picture of binding. To address this limitation and test the impact of ion-ion interactions across multiple solvents, we quantified chloride binding to a cationic receptor after accounting for ion pairing. In these studies, we created a chelate receptor using aryl-triazole CH donors and a quinolinium unit that directs its cationic methyl inside the binding pocket. In low-polarity dichloromethane, the 1 : 1 complex (log K1 : 1 ~ 7.3) is more stable than neutral chelates, but fortuitously comparable to a preorganized macrocycle (log K1 : 1 ~ 6.9). Polar acetonitrile and DMSO diminish stabilities of the charged receptor (log K1 : 1 ~ 3.7 and 1.9) but surprisingly 100-fold more than the macrocycle. While both receptors lose stability by dielectric screening of electrostatic stability, the cationic receptor also pays additional costs of organization. Thus even though the charged receptor has stronger binding in apolar solvents, the uncharged receptor has more anion affinity in polar solvents.

Aromatic pentaamide macrocycles bind anions with high affinity for transport across biomembranes

The convergent positioning of functional groups in biomacromolecules leads to good binding, catalytic and transport capabilities. Synthetic frameworks capable of convergently locking functional groups with minimized conformational uncertainty-leading to similar properties-are highly desirable but rare. Here we report C5-symmetric aromatic pentaamide macrocycles synthesized in one pot from the corresponding monomers. Their crystal structures reveal a star-shaped, fully constrained backbone that causes ten alternating NH/CH hydrogen-bond donors and five large amide dipoles to orient towards the centre of the macrocycle. With a highly electropositive cavity in a high-energy unbound state, the macrocycles bind anions in a 1:1 stoichiometry in solution, with high affinity for halides and very high affinity for oxoanions. We demonstrate that such macrocycles are able to transport anions across lipid bilayers with a high chloride selectivity and restore the depleted airway surface liquid of cystic fibrosis airway cell cultures.

Tripodal Organic Cages with Unconventional CH···O Interactions for Perchlorate Remediation in Water

Perchlorate anions used in industry are harmful pollutants in groundwater. Therefore, selectively binding perchlorate provides solutions for environmental remediation. Here, we synthesized a series of tripodal organic cages with highly preorganized Csp3-H bonds that exhibit selectively binding to perchlorate in organic solvents and water. These cages demonstrated binding affinities to perchlorate of 105-106 M-1 at room temperature, along with high selectivity over competing anions, such as iodide and nitrate. Through single crystal structure analysis and density functional theory calculations, we identified unconventional Csp3-H···O interactions as the primary driving force for perchlorate binding. Additionally, we successfully incorporated this cage into a 3D-printable polymer network, showcasing its efficacy in removing perchlorate from water.

Steric Control over the Threading of Pyrophosphonates with One or Two Cyanostar Macrocycles during Pseudorotaxane Formation

The supramolecular recognition of anions is increasingly harnessed to achieve the self-assembly of supramolecular architectures, ranging from cages and polymers to (pseudo)rotaxanes. The cyanostar (CS) macrocycle has previously been shown to form 2 : 1 complexes with organophosphate anions that can be turned into [3]rotaxanes by stoppering. Here we achieved steric control over the assembly of pseudorotaxanes comprising the cyanostar macrocycle and a thread that is based, for the first time, on organo-pyrophosphonates. Subtle differences in steric bulk on the threads allowed formation of either [3]pseudorotaxanes or [2]pseudorotaxanes. We demonstrate that the threading kinetics are governed by the steric demand of the organo-pyrophosphonates and in one case, slows down to the timescale of minutes. Calculations show that the dianions are sterically offset inside the macrocycles. Our findings broaden the scope of cyanostar-anion assemblies and may have relevance for the design of molecular machines whose directionality is a result of relatively slow slipping.

Nonspherical anion sequestration by C-H hydrogen bonding

Macrocyclic arenes laid the foundations of supramolecular chemistry and their study established the fundamentals of noncovalent interactions. Advancing their frontier, here we designed rigidified resorcin[4]arenes that serve as hosts for large nonspherical anions. In one synthetic step, we vary the host's anion affinity properties by more than seven orders of magnitude. This is possible by engineering electropositive aromatic C–H bond donors in an idealized square planar geometry embedded within the host's inner cavity. The hydrogen atom's electropositivity is tuned by introducing fluorine atoms as electron withdrawing groups. These novel macrocycles, termed fluorocages, are engineered to sequester large anions. Indeed, experimental data shows an increase in the anion association constant (K_a) as the number of F atoms increase. The observed trend is rationalized by DFT calculations of Hirshfeld Charges (HCs). Most importantly, fluorocages in solution showed weak-to-medium binding affinity for large anions like [PF₆]⁻ (10²< K_a <10⁴ M⁻¹), and high affinity for [MeSO₃]⁻ (K_a >10⁶).

Fluorocages: new class of rigidified host utilizing nontraditional C–H hydrogen bonds to capture the nonspherical anions.

Anion-Selective Electrodes Based On a CH-Hydrogen Bonding Bis-macrocyclic Ionophore with a Clamshell Architecture

CH-hydrogen bonding provides access to new building blocks for making macrocyclic ionophores with high degrees of preorganization and selective anion recognition. In this study, an anion-binding ionophore in the shape of a clamshell (ClS) was employed that is composed of two cyanostar (CNstar) macrocycles with preorganized cavities linked with a 12-carbon chain. This ionophore allows for anion complexation by CH-hydrogen bonding. The potentiometric performance of membrane-based ion-selective electrodes incorporating this ionophore was evaluated. Different membrane compositions were prepared to determine the optimum concentrations of the ionophore and lipophilic additive in the membrane. The optimized electrode had a slope of -58.2 mV/decade and demonstrated an anti-Hofmeister selectivity pattern toward iodide with a nanomolar detection limit. Electrospray ionization mass spectrometry was employed to study the relative association strengths of ClS with various anions. The observed mass peaks of the ion-ionophore complexes were found to be consistent with the potentiometric selectivity pattern of the corresponding electrodes. Overall, the selectivity of the electrode could be altered by using an ionophore in which the two CNstar macrocycles are linked together with a flexible 12-carbon chain to control the molecularity of the binding event.

Chain Entropy Beats Hydrogen Bonds to Unfold and Thread Dialcohol Phosphates inside Cyanostar Macrocycles To Form [3]Pseudorotaxanes

The recognition of substituted phosphates underpins many processes including DNA binding, enantioselective catalysis, and recently template-directed rotaxane synthesis. Beyond ATP and a few commercial substrates, however, little is known about how substituents effect organophosphate recognition. Here, we examined alcohol substituents and their impact on recognition by cyanostar macrocycles. The organophosphates were disubstituted by alcohols of various chain lengths, dipropanol, dihexanol, and didecanol phosphate, each accessed using modular solid-phases syntheses. Based on the known size-selective binding of phosphates by π-stacked dimers of cyanostars, threaded [3]pseudorotaxanes were anticipated. While seen with butyl substituents, pseudorotaxane formation was disrupted by competitive OH···O- hydrogen bonding between both terminal hydroxyls and the anionic phosphate unit. Crystallography also showed formation of a backfolded propanol conformation resulting in an 8-membered ring and a perched cyanostar assembly. Motivated by established entropic penalties accompanying ring formation, we reinstated [3]pseudorotaxanes by extending the size of the substituent to hexanol and decanol. Chain entropy overcomes the enthalpically favored OH···O- contacts to favor random-coil conformations required for seamless, high-fidelity threading of dihexanol and didecanol phosphates inside cyanostars. These studies highlight how chain length and functional groups on phosphate's substituents can be powerful design tools to regulate binding and control assembly formation during phosphate recognition.

Zero-Overlap Fluorophores for Fluorescent Studies at Any Concentration

Fluorophores are powerful tools for the study of chemistry, biology, and physics. However, fluorescence is severely impaired when concentrations climb above 5 μM as a result of effects like self-absorption and chromatic shifts in the emitted light. Herein, we report the creation of a charge-transfer (CT) fluorophore and the discovery that its emission color seen at low concentrations is unchanged even at 5 mM, some 3 orders of magnitude beyond typical limits. The fluorophore is composed of a triphenylamine-substituted cyanostar macrocycle, and it exhibits a remarkable Stokes shift of 15 000 cm^-1 to generate emission at 633 nm. Crucial to the performance of this fluorophore is the observation that its emission spectrum shows near-zero overlap with the absorption band at 325 nm. We propose that reducing the spectral overlap to zero is a key to achieving full fluorescence across all concentrations. The triphenylamine donor and five cyanostilbene acceptor units of the macrocycle generate an emissive CT state. Unlike closely related donor-acceptor control compounds showing dual emission, the cyanostar framework inhibited emission from the second state to create a zero-overlap fluorophore. We demonstrated the use of emission spectroscopy for characterization of host-guest complexation at millimolar concentrations, which are typically the exclusive domain of NMR spectroscopy. The binding of the PF₆^- anion generates a 2:1 sandwich complex with blue-shifted emission. Distinct from twisted intramolecular charge-transfer (TICT) states, experiment-supported density functional theory shows a 67° twist inside an acceptor unit in the CT state instead of displaying a twist between the donor and acceptor; it is TICT-like. Inspired by the findings, we uncovered similar concentration-independent behavior from a control compound, strongly suggesting this behavior may be latent to other large Stokes-shift fluorophores. We discuss strategies capable of generating zero-overlap fluorophores to enable accurate fluorescence characterization of processes across all practical concentrations.

The road to aryl CHanion binding was paved with good intentions: fundamental studies, host design, and historical perspectives in CH hydrogen bonding

Throughout the design and development of supramolecular receptors for anion binding, many different non-covalent anion-binding motifs have been employed. One motif seen in many host-guest systems is the sometimes weaker, 'non-traditional' aryl CH hydrogen bond. From June Sutor's discovery of the interaction and its subsequent dismissal by the field in the 1960s to today's use of the aryl CH hydrogen bond in synthetic anion receptors, the path our lab took to begin studying this interaction has been influenced by many other researchers in the field. This feature article highlights the history and properties of the CH hydrogen bond, with a particular focus on aryl CH hydrogen bonds in anion recognition. We highlight select recent developments in the field of anion receptors utilizing aryl CH hydrogen bonds, with an emphasis on how this has influenced the evolution of our approach in designing fundamental studies on CH hydrogen bonding and exploiting this interaction in efforts aimed toward preferential anion binding.

The Chaotropic Effect as an Assembly Motif in Chemistry

Following up on scattered reports on interactions of conventional chaotropic ions (for example, I- , SCN- , ClO4- ) with macrocyclic host molecules, biomolecules, and hydrophobic neutral surfaces in aqueous solution, the chaotropic effect has recently emerged as a generic driving force for supramolecular assembly, orthogonal to the hydrophobic effect. The chaotropic effect becomes most effective for very large ions that extend beyond the classical Hofmeister scale and that can be referred to as superchaotropic ions (for example, borate clusters and polyoxometalates). In this Minireview, we present a continuous scale of water-solute interactions that includes the solvation of kosmotropic, chaotropic, and hydrophobic solutes, as well as the creation of void space (cavitation). Recent examples for the association of chaotropic anions to hydrophobic synthetic and biological binding sites, lipid bilayers, and surfaces are discussed.

Inchworm movement of two rings switching onto a thread by biased Brownian diffusion represent a three-body problem

The coordinated motion of many individual components underpins the operation of all machines. However, despite generations of experience in engineering, understanding the motion of three or more coupled components remains a challenge, known since the time of Newton as the "three-body problem." Here, we describe, quantify, and simulate a molecular three-body problem of threading two molecular rings onto a linear molecular thread. Specifically, we use voltage-triggered reduction of a tetrazine-based thread to capture two cyanostar macrocycles and form a [3]pseudorotaxane product. As a consequence of the noncovalent coupling between the cyanostar rings, we find the threading occurs by an unexpected and rare inchworm-like motion where one ring follows the other. The mechanism was derived from controls, analysis of cyclic voltammetry (CV) traces, and Brownian dynamics simulations. CVs from two noncovalently interacting rings match that of two covalently linked rings designed to thread via the inchworm pathway, and they deviate considerably from the CV of a macrocycle designed to thread via a stepwise pathway. Time-dependent electrochemistry provides estimates of rate constants for threading. Experimentally derived parameters (energy wells, barriers, diffusion coefficients) helped determine likely pathways of motion with rate-kinetics and Brownian dynamics simulations. Simulations verified intercomponent coupling could be separated into ring-thread interactions for kinetics, and ring-ring interactions for thermodynamics to reduce the three-body problem to a two-body one. Our findings provide a basis for high-throughput design of molecular machinery with multiple components undergoing coupled motion.

Flexible imidazolium macrocycles: building blocks for anion-induced self-assembly

This feature article summarises recent contributions of the authors in the area of anion-induced supramolecular self-assembly. It is based on the chemistry of a set of tetracationic imidazolium macrocycles, specifically the so-called 'Texas-sized' molecular box, cyclo[2](2,6-di(1H-imidazol-1-yl)pyridine)[2](1,4-dimethylenebenzene) (1⁴⁺), and its congeners, cyclo[2](2,6-di(1H-imidazol-1-yl)pyridine)[2](1,2-dimethylenebenzene) (2⁴⁺), cyclo[2](2,6-di(1H-imidazol-1-yl)pyridine)[2](1,3-dimethylenebenzene) (3⁴⁺), and cyclo[2](2,6-di(1H-imidazol-1-yl)pyridine)[2](2,6-dimethylenepyridine) (4⁴⁺). These systems collectively have been demonstrated as being versatile building blocks that interact with organic carboxylate or sulfonate anions, as well as substrates (e.g., neutral molecules or metal cations). Most work to date has been carried out with 1⁴⁺, a system that has been found to support the construction of a number of stimuli responsive self-assembled ensembles. This macrocycle and others of the 'Texas-sized' box family also show the potential to react as carbene precursors and to undergo post-synthetic modification (PSM) to produce new functional macrocycles, such as trans- and cis-cyclo[2]((Z)-N-(2-((6-(1H-imidazol-1-yl)pyridin-2-yl)amino)vinyl)formamide)[2](1,4-bismethylbenzene) (5²⁺ and 6²⁺, respectively). On the basis of the work reviewed in this Feature article, we propose that the imidazolium macrocycles 1⁴⁺-4⁴⁺ can be considered as useful tools for the construction of ensembles with environmentally responsive features, including control over self-assembly and an ability to undergo precursor-specific PSM.

Phosphate-phosphate oligomerization drives higher order co-assemblies with stacks of cyanostar macrocycles

The importance of phosphate in biology and chemistry has long motivated investigation of its recognition. Despite this interest, phosphate's facile oligomerization is only now being examined following the discovery of complexes of anion-anion dimers of hydroxyanions. Here we address how oligomerization dictates phosphate's recognition properties when engaged with planar cyanostar macrocycles that can also oligomerize by stacking. The crystal structure of cyanostar with phosphate shows an unprecedented tetrameric stack of cyanostar macrocycles threaded by a phosphate trimer, [H₂PO₄···H₂PO₄···H₂PO₄]^3-. The solution behaviour, studied as a function of solvent quality, highlights how dimers and trimers of phosphate drive formation of higher order stacks of cyanostar into dimer, trimer and tetramer co-assemblies. Solution behaviors differ significantly from simpler complexes of bisulfate hydroxyanion dimers. Phosphate oligomerization is: (1) preferred over ion pairing with tetrabutylammonium cations, (2) inhibits disassembly of the complexes upon dilution, and (3) resists interference from competitive anion solvation. The phosphate oligomers also appear critical for stability; complexation of just one phosphate with cyanostars is unfavored. The cyanostar's ability to self-assemble is found to create a tubular, highly electropositive cavity that complements the size and shape of the phosphate oligomers as well as their higher charge. When given the opportunity, phosphate will cooperate with the receptor to form co-assembled architectures.

Anion-coordination-directed self-assemblies

This review introduces the interplay of anion coordination and supramolecular self-assembly, presenting recent progress in anion-induced and anion-coordination-based self-assemblies.

Triazole-bearing calixpyrroles: strong halide binding affinities through multiple N–H and C–H hydrogen bonds

Triazole-bearing calixpyrroles (TCPs) were synthesized as artificial anion binding receptors.

Anion Recognition as a Supramolecular Switch of Cell Internalization

The cell internalization of designed oligoarginine peptides equipped with six glutamic acid residues and an anionic pyranine at the N-terminus is triggered upon addition of a supramolecular host. This host binds specifically to the pyranine moiety, enabling the complex to traverse the cell membrane. Interestingly, none of the components, neither the host nor the guest, are able to cross the cell membrane on their own.

Triamide macrocyclic chloride receptors via a one-pot tandem reduction–condensation–cyclization reaction

A chloride binding triamide macrocycle has been developed in one pot from the corresponding monomer via tandem reduction–condensation–cyclization reactions.

Macrocyclic shape-persistency of cyclo[6]aramide results in enhanced multipoint recognition for the highly efficient template-directed synthesis of rotaxanes

Examples of using two-dimensional shape-persistent macrocycles, i.e. those having noncollapsible and geometrically well-defined skeletons, for constructing mechanically interlocked molecules are scarce, which contrasts the many applications of these macrocycles in molecular recognition and functional self-assembly. Herein, we report the crucial role played by macrocyclic shape-persistency in enhancing multipoint recognition for the highly efficient template-directed synthesis of rotaxanes. Cyclo[6]aramides, with a near-planar conformation, are found to act as powerful hosts that bind bipyridinium salts with high affinities. This unique recognition module, composed of two macrocyclic molecules with one bipyridinium ion thread through the cavity, is observed both in the solid state and in solution, with unusually high binding constants ranging from ∼10¹³ M^-2 to ∼10¹⁵ M^-2 in acetone. The high efficacy of this recognition motif is embodied by the formation of compact [3]rotaxanes in excellent yields based on either a "click-capping" (91%) or "facile one-pot" (85%) approach, underscoring the great advantage of using H-bonded aromatic amide macrocycles for the highly efficient template-directed synthesis of mechanically interlocked structures. Furthermore, three cyclo[6]aramides bearing different peripheral chains 1-3 demonstrate high specificity in the synthesis of a [3]rotaxane from 1 and 2, and a [2]rotaxane from 3via a "facile one-pot" approach, in each case as the only isolated product. Analysis of the crystal structure of the [3]rotaxane reveals a highly compact binding mode that would be difficult to access using other macrocycles with a flexible backbone. Leveraging this unique recognition motif, resulting from the shape-persistency of these oligoamide macrocycles, in the template-directed synthesis of compact rotaxanes may open up new opportunities for the development of higher order interlocked molecules and artificial molecular machines.

Anions Stabilize Each Other inside Macrocyclic Hosts

Contrary to the simple expectations from Coulomb's law, Weinhold proposed that anions can stabilize each other as metastable dimers, yet experimental evidence for these species and their mutual stabilization is missing. We show that two bisulfate anions can form such dimers, which stabilize each other with self-complementary hydrogen bonds, by encapsulation inside a pair of cyanostar macrocycles. The resulting 2:2 complex of the bisulfate homodimer persists across all states of matter, including in solution. The bisulfate dimer's OH⋅⋅⋅O hydrogen bonding is seen in a ¹ H NMR peak at 13.75 ppm, which is consistent with borderline-strong hydrogen bonds.

A high-yield synthesis and acid–base response of phosphate-templated [3]rotaxanes

We show a high-yielding synthesis (80%) of [3]rotaxanes using shape-persistent macrocycles, cyanostars, and anionic organo-phosphate templates catalyzed by low steric-demand click chemistry.