Molecular recognition of peptides and proteins by cucurbit[n]urils: systems and applications

The development of methodology for attaching ligand binding sites to proteins of interest has accelerated biomedical science. Such protein tags have widespread applications as well as properties that significantly limit their utility. This review describes the mechanisms and applications of supramolecular systems comprising the synthetic receptors cucurbit[7]uril (Q7) or cucurbit[8]uril (Q8) and their polypeptide ligands. Molecular recognition of peptides and proteins occurs at sites of 1-3 amino acids with high selectivity and affinity via several distinct mechanisms, which are supported by extensive thermodynamic and structural studies in aqueous media. The commercial availability, low cost, high stability, and biocompatibility of these synthetic receptors has led to the development of myriad applications. This comprehensive review compiles the molecular recognition studies and the resulting applications with the goals of providing a valuable resource to the community and inspiring the next generation of innovation.

Pillar[n]arene-Based Fluorescence Turn-On Chemosensors for the Detection of Spermine, Spermidine, and Cadaverine in Saline Media and Biofluids

Polyamines are essential analytes due to their critical role in various biological processes and human health in general. Due to their role as regulators for cell growth and proliferation (putrescine and spermine), as neuroprotectors, gero-, and cardiovascular protectors (spermidine), and as bacterial growth indicators (cadaverine), rapid, simple, and cost-effective methods for polyamine detection in biofluids are in demand. The present study focuses on the development and investigation of self-assembled and fluorescent host⋅dye chemo-sensors based on sulfonated pillar[5]arene for the specific detection of polyamines. Binding studies, as well as stability and functionality assessments of the turn-on chemosensors for selective polyamine detection in saline and biologically relevant media, are shown. Furthermore, the practical applicability of the developed chemo-sensors is demonstrated in biofluids such as human urine and saliva.

A fluorescent sensor array based on a single cucurbit[5]uril-truxene probe for simultaneous identification of five heavy metal ions

There is a need to develop simple and effective strategies for the rapid detection of heavy metal ions (HMIs) in order to protect the environment and human health. A simple fluorescent sensor array based on a single cucurbit[5]uril-truxene probe was proposed to simultaneously identify five HMIs (Pb2+, Cu2+, Ag+, Fe2+ and Fe3+). This probe was synthesized using monohydroxyl cucurbit[5]uril and monobromohexyl truxene by a substitution reaction between them. It could be observed that the fluorescence response of this synthesized probe to HMIs was closely related to the pH of the aqueous solution, exhibiting different fluorescence intensities at pH 3.0, 7.0, and 9.0. Based on this phenomenon, a fluorescent sensor array based on a single cucurbit[5]uril-truxene probe was then constructed by simply altering the pH in the sensor element. These unique fluorescence responses were analyzed using linear discriminant analysis (LDA) to identify metal ions. A concentration limit classification of 0.1 μM was applied to the above five HMIs. Moreover, the quantification of metal ions was implemented even at low concentrations of 48-121 nM. This array showed good results in the recognition of metal ions in real water samples (lake water and tap water samples), which shows its broad application prospects in many fields, including monitoring of the environmental water quality and so on.

Overcoming barriers with non-covalent interactions: supramolecular recognition of adamantyl cucurbit[n]uril assemblies for medical applications

Adamantane, a staple in medicinal chemistry, recently became a cornerstone of a supramolecular host-guest drug delivery system, ADA/CB[n]. Owing to a good fit between the adamantane cage and the host cavity of the cucurbit[n]uril macrocycle, formed strong inclusion complexes find applications in drug delivery and controlled drug release. Note that the cucurbit[n]uril host is not solely a delivery vehicle of the ADA/CB[n] system but rather influences the bioactivity and bioavailability of drug molecules and can tune drug properties. Namely, as host-guest interactions are capable of changing the intrinsic properties of the guest molecule, inclusion complexes can become more soluble, bioavailable and more resistant to metabolic conditions compared to individual non-complexed molecules. Such synergistic effects have implications for practical bioapplicability of this complex system and provide a new viewpoint to therapy, beyond the traditional single drug molecule approach. By achieving a balance between guest encapsulation and release, the ADA/CB[n] system has also found use beyond just drug delivery, in fields like bioanalytics, sensing assays, bioimaging, etc. Thus, chemosensing in physiological conditions, indicator displacement assays, in vivo diagnostics and hybrid nanostructures are just some recent examples of the ADA/CB[n] applicability, be it for displacements purposes or as cargo vehicles.

Delving into the Variability of Supramolecular Affinity: Self-Ion Pairing as a Central Player in Aqueous Host-Guest Chemistry

The determination of binding constants is a key matter in evaluating the strength of host-guest interactions. However, the profound impact of self-ion pairing on this parameter is often underrated in aqueous solution, leading in some cases to a misinterpretation of the true potential of supramolecular assemblies. In the present study, we aim to shed further light on this critical factor by exploring the concentration-dependent behavior of a multicharged pillararene in water. Our observations reveal an extraordinary 1-million-fold variability in the affinity of this macrocycle toward a given anion, showcasing the highly dynamic character of electrostatic interactions. We argue that these findings bring to the forefront the inherent determinism that underlies the estimation of affinity constants, a factor profoundly shaped by both the sensitivity of the instrumental technique in use and the intricacies of the experimental design itself. In terms of applications, these results may provide the opportunity to optimize the operational concentrations of multicharged hosts in different scenarios, aiming to achieve their maximum efficiency based on the intended application. Unlocking the potential of this hidden variability may pave the way for the creation of novel molecular materials with advanced functionalities.

N-Methyl- and N-Phenylpiperazine Functionalized Styryl Dyes Inside Cucurbiturils: Theoretical Assessment of the Factors Governing the Host-Guest Recognition

The family of cucurbiturils (CBs), the unique pumpkin-shaped macrocycles, has received great attention over the past four decades owing to their remarkable recognition properties. They have found diverse applications including biosensing and drug delivery technologies. The cucurbituril complexation of guest molecules can modulate their pKas, improve their solubility in aqueous solution, and reduce the adverse effects of the drugs, as well as enhance the stability and/or enable targeted delivery of the drug molecule. Employing twelve cationic styryl dyes with N-methyl- and N-phenylpiperazine functionality as probes, we attempted to understand the factors that govern the host-guest complexation of such molecules within CB[7] and CB[8] host systems. Various key factors determining the process were recognized, such as the pH and dielectric constant of the medium, the cavity size of the host, the chemical characteristics of the substituents in the guest entity, and the presence/absence of metal cations. The presented results add to our understanding (at the molecular level) of the mechanism of encapsulation of styryl dyes by cucurbiturils, thus shedding new light on various aspects of the intriguing complexation chemistry and the underlying recognition processes.

Stabilization of Guest Molecules inside Cation-Lidded Cucurbiturils Reveals that Hydration of Receptor Sites Can Impede Binding

Docking of alkali metal ions to water-soluble macrocyclic receptors generally reduces the affinity of guest molecules due to competitive binding. The idea that solvation water molecules could display a larger steric hindrance towards guest binding than cations has not been considered to date. We show that the docking of large cations to cucurbit[5]uril (CB5) unexpectedly increases (by a factor of 5-8) the binding of hydrophobic guests, methane and ethane. This is due to the removal of water molecules from the carbonyl portals of CB5 during cation binding, which frees up space for hydrophobe encapsulation. In contrast, smaller cations like sodium protrude deeply into the cavity of CB5 and cause the expected decrease in binding, such that the rational selection of alkali cations allows for a variation of up to a factor of 20 in binding of methane and ethane. The statistical analysis of crystallographic data shows that the cavity volume of CB5 can be enlarged by placing large alkali ions (Rb+ and Cs+ ) centro-symmetrically at the portals. The results reveal a hitherto elusive steric hindrance of solvation water molecules near receptor binding sites, which is pertinent for the design of supramolecular catalysts and the understanding of biological receptors.

Solvent-controlled formation of alkali and alkali-earth-secured cucurbituril/guest trimers

Cucurbit[7]uril (CB[7]) encapsulates adamantyl and trimethylsilyl substituents of positively charged guests in dimethyl sulfoxide (DMSO). Unlike in water or deuterium oxide, addition of a selection of alkali and alkali-earth cations with van der Waals radii between 1.0 and 1.4 Å (Na+, K+, Ca2+, Sr2+, Ba2+ and Eu3+) to the CB[7]/guest complexes triggers their cation-mediated trimerization, a process that is very slow on the nuclear magnetic resonance (NMR) time scale. Smaller (Li+, Mg2+) or larger cations (Rb+, Cs+ or NH4+) are inert. The trimers display extensive CH-O interactions between the equatorial and pseudo-equatorial hydrogens of CB[7] and the carbonyl rim of the neighboring CB[7] unit in the trimer, and a deeply nested cation between the three interacting carbonylated CB[7] rims; a counteranion is likely perched in the shallow cavity formed by the three outer walls of CB[7] in the trimer. Remarkably, a guest must occupy the cavity of CB[7] for trimerization to take place. Using a combination of semi-empirical and density functional theory techniques in conjunction with continuum solvation models, we showed that trimerization is favored in DMSO, and not in water, because the penalty for the partial desolvation of three of the six CB[7] portals upon aggregation into a trimer is less unfavorable in DMSO compared to water.

Supramolecular Polymer Brushes Grown by Surface-Initiated Atom Transfer Radical Polymerization from Cucurbit[7]uril-based Non-Covalent Initiators

Polymer brushes are densely grafted, chain end-tethered assemblies of polymers that can be produced via surface-initiated polymerization. Typically, this is accomplished using initiators or chain transfer agents that are covalently attached to the substrate. This manuscript reports an alternative route towards polymer brushes, which involves the use of non-covalent cucurbit[7]uril-adamantane host-guest interactions to surface-immobilize initiators for atom transfer radical polymerization. These non-covalent initiators can be used for the surface-initiated atom transfer radical polymerization of a variety of water-soluble methacrylate monomers to generate supramolecular polymer brushes with film thicknesses of more than 100 nm. The non-covalent nature of the initiator also allows facile access to patterned polymer brushes, which can be produced in straightforward fashion by drop-casting a solution of the initiator-modified guest molecules onto a substrate that presents the cucurbit[7]uril host.

Supramolecular Complexation of Azobenzene Dyes by Cucurbit[7]uril

This report describes cucurbit[7]uril (CB7) complexation of azobenzene dyes that have a 4-(N,N'-dimethylamino) or 4-amino substituent. Absorption and NMR data show that CB7 encapsulates the protonated form of the azobenzene and that the complexed dye exists as its azonium tautomer with a trans azo conformation and substantial quinoid resonance character. Because CB7 complexation stabilizes the dye conjugate acid, there is an upward shift in its pKa, and in one specific case, the pKa of the protonated azobenzene is increased from 3.09 to 4.47. Molecular modeling indicates that the CB7/azobenzene complex is stabilized by three major noncovalent factors: (i) ion-dipole interactions between the partially cationic 4-(N,N'-dimethylamino) or 4-amino group on the encapsulated protonated azobenzene and the electronegative carbonyl oxygens on CB7, (ii) inclusion of the upper aryl ring of the azobenzene within the hydrophobic CB7 cavity, and (iii) a hydrogen bond between the proton on the azo nitrogen and CB7 carbonyls. CB7 complexation enhances azobenzene stability and increases azobenzene hydrophilicity; thus, it is a promising way to improve azobenzene performance as a pigment or prodrug. In addition, the striking yellow/pink color change that accompanies CB7 complexation can be exploited to create azobenzene dye displacement assays with naked eye detection.

Fluorophore-based host-guest assembly complexes for imaging and therapy

Recently, supramolecular chemistry with its unique properties has received considerable attention in many fields. Supramolecular fluorescent systems constructed on the basis of macrocyclic hosts are not only effective in overcoming the limitations of imaging and diagnostic reagents, but also in enhancing their performances. This paper summarizes the recent advances in supramolecular fluorescent systems based on host-guest interactions and their application in bioimaging and therapy as well as the challenges and prospects in developing novel supramolecular fluorescent systems.

A supramolecular cucurbit[8]uril-based rotaxane chemosensor for the optical tryptophan detection in human serum and urine

Sensing small biomolecules in biofluids remains challenging for many optical chemosensors based on supramolecular host-guest interactions due to adverse interplays with salts, proteins, and other biofluid components. Instead of following the established strategy of developing alternative synthetic binders with improved affinities and selectivity, we report a molecular engineering approach that addresses this biofluid challenge. Here we introduce a cucurbit[8]uril-based rotaxane chemosensor feasible for sensing the health-relevant biomarker tryptophan at physiologically relevant concentrations, even in protein- and lipid-containing human blood serum and urine. Moreover, this chemosensor enables emission-based high-throughput screening in a microwell plate format and can be used for label-free enzymatic reaction monitoring and chirality sensing. Printed sensor chips with surface-immobilized rotaxane-microarrays are used for fluorescence microscopy imaging of tryptophan. Our system overcomes the limitations of current supramolecular host-guest chemosensors and will foster future applications of supramolecular sensors for molecular diagnostics.

Mechanochemical Defluorinative Arylation of Trifluoroacetamides: An Entry to Aromatic Amides

The amide bond is prominent in natural and synthetic organic molecules endowed with activity in various fields. Among a wide array of amide synthetic methods, substitution on a pre-existing (O)C-N moiety is an underexplored strategy for the synthesis of amides. In this work, we disclose a new protocol for the defluorinative arylation of aliphatic and aromatic trifluoroacetamides yielding aromatic amides. The mechanochemically induced reaction of either arylboronic acids, trimethoxyphenylsilanes, diaryliodonium salts, or dimethyl(phenyl)sulfonium salts with trifluoroacetamides affords substituted aromatic amides in good to excellent yields. These nickel-catalyzed reactions are enabled by C-CF₃ bond activation using Dy₂O₃ as an additive. The current protocol provides versatile and scalable routes for accessing a wide variety of substituted aromatic amides. Moreover, the protocol described in this work overcomes the drawbacks and limitations in the previously reported methods.

Trapping Alkali Halide Cluster Ions Inside the Cucurbit[7]uril Cavity

In this study, the distinctive behavior of cucurbit[n]uril (CB[n]), which captures a variety of alkali halide clusters inside the cavity during the droplet evaporation, has been investigated by using ion mobility spectrometry-mass spectrometry. Complexes of CB[7] with various alkali chloride cluster cations or anions generated during the electrospray ionization were studied, and their collision cross-section (CCS) values were obtained to determine whether these clusters were trapped inside the cavity or not. It was found that the clusters smaller than a specific critical size were trapped inside the CB[7] cavity in the gas phase, although trapping of alkali halide clusters at the given concentration is supposed to be unfavorable in solution. We suggest that the rapid solvent evaporation rapidly increases ion concentrations and subsequently forms alkali-chloride contact ion pairs; therefore, it may provide a specific environment to enable the formation of the inclusion complexes.

A combination of a graphene quantum dots-cationic red dye donor-acceptor pair and cucurbit[7]uril as a supramolecular sensor for ultrasensitive detection of cancer biomarkers spermine and spermidine

In a unique approach, the combination of a donor-acceptor pair of hydroxy graphene quantum dots (GQDs-OH) and a red-emissive donor-two-acceptor (D-2-A) type dye with pyridinium units (BPBP) and the well-known host cucurbit[7]uril (CB[7]) has been exploited as a supramolecular sensing assembly for the detection of cancer biomarkers spermine and spermidine in aqueous media at the sub-ppb level based on the affinity-driven exchange of guests from the CB[7] portal. In the binary conjugate, green fluorescent GQDs-OH transfers energy to trigger the emission of the dye BPBP and itself remains in the turn-off state. CB[7] withdraws the dye from the surface of GQDs-OH by strong host-guest interactions with its portal, making GQDs-OH fluoresce again to produce a ratiometric response. In the presence of spermine (SP) or spermidine (SPD), their strong affinity with CB[7] forces the ejection of the fluorophore to settle on the GQDs-OH surface, and the strong green emission of GQDs-OH turns off to device a supramolecular sensor for the detection of SP/SPD. The DFT studies revealed interesting excited-state charge-transfer conjugate formation between BPBP and GQDs leading to turn-on emission of the dye, and further supported the stronger binding modes of BPBP-CB[7], indicating the retrieval of the emission of GQDs. The assembly-disassembly based sensing mechanism was also established by Job's plot analysis, particle size analysis, zeta potential, time-resolved spectroscopy, ITC studies, microscopic studies, etc. The supramolecular sensing assembly is highly selective to SP and SPD, and showed nominal interference from other biogenic amines, amino acids, various metal ions, and anions. The limits of detection (LODs) were 0.1 ppb and 0.9 ppb for spermine and spermidine, respectively. The potential for the real-world application of this sensing assembly was demonstrated by spiking SP and SPD in human urine and blood serum with a high %recovery.

Chemiluminescent Cucurbit[n]uril-Based Chemosensor for the Detection of Drugs in Biofluids

Chemiluminescence-based detection methods offer a superior signal-to-noise ratio and are commonly adopted for biosensors. This work presents the design and implementation of a supramolecular assay based on a chemiluminescent chemosensor. Specifically, an indicator displacement assay (IDA) with the supramolecular host-guest complex of chemiluminescent phenoxy 1,2-dioxetane and cucurbit[8]uril enables the low-micromolar detection of drugs in human urine and human serum samples. Cucurbit[8]uril thereby acts as a non-surfactant chemiluminescence enhancer and a synthetic receptor. Additionally, we show that adding an equimolar amount of cucurbit[8]uril to a commercially available dioxetane used in standard enzymatic chemiluminescence immunoassays enhances the chemiluminescence by more than 15 times. Finally, we demonstrate that a chemiluminescence resonance energy transfer between a unimolecular macrocyclic cucurbit[7]uril-dye conjugate and a phenoxy 1,2-dioxetane can be utilized to detect the herbicide paraquat at a micromolar concentration in aqueous media.

Cucurbit[7]uril Complexation of Near-Infrared Fluorescent Azobenzene-Cyanine Conjugates

Two new azobenzene heptamethine cyanine conjugates exist as dispersed monomeric molecules in methanol solution and exhibit near-infrared (NIR) cyanine absorption and fluorescence. Both conjugates form non-emissive cyanine H-aggregates in water, but the addition of cucurbit[7]uril (CB7) induces dye deaggregation and a large increase in cyanine NIR fluorescence emission intensity. CB7 encapsulates the protonated azonium tautomer of the 4-(N,N-dimethylamino)azobenzene component of each azobenzene-cyanine conjugate and produces a distinctive new absorption band at 534 nm. The complex is quite hydrophilic, which suggests that CB7 can be used as a supramolecular additive to solubilize this new family of NIR azobenzene-cyanine conjugates for future biomedical applications. Since many azobenzene compounds are themselves potential drug candidates or theranostic agents, it should be possible to formulate many of them as CB7 inclusion complexes with improved solubility, stability, and pharmaceutical profile.

Host-guest complexation between cucurbit[7]uril and doxepin induced supramolecular assembly

The supramolecular complexation of doxepin (DOX) with cucurbit[7]uril (CB7) was investigated in aqueous solution. The results indicated the formation of a host-guest complex, as verified by complexation-induced chemical shifts in the NMR experiments and supported by quantum-chemical calculations, in which the alkylammonium tail of DOX was found to be encapsulated inside the CB7 cavity, while the tricyclic moiety remained exposed to bulk water. Isothermal titration calorimetry and dye-displacement experiments provided a moderate binding affinity (10⁴ M^-1). Interestingly, the partial encapsulation of DOX by the CB7 macrocycle led to the development of a supramolecular assembly at a low millimolar concentration, as verified by NMR and dynamic light scattering (DLS) measurements, which showed homogeneous size distributions with an average diameter of 1700 nm.

The Role of Packing, Dispersion, Electrostatics, and Solvation in High-Affinity Complexes of Cucurbit[n]urils with Uncharged Polar Guests

The rationalization of non-covalent binding trends is both of fundamental interest and provides new design concepts for biomimetic molecular systems. Cucurbit[n]urils (CBn) are known for a long time as the strongest synthetic binders for a wide range of (bio)organic compounds in water. However, their host-guest binding mechanism remains ambiguous despite their symmetric and simple macrocyclic structure and the wealth of literature reports. We herein report experimental thermodynamic binding parameters (ΔG, ΔH, TΔS) for CB7 and CB8 with a set of hydroxylated adamantanes, di-, and triamantanes as uncharged, rigid, and spherical/ellipsoidal guests. Binding geometries and binding energy decomposition were obtained from high-level theory computations. This study reveals that neither London dispersion interactions, nor electronic energies or entropic factors are decisive, selectivity-controlling factors for CBn complexes. In contrast, peculiar host-related solvation effects were identified as the major factor for rationalizing the unique behavior and record-affinity characteristics of cucurbit[n]urils.

Supramolecular Mitigation of the Cyanine Limit Problem

Currently, there is a substantial research effort to develop near-infrared fluorescent polymethine cyanine dyes for biological imaging and sensing. In water, cyanine dyes with extended conjugation are known to cross over the "cyanine limit" and undergo a symmetry breaking Peierls transition that favors an unsymmetric distribution of π-electron density and produces a broad absorption profile and low fluorescence brightness. This study shows how supramolecular encapsulation of a newly designed series of cationic, cyanine dyes by cucurbit[7]uril (CB7) can be used to alter the π-electron distribution within the cyanine chromophore. For two sets of dyes, supramolecular location of the surrounding CB7 over the center of the dye favors a nonpolar ground state, with a symmetric π-electron distribution that produces a sharpened absorption band with enhanced fluorescence brightness. The opposite supramolecular effect (i.e., broadened absorption and partially quenched fluorescence) is observed with a third set of dyes because the surrounding CB7 is located at one end of the encapsulated cyanine chromophore. From the perspective of enhanced near-infrared bioimaging and sensing in water, the results show how that the principles of host/guest chemistry can be employed to mitigate the "cyanine limit" problem.

Effect of Na+ and K+ on the cucurbituril-mediated hydrolysis of a phenyl acetate

The environment around the active site affects the catalytic activity of enzymes. Studying the cucurbit[7]uril-promoted acid hydrolysis of a cationic phenyl acetate derivative, we found that the hydrophobic cavity of the macrocycle screens the reaction centre from the positively charged neighbouring group. Moreover, the chelation of alkali metal cations with the cucurbit[7]uril portal and acetyl group of the substrate reduces the hydrolysis rate of the encapsulated ester in an aqueous solution. This type of inhibition corresponds to a rare uncompetitive model in contrast to the more common competitive model that relies on substrate displacement.

When Molecules Meet in Water-Recent Contributions of Supramolecular Chemistry to the Understanding of Molecular Recognition Processes in Water

Molecular recognition processes in water differ from those in organic solvents in that they are mediated to a much greater extent by solvent effects. The hydrophobic effect, for example, causes molecules that only weakly interact in organic solvents to stay together in water. Such water-mediated interactions can be very efficient as demonstrated by many of the synthetic receptors discussed in this review, some of which have substrate affinities matching or even surpassing those of natural binders. However, in spite of considerable success in designing such receptors, not all factors determining their binding properties in water are fully understood. Existing concepts still provide plausible explanations why the reorganization of water molecules often causes receptor-substrate interactions in water to be strongly exothermic rather than entropically favored as predicted by the classical view of the hydrophobic effect.

HPLC-potentiometric method for determination of biogenic amines in alcoholic beverages: A reliable approach for food quality control

Determination of ten biogenic amines in alcoholic beverages by HPLC coupled to a potentiometric detector for food quality control is herein presented. Biogenic amines were separated by ion-pair chromatography on a C18 column using a gradient mobile phase of acetic acid, acetonitrile, and butane-sulfonic acid. Detection was accomplished by a miniaturized amine-selective electrode. The method was validated following ICH and Eurachem guidelines. Linear regression models provided R² values from 0.9870 ± 0.0019 to 0.9991 ± 0.0014 for tyramine and cadaverine, respectively. Detection and quantification limits depend on the molecular weight of BAs, ranging from 9.3 to 60.5 and from 31.1 to 202.3 µg L^-1 for methylamine and spermine, respectively. Repeatability and intermediate precision showed RSD values lower than 5.8 and 8.3%, respectively. Accuracy of assays yielded recovery values from 86.4 to 109.9%. The biogenic amines content in red wine, white wine, and beer samples were 7.54, 5.24, and 4.58 mg L^-1, respectively.

Molecular Probes, Chemosensors, and Nanosensors for Optical Detection of Biorelevant Molecules and Ions in Aqueous Media and Biofluids

Synthetic molecular probes, chemosensors, and nanosensors used in combination with innovative assay protocols hold great potential for the development of robust, low-cost, and fast-responding sensors that are applicable in biofluids (urine, blood, and saliva). Particularly, the development of sensors for metabolites, neurotransmitters, drugs, and inorganic ions is highly desirable due to a lack of suitable biosensors. In addition, the monitoring and analysis of metabolic and signaling networks in cells and organisms by optical probes and chemosensors is becoming increasingly important in molecular biology and medicine. Thus, new perspectives for personalized diagnostics, theranostics, and biochemical/medical research will be unlocked when standing limitations of artificial binders and receptors are overcome. In this review, we survey synthetic sensing systems that have promising (future) application potential for the detection of small molecules, cations, and anions in aqueous media and biofluids. Special attention was given to sensing systems that provide a readily measurable optical signal through dynamic covalent chemistry, supramolecular host-guest interactions, or nanoparticles featuring plasmonic effects. This review shall also enable the reader to evaluate the current performance of molecular probes, chemosensors, and nanosensors in terms of sensitivity and selectivity with respect to practical requirement, and thereby inspiring new ideas for the development of further advanced systems.

The cucurbit[7]uril effect on reference substances for NMR in deuterium oxide solution

The effect of macrocyclic molecule cucurubit[7]uril on the chemical shifts of internal reference substances for NMR studies in deuterium oxide solution and the cause were investigated.

Electrogenerated chemiluminescence sensor for silver ions based on their coordination interaction with cucurbit[6]uril

Strong luminol ECL was obtained at the Q[6]/GCE. The interaction between Ag+ and Q[6] could decrease ECL signal. An ECL sensor for the detection of Ag+ was proposed based on the competitive interaction between luminol, silver ions and Q[6].

Inclusion complexation and self-association of cucurbit[n]uril (n = 6, 7) and diquat under pseudo-physiological conditions

The formation and steric structure of the inclusion complex of cucurbit[n]uril (CB[n]; n = 6, 7) and diquat (DQ) were investigated through NMR measurements under the pH conditions of human pseudo-gastric or body fluids, in physiological saline.

Controllable synthesis of Co nanoparticles with the assistance of cucurbit[6]uril and its efficient photoelectrochemical catalysis in water splitting on a g-C3N4 photoanode

An innovative photoanode was developed for efficient PEC water splitting by the deposition of a Co nano-catalyst on the surface of a g-C3N4 film, producing the significant photocurrent density of 393 μA cm−2 at 1.23 V vs. RHE.

DFT-D4 Insight into the Inclusion of Amphetamine and Methamphetamine in Cucurbit[7]uril: Energetic, Structural and Biosensing Properties

The host-guest interactions of cucurbit[7]uril (CB[7]) as host and amphetamine (AMP), methamphetamine (MET) and their enantiomeric forms (S-form and R-form) as guests were computationally investigated using density functional theory calculations with the recent D4 atomic-charge dependent dispersion corrections. The analysis of energetic, structural and electronic properties with the aid of frontier molecular orbital analysis, charge decomposition analysis (CDA), extended charge decomposition analysis (ECDA) and independent gradient model (IGM) approach allowed to characterize the host-guest interactions in the studied systems. Energetic results indicate the formation of stable non-covalent complexes where R-AMP@CB[7] and S-AMP@CB[7] are more stable thermodynamically than R-MET@CB[7] and S-MET@CB[7] in gas phase while the reverse is true in water solvent. Based on structural analysis, a recognition mechanism is proposed, which suggests that the synergistic effect of van der Waals forces, ion-dipole interactions, intermolecular charge transfer interactions and intermolecular hydrogen bonding is responsible for the stabilization of the complexes. The geometries of the complexes obtained theoretically are in good agreement with the X-ray experimental structures and indicate that the phenyl ring of amphetamine and methamphetamine is deeply buried into the cavity of CB[7] through hydrophobic interactions while the ammonium group remains outside the cavity to establish hydrogen bonds with the portal oxygen atoms of CB[7].

Encapsulation of Metronidazole in Biocompatible Macrocycles and Structural Characterization of Its Nano Spray-Dried Nanostructured Composite

Due to the great potential of biocompatible cucurbit[7]uril (CB7) and 4-sulfonatocalix[4]arene (SCX4) macrocycles in drug delivery, the confinement of the pharmaceutically important metronidazole as an ionizable model drug has been systematically studied in these cavitands. Absorption and fluorescence spectroscopic measurements gave 1.9 × 10⁵ M⁻¹ and 1.0 × 10⁴ M⁻¹ as the association constants of the protonated metronidazole inclusion in CB7 and SCX4, whereas the unprotonated guests had values more than one order of magnitude lower, respectively. The preferential binding of the protonated metronidazole resulted in 1.91 pH unit pK_a diminution upon encapsulation in CB7, but the complexation with SCX4 led to a pK_a decrease of only 0.82 pH unit. The produced protonated metronidazole–SCX4 complex induced nanoparticle formation with protonated chitosan by supramolecular crosslinking of the polysaccharide chains. The properties of the aqueous nanoparticle solutions and the micron-sized solid composite produced therefrom by nano spray drying were unraveled. The results of the present work may find application in the rational design of tailor-made self-assembled drug carrier systems.

Exploring the pH-dependent kinetics, thermodynamics and photochemistry of a flavylium-based pseudorotaxane

Flavylium-based molecular switches are attractive molecular components to devise stimuli-responsive host-guest systems such as rotaxanes and pseudorotaxanes. These compounds display a pH-dependent reaction network of several species that reversibly interconvert within different time scales. Therefore, to explore and take profit of exceptional stimuli-responsive properties of these systems, detailed kinetic and thermodynamic characterizations are often required. In this work, we present the results of such characterization for a new flavylium compound decorated with a trimethylalkylammonium substituent designed to form a pseudorotaxane with cucurbit[7]uril (CB7). The formation of the pseudorotaxane was characterized in detail, and the thermodynamic and kinetic aspects of the flavylium interconversion reactions in the assembly were investigated and compared with the free molecular switch.

A reference scale of cucurbit[7]uril binding affinities

The accurate determination of ultra-high binding affinities in supramolecular host-guest chemistry is a challenging endeavour because direct binding titrations are generally limited to affinities <10⁶ M^-1 due to sensitivity constraints of common titration methods. To determine higher affinities, competitive titrations are usually performed, in which one compound with a well established binding affinity serves as a reference. Herein, we propose a reference scale for such competitive titrations with the host cucurbit[7]uril (CB7) comprising binding affinities in the range from 10³ to 10¹⁵ M^-1. The suggested reference compounds are commercially available and will aid in the future determination of CB7 binding affinities for stimuli-responsive host-guest systems.

Toward Light-Controlled Supramolecular Peptide Dimerization

The selective photodeprotection of the NVoc-modified FGG tripeptide yields the transformation of its 1:1 receptor-ligand complex with cucurbit[8]uril into a homoternary FGG₂@CB8 assembly. The resulting light-induced dimerization of the model peptide provides a tool for the implementation of stimuli-responsive supramolecular chemistry in biologically relevant contexts.

Calculation of absolute molecular entropies and heat capacities made simple

We propose a fully-automated composite scheme for the accurate and numerically stable calculation of molecular entropies by efficiently combining density-functional theory (DFT), semi-empirical methods (SQM), and force-field (FF) approximations. The scheme is systematically expandable and can be integrated seamlessly with continuum-solvation models. Anharmonic effects are included through the modified rigid-rotor-harmonic-oscillator (msRRHO) approximation and the Gibbs-Shannon formula for extensive conformer ensembles (CEs), which are generated by a metadynamics search algorithm and are extrapolated to completeness. For the first time, variations of the ro-vibrational entropy over the CE are consistently accounted-for through a Boltzmann-population average. Extensive tests of the protocol with the two standard DFT approaches B97-3c and B3LYP-D3 reveal an unprecedented accuracy with mean deviations <1 cal mol-1 K-1 (about <1-2%) for the total gas phase molecular entropy of medium-sized molecules. Even for the hardship case of extremely flexible linear alkanes (C14H30-C16H34), errors are only about 3 cal mol-1 K-1. Comprehensive tests indicate a relatively strong variation of the conformational entropy on the underlying level of theory for typical drug molecules, inferring the complex potential energy surfaces as the main source of error. Furthermore, we show some application examples for the calculation of free energy differences in typical chemical reactions.

Macrocyclic and acyclic supramolecular elements for co-precipitation of square-planar gold(iii) tetrahalide complexes

Non-covalent interactions control the solid-state packing of AuX₄⁻ anions (yellow circles) co-precipitated with different supramolecular elements.

Elucidating dissociation activation energies in host-guest assemblies featuring fast exchange dynamics

The ability to mediate the kinetic properties and dissociation activation energies (E _a) of bound guests by controlling the characteristics of "supramolecular lids" in host-guest molecular systems is essential for both their design and performance. While the synthesis of such systems is well advanced, the experimental quantification of their kinetic parameters, particularly in systems experiencing fast association and dissociation dynamics, has been very difficult or impossible with the established methods at hand. Here, we demonstrate the utility of the NMR-based guest exchange saturation transfer (GEST) approach for quantifying the dissociation exchange rates (k _out) and activation energy (E _a,out) in host-guest systems featuring fast dissociation dynamics. Our assessment of the effect of different monovalent cations on the extracted E _a,out in cucurbit[7]uril:guest systems with very fast k _out highlights their role as "supramolecular lids" in mediating a guest's dissociation E _a. We envision that GEST could be further extended to study kinetic parameters in other supramolecular systems characterized by fast kinetic properties and to design novel switchable host-guest assemblies.

Nonlinear Dependence on Na+ Ions for the Binding Dynamics of Cucurbit[6]uril with the trans-1-Methyl-4-(4-hydroxystyryl)pyridinium Cation

The binding dynamics of the trans-1-methyl-4-(4-hydroxystyryl)pyridinium cation (HSP⁺) to cucurbit[6]uril (CB[6]) in the presence of Na⁺ cations were studied to establish the effect of the relative concentrations of the system's components (HSP⁺, CB[6], and Na⁺) on these dynamics. The formation of the HSP⁺@CB[6] complex was temporally uncoupled from the photoisomerization of trans-HSP⁺, while a nonlinear effect of the Na⁺ cation concentration on the HSP⁺@CB[6] dynamics was observed. This nonlinearity is a consequence of Na⁺ having the opposite effect on the association and dissociation rate constants for the HSP⁺@CB[6] complex, creating a conceptual framework for using such nonlinearities to control multistep reactions in cucurbit[n]uril chemistry.

Binding Modes of a Phenylpyridinium Styryl Fluorescent Dye with Cucurbiturils

In order to explore how cucurbituril hosts accommodate an N-phenyl-pyridinium derivative guest, the complexation of the solvatochromic dye, 4-(4-(dimethylamino)styryl)-1-phenylpyridinium iodide (PhSt) with ,',δ,δ'-tetramethyl-cucurbit[6]uril (Me4CB6) and cucurbit[7]uril (CB7) was investigated by absorption spectroscopic, fluorescence and NMR experiments. In aqueous solutions, PhSt forms 1:1 complexes with both cucurbiturils, the complex with CB7 has a higher stability constant (Ka = 6.0 × 106 M-1) than the complex with Me4CB6 (Ka = 1.1 × 106 M-1). As revealed by NMR experiments and confirmed by theoretical calculations, CB7 encapsulates the whole phenylpyridinium entity of the PhSt cation guest, whereas the cavity of Me4CB6 includes only the phenyl ring, the pyridinium ring is bound to the carbonyl rim of the host. The binding of PhSt to cucurbiturils is accompanied by a strong enhancement of the fluorescence quantum yield due to the blocking of the deactivation through a twisted intramolecular charge transfer (TICT) state. The TICT mechanism in PhSt was characterized by fluorescence experiments in polyethylene glycol (PEG) solvents of different viscosities. The PhSt-CB7 system was tested as a fluorescence indicator displacement (FID) assay, and it recognized trimethyl-lysine selectively over other lysine derivatives.

Covalent cucurbit[7]uril-dye conjugates for sensing in aqueous saline media and biofluids

Non-covalent chemosensing ensembles of cucurbit[n]urils (CBn) have been widely used in proof-of-concept sensing applications, but they are prone to disintegrate in saline media, e.g. biological fluids. We show here that covalent cucurbit[7]uril-indicator dye conjugates are buffer- (10× PBS buffer) and saline-stable (up to 1.4 M NaCl) and allow for selective sensing of Parkinson's drug amantadine in human urine and saliva, where the analogous non-covalent CB7⊃dye complex is dysfunctional. The in-depth analysis of the covalent host-dye conjugates in the gas-phase, and deionized versus saline aqueous media revealed interesting structural, thermodynamic and kinetic effects that are of general interest for the design of CBn-based supramolecular chemosensors and systems. This work also introduces a novel high-affinity indicator dye for CB7 through which fundamental limitations of indicator displacement assays (IDA) were exposed, namely an impractical slow equilibration time. Unlike non-covalent CBn⊃dye reporter pairs, the conjugate chemosensors can also operate through a SN2-type guest-dye exchange mechanism, which shortens assay times and opens new avenues for tailoring analyte-selectivity.

Complexation of biologically essential (mono- and divalent) metal cations to cucurbiturils: a DFT/SMD evaluation of the key factors governing the host-guest recognition

Supramolecular complexes based on classical synthetic macrocyclic host molecules such as cyclodextrins and calixarenes have received much attention recently due to their broad applications as biological and chemical sensors, bioimaging agents, drug delivery carriers, light-emitting materials, etc. Cucurbit[n]urils comprise another group of cavitands known for their high affinity for various guest molecules. Nonetheless, some aspects of their coordination chemistry remain enigmatic. Although they are recognized as potential biomimetic scaffolds, they are still not tested as metalloenzyme models and not much is known about their metal-binding properties. Furthermore, there is no systematic study on the key factors controlling the processes of metal coordination to these systems. In the computational study herein, DFT molecular modeling has been employed in order to investigate the interactions of biologically essential (mono- and divalent) metal cations to cucurbit[n]urils and evaluate the major determinants shaping the process. The thermodynamic descriptors (Gibbs energies in the gas phase and in a water medium) of the corresponding complexation reactions have been estimated. The results obtained shed light on the mechanism of host-guest recognition and disclose which factors more specifically affect the metal binding process.

Influence of cyclic and acyclic cucurbiturils on the degradation pathways of the chemical warfare agent VX

The highly toxic nerve agent VX is a methylphosphonothioate that degrades via three pathways in aqueous solution, namely through the hydrolysis of the P-O or P-S bonds, or the cleavage of the C-S bond at the 2-aminoethyl residue. In the latter case, an aziridinium ion and a phosphonothioate is formed. Here it is shown that acyclic or cyclic cucurbiturils inhibit these reactions in phosphate buffer at physiological pH and thus stabilise the nerve agent. When using unbuffered basic solutions as the reaction medium, however, in which the P-S or P-O bonds are normally hydrolysed preferentially, cucurbiturils turned out to strongly shift VX degradation towards the cleavage of the C-S bond. Cucurbit[7]uril, in particular, has a so pronounced effect under suitable conditions that it almost completely suppresses the formation of products resulting from the other degradation pathways. Investigations involving VX analogues in combination with computational methods suggest that one reason for the reaction control exerted by the cucurbiturils is the preorganisation of VX for aziridinium ion formation. In addition, cucurbit[7]uril also lowers the transition state of the reaction by stabilising the positive charge developing on the way to the product. Cucurbiturils thus have a marked effect on the reactivity of a highly toxic nerve agent, which potentially allows using them for decontamination purposes.

Teaching old indicators even more tricks: binding affinity measurements with the guest-displacement assay (GDA)

A simple change has important consequences: the guest-displacement assay (GDA) is introduced which allows for binding affinity determinations of supramolecular complexes with spectroscopically silent hosts and guests. GDA is complementary to indicator-displacement assay for affinity measurements with soluble components, but is superior for insoluble or for weakly binding guests.

Site-selective modification of proteins using cucurbit[7]uril as supramolecular protection for N-terminal aromatic amino acids

Cucurbit[7,8]urils are known to form inclusion complexes with aromatic amino acids, hosting the hydrohobic side chains within the cavity and adjacent cations within the portal of the macrocyclic host. Here we show that cucurbit[7]uril binding with N-terminal phenylalanine significantly reduces the nucleophilicity of the amine, likely due to an increase in stability of the ammonium ion, rendering it unreactive at neutral pH. Using insulin as a model protein, we show that this supramolecular protection strategy can drive selectivity of N-terminal amine conjugation away from the preferred B chain N-terminal phenylalanine towards the A chain N-terminal glycine. Cucurbit[7]uril can therefore be used as a supramolecular protecting group for site-selective protein modification.