PCage: Fluorescent Molecular Temples for Binding Sugars in Water

A Macrocyclic Tweezers-Shaped Receptor for the Biomimetic Recognition of the Gal(α1-3)Gal Disaccharide of the α-Gal Antigen

The Gal(α1-3)Gal is the terminal disaccharide unit of the α-Gal epitope [Gal(α1-3)Gal(β1-4)GlcNAc], an exogenous antigenic determinant with several clinical implications, found in all non-primate mammals and in several dangerous pathogens, including certain protozoa and mycobacteria. Its absence in humans makes the α-Gal epitope an interesting target for several infectious diseases. Here we present the development of a macrocyclic tweezers-shaped receptor, resulting from the combination of the structural features of two predecessors belonging to the family of diaminocarbazole receptors, which exhibits binding properties in the low millimolar range toward the Gal(α1-3)Gal disaccharide of the α-Gal antigen.

Uncovering tetrazoles as building blocks for constructing discrete and polymeric assemblies

Metal-organic self-assembly with flexible moieties is a budding field of research due to the possibility of the formation of unique architectures. Tetrazole, characterised by four nitrogen atoms in a five-member ring, exhibits immense potential as a component. Tetrazole offers four coordination sites for binding to the metal centre with nine distinct binding modes, leading to various assemblies. This review highlights different polymeric and discrete tetrazole-based assemblies and their functions. The meticulous manipulation of stoichiometry, ligands, and metal ions required for constructing discrete assemblies has also been discussed. The different applications of these architectures in separation, catalysis and detection have also been accentuated. The latter section of the review consolidates tetrazole-based cage composites, highlighting their applications in cell imaging and photocatalytic applications.

Water-Soluble Triazolium Covalent Cages for ATP Sensing

Water-soluble organic cages are attractive targets for their molecular recognition and sensing features of biologically relevant molecules. Here, we have successfully designed and synthesized a pair of water-soluble cationic cages employing click reaction as the fundamental step followed by the N-methylation of the triazole rings. The rigid and shape-persistent 3D hydrophobic cavity, positively charged surface, H-bonding triazolium rings, and excellent water solubility empower both cages to exhibit a superior affinity and selectivity for binding with adenosine-5'-triphosphate (ATP) compared to cyclophanes and other macrocyclic receptors. Both cage molecules (PCC⋅Cl and BCC⋅Cl) can bind a highly emissive dye HPTS (8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt) to form non-fluorescent complexes. The addition of ATP resulted in the stronger cage⊂ATP complexes with the retention of HPTS emission upon its displacement. The resultant indicator-displacement assay system can efficiently sense and quantify ATP in nanomolar detection limits in buffer solutions and human serum matrix. Spectroscopic and theoretical studies revealed the synergistic effect of π⋅⋅⋅π stacking interaction between the aromatic moiety of the cationic cages and the adenine moiety of ATP, as well as the electrostatic and hydrogen bonding interaction between the phosphate anion of ATP and triazole protons of cages, played the pivotal roles in the sensing process.

Tailored Water-Soluble Covalent Organic Cages for Encapsulation of Pyrene and Information Encryption

Forming pyridine salts to construct covalent organic cages is an effective strategy for constructing covalent cage compounds. Covalent organic cages based on pyridine salt structures are prone to form water-soluble supramolecular compounds. Herein, we designed and synthesized a triangular prism-shaped hexagonal cage with a larger cavity and relatively flexible conformation. The supramolecular cage structure was also applied to the encapsulation of pyrene and information encryption.

Precise Recognition in Water by an Endo-Functionalized Cavity: Tuning the Complementarity of Binding Sites

Precise binding towards structurally similar substrates is a common feature of biomolecular recognition. However, achieving such selectivity-especially in distinguishing subtle differences in substrates-with synthetic hosts can be quite challenging. Herein, we report a novel design strategy involving the combination of different rigid skeletons to adjust the distance between recognition sites within the cavity, which allows for the highly selective recognition of hydrogen-bonding complementary substrates, such as 4-chromanone. X-ray single-crystal structures and density functional theory calculations confirmed that the distance of endo-functionalized groups within the rigid cavity is crucial for achieving high binding selectivity through hydrogen bonding. The thermodynamic data and molecular dynamics simulations revealed a significant influence of the hydrophobic cavity on the binding affinity. The new receptor possesses both high selectivity and high affinity, which provide valuable insights for the design of customized receptors.

Exciplex Emission and Förster Resonance Energy Transfer in Polycyclic Aromatic Hydrocarbon-Based Bischromophoric Cyclophanes and Homo[2]catenanes

Energy transfer and exciplex emission are not only crucial photophysical processes in many living organisms but also important for the development of smart photonic materials. We report, herein, the rationally designed synthesis and characterization of two highly charged bischromophoric homo[2]catenanes and one cyclophane incorporating a combination of polycyclic aromatic hydrocarbons, i.e., anthracene, pyrene, and perylene, which are intrinsically capable of supporting energy transfer and exciplex formation. The possible coconformations of the homo[2]catenanes, on account of their dynamic behavior, have been probed by Density Functional Theory calculations. The unique photophysical properties of these exotic molecules have been explored by steady-state and time-resolved absorption and fluorescence spectroscopies. The tetracationic pyrene-perylene cyclophane system exhibits emission emanating from a highly efficient Förster resonance energy transfer (FRET) mechanism which occurs in 48 ps, while the octacationic homo[2]catenane displays a weak exciplex photoluminescence following extremely fast (<0.3 ps) exciplex formation. The in-depth fundamental understanding of these photophysical processes involved in the fluorescence of bischromophoric cyclophanes and homo[2]catenanes paves the way for their use in future bioapplications and photonic devices.

Emergence of Cooperative Glucose-Binding Networks in Adaptive Peptide Systems

Minimalistic peptide-based systems that bind sugars in water are challenging to design due to the weakness of interactions and required cooperative contributions from specific amino-acid side chains. Here, we used a bottom-up approach to create peptide-based adaptive glucose-binding networks by mixing glucose with selected sets of input dipeptides (up to 4) in the presence of an amidase to enable in situ reversible peptide elongation, forming mixtures of up to 16 dynamically interacting tetrapeptides. The choice of input dipeptides was based on amino-acid abundance in glucose-binding sites found in the protein data bank, with side chains that can support hydrogen bonding and CH-π interactions. Tetrapeptide sequence amplification patterns, determined through LC-MS analysis, served as a readout for collective interactions and led to the identification of optimized binding networks. Systematic variation of dipeptide input revealed the emergence of two networks of non-covalent hydrogen bonding and CH-π interactions that can co-exist, are cooperative and context-dependent. A cooperative binding mode was determined by studying the binding of the most amplified tetrapeptide (AWAD) with glucose in isolation. Overall, these results demonstrate that the bottom-up design of complex systems can recreate emergent behaviors driven by covalent and non-covalent self-organization that are not observed in reductionist designs and lead to the identification of system-level cooperative binding motifs.

Selectivity Rule of Cryptands for Anions: Molecular Rigidity and Bonding Site

Cryptands utilize inside CH or NH groups as hydrogen bond (H-bond) donors to capture anions such as halides. In this work, the nature and selectivity of confined hydrogen bonds inside cryptands were computationally analyzed with the energy decomposition scheme based on the block-localized wavefunction method (BLW-ED), aiming at an elucidation of governing factors in the binding between cryptands and anions. It was revealed that the intrinsic strengths of inward hydrogen bonds are dominated by the electrostatic attraction, while the anion preferences (selectivity) of inner CH and NH hydrogen bonds are governed by the Pauli exchange repulsion and electrostatic interaction, respectively. Typical conformers of cages are classified into two groups, including the C_3(h) -symmetrical conformers, in which all halide anions are located near the centroids of cages, and the "semi-open" conformers, which exhibit shifted bonding sites for different halide anions. Accordingly, the difference in governing factors of selectivity is attributed to either the rigidity of cages or the binding site of anions for these two groups. In details, the C₃ conformers of NH cryptands can be enlarged more remarkably than the C_3(h) -symmetrical conformers of CH cryptands as the size of anion (ionic radius) increases, resulting in the relaxation of the Pauli repulsion and a dramatic reduction in electrostatic attraction, which eventually rules the selectivity of NH cryptands for halide anions. By contrary, the CH cryptands are more rigid and cannot effectively reduce the Pauli repulsion, which subsequently governs the anion preference. Unlike C₃ conformers whose rigidity determines the selectivity, semi-open conformers exhibit different binding sites for different anions. From F^- to I^- , the bonding site shifts toward the outside end of the pocket inside the semi-open NH cryptand, leading to the significant reduction of the electrostatic interaction that dominates the anion preference. Differently, binding sites are much less affected by the size of anion inside the semi-open CH cryptand, in which the Pauli exchange repulsion remains the key factor for the selectivity of inner hydrogen bonds.

Tricyclic octaurea "Temples" for the recognition of polar molecules in water

Two water-soluble tricyclic "Temple" macrocycles featuring pyrene roof/floor units and bis-urea spacers have been synthesised and studied as receptors for aromatic compounds in aqueous media. The tricycles show good selectivity for methylated purine alkaloids such as caffeine versus unsubstituted heterocycles such as adenine and indole. Binding is signalled by major changes in fluorescence, apparently due to the break-up of intramolecular excimers. The formation of excimers implies cavity collapse in the absence of guests explaining why, unlike an earlier relative, these receptors do not bind carbohydrates. Naphthalenediimides (NDIs) have also been studied as geometrically complementary guests, and indeed bind especially strongly (K_a > 10⁷ M^-1); this powerful and selective association suggests potential applications in supramolecular self-assembly.

Molecular Level Sucrose Quantification: A Critical Review

Sucrose is a primary metabolite in plants, a source of energy, a source of carbon atoms for growth and development, and a regulator of biochemical processes. Most of the traditional analytical chemistry methods for sucrose quantification in plants require sample treatment (with consequent tissue destruction) and complex facilities, that do not allow real-time sucrose quantification at ultra-low concentrations (nM to pM range) under in vivo conditions, limiting our understanding of sucrose roles in plant physiology across different plant tissues and cellular compartments. Some of the above-mentioned problems may be circumvented with the use of bio-compatible ligands for molecular recognition of sucrose. Nevertheless, problems such as the signal-noise ratio, stability, and selectivity are some of the main challenges limiting the use of molecular recognition methods for the in vivo quantification of sucrose. In this review, we provide a critical analysis of the existing analytical chemistry tools, biosensors, and synthetic ligands, for sucrose quantification and discuss the most promising paths to improve upon its limits of detection. Our goal is to highlight the criteria design need for real-time, in vivo, highly sensitive and selective sucrose sensing capabilities to enable further our understanding of living organisms, the development of new plant breeding strategies for increased crop productivity and sustainability, and ultimately to contribute to the overarching need for food security.

Cycloalkyl Groups as Building Blocks of Artificial Carbohydrate Receptors: Studies with Macrocycles Bearing Flexible Side-Arms

The cyclopentyl group was expected to act as a building block for artificial carbohydrate receptors and to participate in van der Waals contacts with the carbohydrate substrate in a similar way as observed for the pyrrolidine ring of proline in the crystal structures of protein-carbohydrate complexes. Systematic binding studies with a series of 1,3,5-trisubstituted 2,4,6-triethylbenzenes bearing various cycloalkyl groups as recognition units provided indications of the involvement of these groups in the complexation process and showed the influence of the ring size on the receptor efficiency. Representatives of compounds that exhibit a macrocyclic backbone and flexible side arms were now chosen as further model systems to investigate whether the previously observed effects represent a general trend. Binding studies with these macrocycles towards β-D-glucopyranoside, an all-equatorial substituted carbohydrate substrate, included 1H NMR spectroscopic titrations and microcalorimetric investigations. The performed studies confirmed the previously observed tendency and showed that the compound bearing cyclohexyl groups displays the best binding properties.

Alkoxy-Substituted Quadrupolar Fluorescent Dyes

Polar and polarizable π-conjugated organic molecules containing push-pull chromophores have been investigated extensively in the past. Identifying unique backbones and building blocks for fluorescent dyes is a timely exercise. Here, we report the synthesis and characterization of a series of fluorescent dyes containing quadrupolar A-D-A constitutions (where A = acceptor and D = donor), which exhibit fluorescence emission at a variety of different wavelengths. We have investigated the effects of different electron-withdrawing groups, located at both termini of a para-terphenylene backbone, by steady-state UV/vis and fluorescence spectroscopy. Pyridine and substituted pyridinium units are also introduced during the construction of the quadrupolar backbones. Depending on the quadrupolarity, fluorescence emission wavelengths cover from 380 to 557 nm. Time-resolved absorption and emission spectroscopy reveal that the photophysical properties of those quadrupolar dyes result from intramolecular charge transfer. One of the dyes we have investigated is a symmetrical box-like tetracationic cyclophane. Its water-soluble tetrachloride, which is non-cytotoxic to cells up to a loading concentration of 1 μM, has been employed in live-cell imaging. When taken up by cells, the tetrachloride emits a green fluorescence emission without any hint of photobleaching or disruption of normal cell behavior. We envision that our design strategy of modifying molecules through the functionalization of the quadrupolar building blocks as chromophores will lead to future generations of fluorescent dyes in which these A-D-A constitutional fragments are incorporated into more complex molecules and polymers for broader photophysical and biological applications.

A Fluorescent Cage for Supramolecular Sensing of 3‐Nitrotyrosine in Human Blood Serum

3‐Nitrotyrosine (NT) is generated by the action of peroxynitrite and other reactive nitrogen species (RNS), and as a consequence it is accumulated in inflammation‐associated conditions. This is particularly relevant in kidney disease, where NT concentration in blood is considerably high. Therefore, NT is a crucial biomarker of renal damage, although it has been underestimated in clinical diagnosis due to the lack of an appropriate sensing method. Herein we report the first fluorescent supramolecular sensor for such a relevant compound: Fluorescence by rotational restriction of tetraphenylethenes (TPE) in a covalent cage is selectively quenched in human blood serum by 3‐nitrotyrosine (NT) that binds to the cage with high affinity, allowing a limit of detection within the reported physiological concentrations of NT in chronic kidney disease.

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.