Precise tuning of cationic cyclophanes toward highly selective fluorogenic recognition of specific biophosphate anions

Unraveling the structure-chirality sensing relationship between achiral anthracene-based tetracationic nanotubes and nucleosides in aqueous host-guest complexation

In biological systems, nucleosides play crucial roles in various physiological processes. In this study, we designed and synthesized four achiral anthracene-based tetracationic nanotubes (1-4) as artificial hosts and chiroptical sensors for nucleosides in aqueous media. Notably, different nanotubes exhibit varied chirality sensing on circular dichroism (CD)/circularly polarized luminescence (CPL) spectra through the host-guest complexation, which prompted us to explore the factors influencing their chiroptical responses. Through systematic host-guest experiments, the structure-chirality sensing relationship between achiral anthracene-based tetracationic nanotubes and nucleosides in the host-guest complexation was unraveled. Firstly, the CD response originates from the anthracene rings situated at the side-wall position, resulting from the right-handed (P)- or left-handed (M)-twisted conformation of the macrocyclic structure. Secondly, the CPL signal is influenced by the presence of anthracene rings at the linking-wall position, which results from intermolecular chiral twisted stacking between these anthracene rings. Therefore, these nanotubes can serve as chiroptical sensor arrays to enhance the accuracy of nucleotide recognition through principal component analysis (PCA) analysis based on the diversified CD spectra. This study provides insights for the construction of adaptive chirality from achiral nanotubes with dynamic conformational nature and might facilitate further design of chiral functional materials for several applications.

Supramolecular Recognition of Cytidine Phosphate in Nucleotides and RNA Sequences

Supramolecular recognition of nucleotides would enable manipulating crucial biochemical pathways like transcription and translation directly and with high precision. Therefore, it offers great promise in medicinal applications, not least in treating cancer or viral infections. This work presents a universal supramolecular approach to target nucleoside phosphates in nucleotides and RNA. The artificial active site in new receptors simultaneously realizes several binding and sensing mechanisms: encapsulation of a nucleobase via dispersion and hydrogen bonding interactions, recognition of the phosphate residue, and a self-reporting feature-"turn-on" fluorescence. Key to the high selectivity is the conscious separation of phosphate- and nucleobase-binding sites by introducing specific spacers in the receptor structure. We have tuned the spacers to achieve high binding affinity and selectivity for cytidine 5' triphosphate coupled to a record 60-fold fluorescence enhancement. The resulting structures are also the first functional models of poly(rC)-binding protein coordinating specifically to C-rich RNA oligomers, e.g., the 5'-AUCCC(C/U) sequence present in poliovirus type 1 and the human transcriptome. The receptors bind to RNA in human ovarian cells A2780, causing strong cytotoxicity at 800 nM. The performance, self-reporting property, and tunability of our approach open up a promising and unique avenue for sequence-specific RNA binding in cells by using low-molecular-weight artificial receptors.

Fluorescent cyclophanes and their applications

With the serendipitous discovery of crown ethers by Pedersen more than half a century ago and the subsequent introduction of host-guest chemistry and supramolecular chemistry by Cram and Lehn, respectively, followed by the design and synthesis of wholly synthetic cyclophanes-in particular, fluorescent cyclophanes, having rich structural characteristics and functions-have been the focus of considerable research activity during the past few decades. Cyclophanes with remarkable emissive properties have been investigated continuously over the years and employed in numerous applications across the field of science and technology. In this Review, we feature the recent developments in the chemistry of fluorescent cyclophanes, along with their design and synthesis. Their host-guest chemistry and applications related to their structure and properties are highlighted.

Synthesis and aqueous anion recognition of an imidazolium-based nonacationic cup

An imidazolium-based nonacationic cup (1·9X; X = PF₆^- or Cl^-) was synthesized via step-by-step S_N2 reactions without using any template. The water-soluble 1·9Cl^- as a molecular container can encapsulate anionic nucleoside triphosphate and dinucleotide molecules (e.g., ATP and NADH) inside its cavity through hydrogen bonds and electrostatic interactions in aqueous solution.

Charge neutral halogen bonding tetradentate-iodotriazole macrocycles capable of anion recognition and sensing in highly competitive aqueous media

A series of neutral tetradentate halogen bonding (XB) macrocycles, comprising of two bis-iodotriazole XB donors were synthesised in 60-70% yields via a stepwise CuAAC-mediated cyclisation strategy. Extensive ¹H NMR anion titration experiments reveal halide binding affinities are critically dependent on the substitution pattern of the xylyl spacer unit. The meta-substituted macrocycle remarkably displays cooperative tetradentate XB-halide anion recognition in highly competitive 40% aqueous-organic D₂O/acetone-d₆ (40 : 60, v/v) solvent mixtures. Integration of para-xylyl and naphthyl spacer units generates extended macrocyclic cavities, capable of selective oxalate recognition. Furthermore, preliminary fluorescence exeperiments reveal dicarboxylate specific sensing can be achieved through monitoring of the naphthylene centred emission.

Photophysical and NMR studies of encapsulation of 2-cyano-6-hydroxy benzothiazole in p-sulfonatocalix[6]arene and its biological applications

This work deals with the study of the interaction between 2-cyano-6-hydroxy benzothiazole (CHBT) and p-sulfonatocalix[6]arene (SCX6) at different pH values in aqueous medium by UV-visible absorption spectroscopy and steady-state fluorescence spectroscopy. The results demonstrate the strong influence of SCX6 on the fluorescence properties of CHBT. The steady-state emission of CHBT shows strong sensitivity to its environment. The mode of inclusion complexation of CHBT and SCX6 has also been investigated using HR-MS, FT-IR, NMR, 2D NMR, and FESEM analysis. With the increase in SCX6 concentration, absorbance decreased with an isosbestic point at 305 nm. The binding constant is calculated by a spectrofluorimetric method and stoichiometry by Job's method. The formation of an inclusion complex has been confirmed by 2D NMR NOESY, COSY, ROESY, HMBC, and HSQC spectroscopic methods. The complex is seen to be stabilized by electrostatic interactions between CHBT and the nanocavity of SCX6. Studies with cellular systems support that the CHBT-SCX6 complex is more effective in killing cancerous cells and hence, SCX6 may prove to be an effective carrier for drug molecules like CHBT.

Hierarchical Two-Level Supramolecular Chirality of an Achiral Anthracene-Based Tetracationic Nanotube in Water

Herein, we report an achiral anthracene-based tetracationic nanotube (1⋅4Cl^- ) that shows two levels of supramolecular chirality: namely, conformationally adaptive host-guest complexation with nucleoside triphosphates (e.g. ATP, GTP, CTP, and UTP) and twisted packing of the chiral host-guest complexes in water. Interestingly, achiral 1⋅4Cl^- exhibits chiral recognition for ATP/GTP and CTP/UTP through structural transformation of its intramolecular M- and P-twisted conformation as the first level of supramolecular chirality, which leads to adaptive chirality with opposite CD responses. Furthermore, the formation of chiral M-1⋅4Cl^- ⊃ATP can promote an intermolecular P-twisted dimeric packing of anthracene rings as the second level of supramolecular chirality to achieve assembled chirality with strong circularly polarized luminescence arising from the excimer ((+)-CPL, g_lum ≈10^-2 ) in water.

Acridino-Diaza-20-Crown-6 Ethers: New Macrocyclic Hosts for Optochemical Metal Ion Sensing

Acridino-diaza-20-crown-6 ether derivatives as new turn-on type fluorescent chemosensors with an excellent functionality and photophysical properties have been designed and synthesized for metal ion-selective optochemical sensing applications. Spectroscopic studies revealed that in an acetonitrile-based semi-aqueous medium, the sensor molecules exhibited a remarkable fluorescence enhancement with high sensitivity only toward Zn2+, Al3+ and Bi3+, among 23 different metal ions. Studies on complexation showed a great coordinating ability of logK > 4.7 with a 1:1 complex stoichiometry in each case. The detection limits were found to be from 59 nM to micromoles. The new ionophores enabled an optical response without being affected either by the pH in the range of 5.5-7.5, or the presence of various anions or competing metal ions. Varying the N-substituents of the new host-backbone provides diverse opportunities in both immobilization and practical applications without influencing the molecular recognition abilities.

Comparison in practical applications of crown ether sensor molecules containing an acridone or an acridine unit – a study on protonation and complex formation

Crown ethers containing an acridone or an acridine unit are successfully applied opto- and electrochemical cation sensors. The heteroaromatic unit of these macrocycles can be in different forms during the applications, which have a strong influence on the sensing behavior. Moreover, in the case of acridono-macrocycles a prototropic equilibrium takes place upon complexation, which is effected by the physicochemical characteristics. A Pb2+-selective acridono-18-crown-6 ether and its 9-phenylacridino-analogue were used as model compounds for comparing the different forms of the heterocyclic units of these sensor molecules. Since in most practical sensor applications of the fluorescent hosts a non-neutral aqueous medium is present, studies on complexation and signaling were carried out from the aspect of the relationship among protonation, coordinating ability, complex stability and tautomeric equilibrium. A strong interdependence among these factors was found and limitations of using unsubstituted acridino- and acridono-sensor molecules in comparison with their 9-substituted-acridino-analogues were discussed. This study will hopefully serve as a useful standpoint for future development of ionophore-based sensors containing an acridone or an acridine unit.

Revisiting imidazolium receptors for the recognition of anions: highlighted research during 2010-2019

Imidazolium based receptors selectively recognize anions, and have received more and more attention. In 2006 and 2010, we reviewed the mechanism and progress of imidazolium salt recognition of anions, respectively. In the past ten years, new developments have emerged in this area, including some new imidazolium motifs and the identification of a wider variety of biological anions. In this review, we discuss the progress of imidazolium receptors for the recognition of anions in the period of 2010-2019 and highlight the trends in this area. We first classify receptors based on motifs, including some newly emerging receptors, as well as new advances in existing receptor types at this stage. Then we discuss separately according to the types of anions, including ATP, GTP, DNA and RNA.

A "turn-on" fluorescent probe for the detection of permanganate in aqueous media

A novel carbazole-based probe was synthesized and found to exhibit fluorescence upon introduction to potassium permanganate in aqueous media. Guided by a series of experimental studies and DFT calculations, the underlying mechanism is proposed to proceed through a series of tandem proton and electron transfer processes.

Molecular Receptors for Recognition and Sensing of Nucleotides

Nucleotides are constituents of nucleic acids and they have a variety of functions in cellular metabolism. Synthetic receptors and sensors are required to reveal the role of nucleotides in living organisms and mechanisms of signal transduction events. In recent years, a large number of nucleotide-selective synthetic receptors have been devised, which utilize different molecular designs and sensing mechanisms. This Minireview presents recent progress in the design of synthetic molecular receptors for selective recognition of nucleotides in aqueous solution. The binding properties of receptors and the origins of their selectivity for a particular nucleotide are discussed.

Development of an anion imprinted polymer for high and selective removal of arsenite from wastewater

A novel cyclic functional monomer (CFM) was used to develop an As(III)-ion imprinted polymer (As-IIP). CFM possesses a positively charged imidazolium moiety and its specific cyclic size matches that of As(III). Batch adsorption experiments showed that the As-IIP has a maximum As(III) adsorption capacity of 55 mg/g, while that of the control polymer (CP) is only 25 mg As(III)/g. Adsorption isotherms for As(III) agree with the Langmuir model, suggesting monolayer adsorption. Kinetic studies showed that the adsorption process followed pseudo-second-order kinetics. The relative selectivity coefficients of As-IIP compared to CP for Cl^-/H₂AsO₃^-, SO₄^2-/H₂AsO₃^-, HPO₄^2-/H₂AsO₃^-, NO₃^-/H₂AsO₃^-, and Mo₇O₂₄^6-/H₂AsO₃^- are 1.03, 1.95, 2.55, 1.52 and 2.51, respectively. The removal efficiency of As-IIP for As(III) in actual industrial wastewater was nearly 100%, which confirms that As-IIP has a high adsorption capacity as well as selectivity for the removal of As(III) from wastewater.

Insight into Water-Soluble Highly Fluorescent Low-Dimensional Host-Guest Supramolecular Polymers: Structure and Energy-Transfer Dynamics Revealed by Polarized Fluorescence Spectroscopy

Water-soluble, highly fluorescent host-guest chromophore-cucurbit[8]uril supramolecular polymer bundles are investigated by polarized time-resolved photoluminescence spectroscopy, structural methods, and quantum chemistry to fully reveal structural organization and heterogeneity but, in particular, energy-transfer dynamics, being of crucial importance for the design of supramolecular artificial light-harvesting systems.

Template Synthesis of Three-Dimensional Hexakisimidazolium Cages

A procedure for the synthesis of three-dimensional hexakisimidazolium cage compounds has been developed. The reaction of the trigonal trisimidazolium salts H₃ L(PF₆ )₃ , decorated with three N-olefinic pendants, and silver oxide yielded trinuclear trisilver(I) hexacarbene molecular cylinders of the type [Ag₃ L₂ ]³⁺ with the olefinic pendants from the two different tricarbene ligands arranged in three pairs. Subsequent UV irradiation gave three cyclobutane links between the two tris-NHC ligands in three [2+2] cycloaddition reactions, thereby generating a three-dimensional hexakis-NHC ligand. Removal of the metal ions resulted in the formation of three-dimensional hexakisimidazolium cages with a large internal cavity.

Synthetic receptor molecules for selective fluorescence detection of 8-oxo-dGTP in aqueous media

A series of 9-hydroxy-1,3-diazaphenoxazine-2-one derivatives were synthesized as fluorescent receptor molecules for 8-oxo-dGTP, which attach the cyclen-zinc complex at the 3-N position as the binding site for the triphosphate and the (2-aryloxycarbonylamino)ethyl group at the 9-O position as the hydrogen bonding site for 8-oxoguanine. Among these molecules, the receptor molecule 5a-Zn constructed of the ethyl linker at 3-N and the (2-benzyloxycarbonyl amino)ethyl group at 9-O displayed the best recognition ability for 8-oxoguanosine triphosphate (8-oxo-dGTP) in aqueous media. The receptor 5a-Zn was also shown to selectively detect 8-oxo-dGTP in a cell lysate solution.

The conformational behavior of multivalent tris(imidazolium)cyclophanes in the hybrids with metal (pseudo)halides or polyoxometalates

Three 3D imidazole or benzimidazole-bearing cages as trivalent cationic templates react with metal (pseudo)halides or polyoxometalates to obtain a series of different organic–inorganic hybrids in which the cages exhibit breathing behavior of expansion and contraction.

Charged probes: turn-on selective fluorescence for RNA

Imidazolium-based charged fluorescent probes for the selective in vitro and in vivo recognition of RNA over other biomolecules.

A self-assembled amphiphilic imidazolium-based ATP probe

A novel amphiphilic imidazolium-based probe containing a dansyl fluorophore and a long cetyl chain has been developed for ATP recognition. The probe forms self-assembled micelle-like aggregates at low concentration in its aqueous solution and can selectively recognize ATP among other bioactive anions with a significant enhancement in fluorescence emission.

Real-time detection and imaging of copper(ii) in cellular mitochondria

L displays high selectivity for Cu²⁺ with a rapidly reversible on–off–on fluorescence switch.

Metal ion-induced supramolecular pKa tuning and fluorescence regeneration of a p-sulfonatocalixarene encapsulated neutral red dye

Supramolecular pK_a shift and fluorescence quenching in a neutral red dye in the presence of p-sulfonatocalix[4/6]arenes have been demonstrated, which are relevant for the off–on switch, ion sensitive electrodes and drug delivery vehicles.

Imidazolium Based Probes for Recognition of Biologically and Medically Relevant Anions

The imidazolium derivatives due to their positive charge possess one of the most polarized and positively charged proton at C2-H to form strong ionic hydrogen bond (also termed as double ionic hydrogen bond) with anions and also provide opportunities for anion - π interactions with electron-deficient imidazolium ring. In the present review article, imidazolium based molecular probes for their ability to recognize inorganic anions like halides, cyanide, perchlorate, carboxylic acids, phosphate, sulfate etc. and their derived molecules viz. nucleotides, DNA, RNA, surfactants, proteins, etc have been discussed. The review covers the literature published after year 2009 and has > 130 references. The previous literature has already been discussed by Yoon et al. in two review articles published in Chem. Soc. Rev. 2006 and 2010.

Detection and quantification of ATP in human blood serum

Two fluorometric sensors based on the tri-serine tri-lactone scaffold and thiourea or sulfonamide moieties serving as hydrogen bond donors allowing for anion binding are described. The sensor utilizing thiourea as a recognition moiety shows fluorescence enhancement while the sensor with sulfonamide shows quenching upon addition of phosphates. Sensor arrays composed of two sensors are able to discriminate structurally similar organic phosphates in the presence of interferents in human blood serum. The quantitative analysis of ATP in human blood serum shows high accuracy (the root mean square error of prediction, 1.65%) without requiring any sample pretreatment.

Halides with Fifteen Aliphatic C-H···Anion Interaction Sites

Since the aliphatic C–H···anion interaction is relatively weak, anion binding using hydrophobic aliphatic C–H (C_ali–H) groups has generally been considered not possible without the presence of additional binding sites that contain stronger interactions to the anion. Herein, we report X-ray structures of organic crystals that feature a chloride anion bound exclusively by hydrophobic C_ali–H groups. An X-ray structure of imidazolium-based scaffolds using C_ali–H···A⁻ interactions (A⁻ = anion) shows that a halide anion is directly interacting with fifteen C_ali–H groups (involving eleven hydrogen bonds, two bidentate hydrogen-bond-type binding interactions and two weakly hydrogen-bonding-like binding interactions). Additional supporting interactions and/or other binding sites are not observed. We note that such types of complexes may not be rare since such high numbers of binding sites for an anion are also found in analogous tetraalkylammonium complexes. The C_ali–H···A⁻ interactions are driven by the formation of a near-spherical dipole layer shell structure around the anion. The alternating layers of electrostatic charge around the anion arise because the repulsions between weakly positively charged H atoms are reduced by the presence of the weakly negatively charged C atoms connected to H atoms.

Violation of DNA neighbor exclusion principle in RNA recognition

DNA intercalation has been very useful for engineering DNA-based functional materials.

DNA intercalation has been very useful for engineering DNA-based functional materials. It is generally expected that the intercalation phenomenon in RNA would be similar to that in DNA. Here we note that the neighbor-exclusion principle is violated in RNA by naphthalene-based cationic probes, in contrast to the fact that it is usually valid in DNA. All the intercalation structures are responsible for the fluorescence, where small naphthalene moieties are intercalated in between bases via π–π interactions. The structure is aided by hydrogen bonds between the cationic moieties and the ribose-phosphate backbone, which results in specific selectivity for RNA over DNA. This experimentally observed mechanism is supported by computationally reproducing the fluorescence and CD data. MD simulations confirm the unfolding of RNA due to the intercalation of probes. Elucidation of the mechanism of selective sensing for RNA over DNA would be highly beneficial for dynamical observation of RNA which is essential for studying its biological roles.

An efficient non-reaction based colorimetric and fluorescent probe for the highly selective discrimination of Pd0 and Pd2+ in aqueous media

A novel anthraquinone-imidazole based colorimetric and fluorogenic probe 1 discriminates the oxidation states of Pd⁰ and Pd²⁺ by naked eye with high selectivity in aqueous media due to the difference in coordination in the pocket of probe molecule.

A terbium(III)-complex-based on-off fluorescent chemosensor for phosphate anions in aqueous solution and its application in molecular logic gates

A new Tb(III) complex based on a tripodal carboxylate ligand has been synthesized for the selective fluorescent recognition of phosphate anions, including inorganic phosphates and nucleoside phosphates (e.g., ATP), in Tris buffer solution. The resulting L · Tb complex shows the characteristic emission bands centered at about 495 and 550 nm from the Tb(III)-centered (5)D4 excited state to (7)FJ transitions with J = 6 and 5, where the chelating ligand acts only as an "antenna". Upon the addition of phosphate anions to the aqueous solution of Tb(III) complex, significant "on-off" fluorescence changes were observed, which were attributed to the inhibition of the "antenna" effect between the ligand and Tb(III) after the incorporation of phosphate anions. Furthermore, this unique Tb(III) complex has been successfully utilized to detect phosphate anions with filter papers and hydrogels. Notably, the Tb(III) complex also can be used for the construction of molecular logic gates with TRANSFER and INHIBIT logic functions by using the above fluorescence changes.

A pyrenesulfonyl-imidazolium derivative as a selective cyanide ion sensor in aqueous media

Unlocking of probe 2 with CN⁻ ions leads to its minimum detection limit of 0.5 μM (13 ppb).

The synthesis of UDP-selective fluorescent probe and its imaging application in living cells

A perylene-based probe was developed for uridine diphosphate (UDP) sensing and cell imaging. The probe presented about 4-fold fluorescence enhancement in the presence or absence of 100equiv UDP. The selectivity toward UDP over other phosphor-containing anions was observed. The selective UDP sensing was speculated to be related to the binding affinities of Zn(2+) ions in sensor with the uridine and phosphate moieties of UDP. Furthermore, this probe was also applied to image of UDP in living cells.