Development of a Cone Homooxacalix[3]arene-Based Fluorescent Chemosensor for the Selective Detection of Biogenic Ammonium Ions in Protic Solvents.

We report here on the development of a fluorescent cone homooxacalix[3]arene-based receptor with a pyrene unit on the wide rim of the macrocycle (Ox3F) for the selective detection of primary ammonium ions, including those of biological importance. Ox3F was synthesized efficiently via an innovative strategy that enables the regio- and iteroselective wide rim functionalization of the readily available p-tBu-substituted homooxacalix[3]arene precursor. Nuclear magnetic resonance studies and in silico methods highlighted the endo-complexation of primary ammonium ions, including the protonated form of biogenic dopamine, tryptamine, serotonin, mexamine, and 3-iodothyronamine. The binding mode is similar for all guests with the ion deeply inserted into the polyaromatic cavity, enabling the NH3+ head to establish three hydrogen bonds with the ethereal oxygens of the macrocycle. Fluorescence quenching of the pyrene unit was observed following the π-π interaction between the pyrene moiety and the aromatic groups of serotonin, mexamine, and 3-iodothyronamine. No quenching was observed upon complexation of the smaller aromatic neurotransmitter dopamine as well as aliphatic amines and polyamines. This study presents a novel approach for biologically relevant ammonium ion chemosensing with ongoing efforts focused on translating these systems for aqueous environment applications.

A Semiflexible Tetrahydrazone Macrocycle for Binding of Pyrophosphate and Smaller Anions.

Macrocyclization has proven to be a useful design strategy in the development of efficient anion receptors. In addition to the ring size, the overall preorganization due to structural rigidity is key. To explore this in the context of developing an efficient pyrophosphate receptor, three macrocycles featuring a 26-membered interior ring size and similar H-bonding motifs have been synthesized, and their anion binding ability has been investigated. Computational studies and nuclear magnetic resonance (NMR) data showed different degrees of preorganization as a result of differences in flexibility. The interaction of the three macrocycles with chloride, dihydrogen phosphate, and dihydrogen pyrophosphate was investigated in solution by NMR and ultraviolet-visible spectroscopy and in the solid state by X-ray crystallography. The tetrahydrazone-based macrocycle featuring intermediate flexibility exhibited the best affinity for all three anions investigated. Our results suggest that in addition to the proper preorganization of binding groups in a macrocycle a certain degree of flexibility is also required for an optimal affinity with the target guest.

Transmembrane Transport of Inorganic Phosphate by a Strapped Calix[4]pyrrole.

Synthetic anion receptors are increasingly being explored for the transport of anions across lipid membranes because of their potential therapeutic applications. A considerable amount of research focuses on the transport of chloride, whereas the transmembrane transport of inorganic phosphate has not been reported to date, despite the biological relevance of this anion. Here we present a calix[4]pyrrole with a bisurea strap that functions as a receptor and transporter for H2PO4-, relying on the formation of eight hydrogen bonds and efficient encapsulation of the anion. Using a phosphate-sensitive lanthanide probe and 31P NMR spectroscopy, we demonstrate that this receptor can transport phosphate into vesicles by H2PO4-/Cl- antiport, H2PO4- uniport, and Cs+/H2PO4- symport mechanisms. This first example of inorganic phosphate transport by a neutral receptor opens perspectives for the future development of transporters for various biological phosphates.

Specific Binding of Primary Ammoniums in Aqueous Media by Homooxacalixarenes Incorporated into Micelles.

The development of artificial receptors for efficient recognition of analytes in water is a challenging task. Homooxacalix[3]arene-based receptor 1, which is selective toward primary ammoniums in organic solvents, was transferred into water following two different strategies: direct solubilization and micellar incorporation. Extensive 1H NMR studies showed that recognition of ammoniums is only observed in the case of micellar incorporation, highlighting the beneficial effect of the microenvironment of the micellar core. The selectivity of the system for primary ammoniums over secondary and tertiary ones was also maintained. The hydrophobic effect plays an important role in the recognition properties, which are counterion-dependent due to the energy penalty for the dissociation of certain ammonium salts in the apolar micellar core. This study shows that the straightforward self-assembly process used for the encapsulation of artificial receptors in micelles is an efficient strategy for developing water-soluble nanosized supramolecular recognition systems.

A Water Molecule Triggers Guest Exchange at a Mono-Zinc Centre Confined in a Biomimetic Calixarene Pocket: a Model for Understanding Ligand Stability in Zn Proteins.

In this study, the ligand exchange mechanism at a biomimetic ZnII centre, embedded in a pocket mimicking the possible constrains induced by a proteic structure, is explored. The residence time of different guest ligands (dimethylformamide, acetonitrile and ethanol) inside the cavity of a calix[6]arene-based tris(imidazole) tetrahedral zinc complex was probed using 1D EXchange SpectroscopY NMR experiments. A strong dependence of residence time on water content was observed with no exchange occurring under anhydrous conditions, even in the presence of a large excess of guest ligand. These results advocate for an associative exchange mechanism involving the transient exo-coordination of a water molecule, giving rise to 5-coordinate ZnII intermediates, and inversion of the pyramid at the ZnII centre. Theoretical modelling by DFT confirmed that the associative mechanism is at stake. These results are particularly relevant in the context of the understanding of kinetic stability/lability in Zn proteins and highlight the key role that a single water molecule can play in catalysing ligand exchange and controlling the lability of ZnII in proteins.

A Water Molecule Triggers Guest Exchange at a Mono-Zinc Centre Confined in a Biomimetic Calixarene Pocket: A Model for Understanding Ligand Stability in Zn Proteins.

Invited for the cover of this issue are Kristin Bartik, Olivia Reinaud and co-workers at the Université libre de Bruxelles and Université Paris Descartes. The image depicts a Zn protein and highlights the role that a single water molecule can play in catalysing ligand exchange. Read the full text of the article at 10.1002/chem.202102184.

Specific Binding of Primary Ammonium Ions and Lysine-Containing Peptides in Protic Solvents by Hexahomotrioxacalix[3]arenes.

The binding of ammonium ions by two homooxacalix[3]arene-based receptors was studied using NMR spectroscopy and in silico methods. Both receptors are shown to endocomplex, even in a protic environment, a large variety of primary ammonium ions, including biomolecules. The binding mode is similar for all guests with the ammonium ion deeply inserted into the polyaromatic cavity and its NH3+ head nearly in the plane defined by the three oxygen atoms of the 18-crown-3 moiety, thus enabling it to establish three H-bonds with the ethereal macrocycle. The remarkable electronic, size, and shape complementarity between primary ammonium ions and the two cavity-based receptors leads to an unprecedented specificity for primary ammonium ions over secondary, tertiary, and quaternary ones. These binding properties were exploited for the selective liquid-liquid extraction of primary ammonium salts from water and for the selective recognition of lysine-containing peptides, opening new perspectives in the field of peptide sensing.

Repositioning Chloride Transmembrane Transporters: Transport of Organic Ion Pairs.

Given the biological importance of organic cations, the facilitated transport of organic ion pairs could find many applications. Calix[6]arene tris(thio)ureas, which possess a cavity that can accommodate primary ammonium ions, can not only act as carriers for Cl- /NO3- antiport but can also perform the cotransport of PrNH3 Cl. Transport was monitored by fluorescence spectroscopy and the presence of the different species inside the vesicles was characterized by 1 H and 35 Cl NMR experiments involving shift reagents. The cotransport of PrNH3 Cl was also observed by receptors deprived of a cavity, but the presence of the cavity conveys an advantage, as the cotransport by calix[6]arenes was observed to be more efficient than the Cl- /NO3- antiport, which is not the case with receptors without a cavity. The role played by the cavity was further highlighted by the disappearance of this advantage when using a bulky ammonium ion, which cannot be complexed within the cavity.

Submerging a Biomimetic Metallo-Receptor in Water for Molecular Recognition: Micellar Incorporation or Water Solubilization? A Case Study.

Molecular recognition in water is an important topic, but a challenging task due to the very competitive nature of the medium. The focus of this study is the comparison of two different strategies for the water solubilization of a biomimetic metallo-receptor based on a poly(imidazole) resorcinarene core. The first relies on a new synthetic path for the introduction of hydrophilic substituents on the receptor, at a remote distance from the coordination site. The second involves the incorporation of the organosoluble metallo-receptor into dodecylphosphocholine (DPC) micelles, which mimic the proteic surrounding of the active site of metallo-enzymes. The resorcinarene ligand can be transferred into water through both strategies, in which it binds ZnII over a wide pH window. Quite surprisingly, very similar metal ion affinities, pH responses, and recognition properties were observed with both strategies. The systems behave as remarkable receptors for small organic anions in water at near-physiological pH. These results show that, provided the biomimetic site is well structured and presents a recognition pocket, the micellar environment has very little impact on either metal ion binding or guest hosting. Hence, micellar incorporation represents an easy alternative to difficult synthetic work, even for the binding of charged species (metal cations or anions), which opens new perspectives for molecular recognition in water, whether for sensing, transport, or catalysis.

A selective calix[6]arene-based fluorescent chemosensor for phosphatidylcholine type lipids.

The development of chemosensors that can selectively detect phosphatidylcholines (PCs) in biological samples is of medical relevance considering the importance of these phospholipids in cell growth and survival. Their selective sensing over phosphatidylethanolamines (PEs) is however a challenging task. We report here on the chemosensing capacities of calix[6]tris-pyrenylurea 1, which is able to selectively interact with phosphatidylcholine-type lipids in organic media. Host 1 also binds them in a biphasic chloroform/water solution, opening the way to the design of selective chemosensors for these lipids in biological media. The results obtained by NMR, fluorescence spectroscopy and modelling studies show that the selectivity is the result of the high degree of complementarity between the lipids' zwitterionic phosphatidylcholine headgroup and the receptor's H-bonding donor site and hydrophobic pocket. The mode of recognition is reminiscent of natural systems, such as human phosphatidylcholine transfer proteins (PC-TPs), validating the biomimetic approach adopted in our work.

Primary amine recognition in water by a calix[6]aza-cryptand incorporated in dodecylphosphocholine micelles.

Water is a unique solvent and the design of selective artificial hosts that can efficiently work in an aqueous medium is a challenging task. It is known that the calix[6]tren zinc complex can recognize neutral guests in organic solvents. This complex was incorporated into dodecylphosphocholine micelles (DPC) and studied by NMR. The incorporated complex is able to extract selectively primary amines from the aqueous environment driven by an important hydrophobic effect which also affects the selectivity of the complex for these amines. This work shows how the incorporation of organo-soluble receptors in micelles can be an elegant and very efficient strategy to obtain water compatible nanosized supramolecular recognition devices which can be prepared via a straightforward self-assembly process.

Fluoride binding in water with the use of micellar nanodevices based on salophen complexes.

The use of micelles to transpose lipophilic receptors, such as uranyl-salophen complexes, into an aqueous environment is a valuable and versatile tool. Receptor 1 incorporated into CTABr micelles forms a supramolecular system that exhibits excellent binding properties towards fluoride in water, despite the competition of the aqueous medium. To fully evaluate the potential of micellar nanodevices, we extended our previous study to other types of surfactants and to a uranyl-salophen receptor with a more extended aromatic surface. Paramagnetic relaxation enhancement experiments were used to obtain information on the location of the two receptors within the micelles and complementary information was obtained from dynamic light scattering experiments. With these data it is possible to account for the key factors necessary to obtain an efficient supramolecular device for anion binding in water.

Fluorescent chemosensors for anions and contact ion pairs with a cavity-based selectivity.

The association of a concave macrocyclic compound to one or multiple fluorophores is an appealing strategy for the design of chemosensors. Indeed, as with biological systems, a cavity-based selectivity can be expected with such fluorescent receptors. Examples of calix[6]arene-based systems using this strategy are rare in the literature, and to our knowledge, no examples of fluorescent receptors that can bind organic contact ion pairs have been reported. This report describes the straightforward synthesis of fluorescent calix[6]arene-based receptors 4a and 4b bearing three pyrenyl subunits and the study of their binding properties toward anions and ammonium salts using different spectroscopies. It was found that receptor 4a exhibits a remarkable selectivity for the sulfate anion in DMSO, enabling its selective sensing by fluorescence spectroscopy. In CDCl3, the receptor is able to bind ammonium ions efficiently only in association with the sulfate anion. Interestingly, this cooperative binding of ammonium sulfate salts was also evidenced in a protic environment. Finally, a cavity-based selectivity in terms of size and shape of the guest was observed with both receptors 4a and 4b, opening interesting perspectives on the elaboration of fluorescent cavity-based systems for the selective sensing of biologically relevant ammonium salts such as neurotransmitters.

Polyoxometalates as a novel class of artificial proteases: selective hydrolysis of lysozyme under physiological pH and temperature promoted by a cerium(IV) Keggin-type polyoxometalate.

Hen-egg-white lysozyme (HEWL) is specifically cleaved at the Trp28-Val29 and Asn44-Arg45 peptide bonds in the presence of a Keggin-type [Ce(α-PW(11)O(39))(2)](10-) polyoxometalate (POM; 1) at pH 7.4 and 37 °C. The reactivity of 1 towards a range of dipeptides was also examined and the calculated reaction rates were comparable to those observed for the hydrolysis of HEWL. Experiments with α-lactalbumin (α-LA), a protein that is structurally highly homologous to HEWL but has a different surface potential, showed no evidence of hydrolysis, which indicates the importance of electrostatic interactions between 1 and the protein surface for the hydrolytic reaction to occur. A combination of spectroscopic techniques was used to reveal the molecular interactions between HEWL and 1 that lead to hydrolysis. NMR spectroscopy titration experiments showed that on protein addition the intensity of the (31)P NMR signal of 1 gradually decreased due to the formation of a large protein/polyoxometalate complex and completely disappeared when the HEWL/1 ratio reached 1:2. Circular dichroism (CD) measurements of HEWL indicate that addition of 1 results in a clear decrease in the signal at λ=208 nm, which is attributed to changes in the α-helical content of the protein. (15)N-(1)H heteronuclear single quantum coherence (HSQC) NMR measurements of HEWL in the presence of 1 reveal that the interaction is mainly observed for residues that are located in close proximity to the first site in the α-helical part of the structure (Trp28-Val29). The less pronounced NMR spectroscopic shifts around the second cleavage site (Asn44-Arg45), which is found in the ß-strand region of the protein, might be caused by weaker metal-directed binding, compared with strong POM-directed binding at the first site.

Calix[6]arenes with halogen bond donor groups as selective and efficient anion transporters.

Here we present the anion binding and anion transport properties of a series of calix[6]arenes decorated on their small rim with either halogen bond or hydrogen bond donating groups. We show that the halogen bond donating iodotriazole groups enable highly selective transport of chloride and nitrate anions, without transport of protons or hydroxide, at rates similar to those observed with thiourea or squaramide groups.

The search for a deterministic origin for the presence of nonracemic amino-acids in meteorites: a computational approach.

Amino-acid enantiomeric excesses (ee's) have been detected in different types of carbonaceous chondrites, all in favor of the L enantiomer. In this article, we discuss possible deterministic causes to the presence of these amino-acid ee's in meteorites and evaluate in particular enantioselective photolysis by circularly polarized light (CPL). The electronic circular dichroism spectra of a set of amino- and hydroxy-acids, all detected in chondritic matter but some with ee's and others without ee's, were calculated and compared. The spectra were calculated for the most stable conformation(s) of the considered molecules using quantum mechanical methods (density functional theory). Our results suggest that CPL photolysis in the gas phase was perhaps not at the origin of the presence of ee's in meteorites and that the search for another, but still unknown, deterministic cause must be seriously undertaken.

Is it useful to have a clear-cut definition of life? On the use of fuzzy logic in prebiotic chemistry.

Many scientists, including one of the authors of the present paper, have devoted time to try to find a definition for life (Bersini and Reisse 2007). It is clear that a consensus will never be reached but, more importantly, it seems that the issue itself could be without major interest. It is indeed impossible to define a "natural" frontier between non-living and living systems and therefore also impossible to define dichotomic criteria which could be used in order to classify systems in one of these two classes (living or non-living). Fuzzy logic provides a natural way to deal with problems where class membership lacks sharply defined criteria. It also offers the possibility to avoid losing time with unnecessary controversies such as deciding whether a virus is, or is not, a living system.

Comparison of the thermodynamics and base-pair dynamics of a full LNA:DNA duplex and of the isosequential DNA:DNA duplex.

Locked nucleic acids (LNA), conformationally restricted nucleotide analogues, are known to enhance pairing stability and selectivity toward complementary strands. With the aim to contribute to a better understanding of the origin of these effects, the structure, thermal stability, hybridization thermodynamics, and base-pair dynamics of a full-LNA:DNA heteroduplex and of its isosequential DNA:DNA homoduplex were monitored and compared. CD measurements highlight differences in the duplex structures: the homoduplex and heteroduplex present B-type and A-type helical conformations, respectively. The pairing of the hybrid duplex is characterized, at all temperatures monitored (between 15 and 37 degrees C), by a larger stability constant but a less favorable enthalpic term. A major contribution to this thermodynamic profile emanates from the presence of a hairpin structure in the LNA single strand which contributes favorably to the entropy of interaction but leads to an enthalpy penalty upon duplex formation. The base-pair opening dynamics of both systems was monitored by NMR spectroscopy via imino protons exchange measurements. The measurements highlight that hybrid G-C base-pairs present a longer base-pair lifetime and higher stability than natural G-C base-pairs, but that an LNA substitution in an A-T base-pair does not have a favorable effect on the stability. The thermodynamic and dynamic data confirm a more favorable stacking of the bases in the hybrid duplex. This study emphasizes the complementarities between dynamic and thermodynamical studies for the elucidation of the relevant factors in binding events.

Protonation linked equilibria and apparent affinity constants: the thermodynamic profile of the alpha-chymotrypsin-proflavin interaction.

Protonation/deprotonation equilibria are frequently linked to binding processes involving proteins. The presence of these thermodynamically linked equilibria affects the observable thermodynamic parameters of the interaction (K(obs), DeltaH(obs)(0) ). In order to try and elucidate the energetic factors that govern these binding processes, a complete thermodynamic characterisation of each intrinsic equilibrium linked to the complexation event is needed and should furthermore be correlated to structural information. We present here a detailed study, using NMR and ITC, of the interaction between alpha-chymotrypsin and one of its competitive inhibitors, proflavin. By performing proflavin titrations of the enzyme, at different pH values, we were able to highlight by NMR the effect of the complexation of the inhibitor on the ionisable residues of the catalytic triad of the enzyme. Using ITC we determined the intrinsic thermodynamic parameters of the different equilibria linked to the binding process. The possible driving forces of the interaction between alpha-chymotrypsin and proflavin are discussed in the light of the experimental data and on the basis of a model of the complex. This study emphasises the complementarities between ITC and NMR for the study of binding processes involving protonation/deprotonation equilibria.

Amino acid induced fractal aggregation of gold nanoparticles: Why and how.

Gold colloids are the object of many studies as they are reported to have potential biological sensing, imaging and drug delivery applications. In the presence of certain amino acids the aggregation of the gold nanoparticles into linear structures is observed, as highlighted by the appearance of a second plasmon band in the UV-Vis spectra of the colloid. The mechanism behind this phenomenon is still under debate. In order to help elucidate this issue, the interaction between gold colloids and different amino acids, modified amino acids and molecules mimicking their side-chain was monitored by UV-Vis absorption, DLS and TEM. The results show that phenomenon can be rationalized in terms of the Diffusion Limited Colloid Aggregation (DLCA) model which gives rise to the fractal aggregation colloids. The global charge of the compound, which influences the ionic strength of the solution, and the ease with which the compound can interact with the GNPs and affect their surface potential, are, the two parameters which control the DLCA regime. Calculations based on the Derjaguin, Landau, Verwey and Overbeek (DLVO) theory confirm all the experimental observations.