Supramolecular Encapsulation of Tetrahedrally Hydrated Guests in a Tetrahedron Host

Diphenylpyrrole-Strapped Calix[4]pyrrole Extractant for the Fluoride and Chloride Anions

The anion binding features of diphenylpyrrole-strapped calix[4]pyrrole 1 have been investigated by means of 1 H NMR spectroscopy and ITC (isothermal titration calorimetry), as well as single crystal X-ray diffraction analyses. Receptor 1 bearing an auxiliary pyrrolic NH donor and solubilizing phenyl groups on the strap was found to bind F- , Cl- , and Br- as their tetrabutylammonium salts with high affinity in DMSO-d6 . In addition, receptor 1 was found to extract the fluoride anion (as both its tetraethylammonium (TEA+ ) and tetrabutylammonium (TBA+ ) salts), as well as the chloride anion into chloroform-d from an aqueous source phase. Cation metathesis using TBAI or the use of a dual host approach involving crown ethers enabled receptor 1 to extract simple alkali metal fluoride or chloride salts from water. Quantitative binding of NaF by receptor 1 was observed in 20 % D2 O-DMSO-d6 allowing for the direct determination of the NaF concentration in an unknown sample.

A tetrahedron from homooxacalix[3]arene, the fifth Platonic polyhedron from calixarenes and uranyl

A self-assembled tetrahedral cage results from two C ₃-symmetry building blocks, namely, homooxacalix[3]arene tricarboxylate and uranyl cation, as demonstrated by X-ray crystallography. In the cage, four metals coordinate at the lower rim with the phenolic and ether oxygen atoms to shape the macrocycle with appropriate dihedral angles for tetrahedron formation, whereas four additional uranyl cations further coordinate at the upper-rim carboxylates to finalize the assembly. Counterions dictate the filling and porosity of the aggregates, whereas potassium induces highly porous structures, and tetrabutylammonium yields compact, densely packed frameworks. The tetrahedron metallo-cage complements our previous report (Pasquale et al., Nat. Commun., 2012, 3, 785) on uranyl-organic frameworks (UOFs) from calix[4]arene and calix[5]arene carboxylates (octahedral/cubic and icosahedral/dodecahedral giant cages, respectively) and completes the assembly of all five Platonic solids from just two chemical components.

Anthracene-Based Amido-Amine Cage Receptor for Anion Recognition under Neutral Aqueous Conditions

A new amido-amine cage receptor, which combines 1,8-anthracene diacarboxamide subunit and a polyammonium azamacrocycle, is reported. Bearing both the hydrogen bond donor and the acceptor binding sites, the receptor is able to bind phosphate selectively under neutral (pH 7.2) aqueous conditions. The recognition events for phosphate and dicarboxylates are accomplished by a fluorescence enhancement in the anthracene emission. As revealed by experimental and theoretical studies, phosphate and oxalate show different recognition modes. Phosphate demonstrates hydrogen bond acceptor properties, while the coordination of oxalate favours the protonation of the receptor.

Macrocycle-Directed Construction of Tetrahedral Anion-π Receptors for Nesting Anions with Complementary Geometry

Manipulation of the emerging anion-π interactions in a highly cooperative manner through sophisticated host design represents a very challenging task. In this work, unprecedented tetrahedral anion-π receptors have been successfully constructed for complementary accommodation of tetrahedral and relevant anions. The synthesis was achieved by a macrocycle-directed approach by using large macrocycle precursors bearing four reactive sites, which enabled a kinetic-favored pathway and afforded the otherwise inaccessible tetrahedral cages in considerable yields. Crystal structure suggested that the tetrahedral cages have an enclosed three-dimensional cavity surrounded by four electron-deficient triazine faces in a tetrahedral array. The complementary accommodation of a series of tetrahedral and relevant anions including BF₄ ^- , ClO₄ ^- , H₂ PO₄ ^- , HSO₄ ^- , SO₄ ^2- and PF₆ ^- was revealed by ESI-MS and DFT calculations. Crystal structures of ClO₄ ^- and PF₆ ^- complexes showed that the anion was nicely encapsulated within the tetrahedral cavity with up to quadruple cooperative anion-π interactions by an excellent shape and size match. The strong anion-π binding was further confirmed by negative ion photoelectron spectroscopy measurements.

Proton-induced fluorescence in modified quino[7,8-h]quinolines: dual sensing for protons and π-donors

The synthesis, as well as spectral, structural and photoluminescence properties of dipyrido[3,2-e:2',3'-h]acenaphthene 5 and quinazolino[7,8-h]quinazolines 6 as representatives of the bidentate -N[double bond, length as m-dash]/-N[double bond, length as m-dash] superbases, are reported. These nitrogen bases being more rigid (5) or π-extended (6) analogs of optically-mute quino[7,8-h]quinoline are both active in terms of fluorescence with quantum yields up to φ = 0.71-0.77. At the same time, their luminescence behavior is opposite to that of peri-NMe₂/NMe₂ naphthalene proton sponges and their hybrid NMe₂/-N[double bond, length as m-dash] analogs. Although 5 and 6 exhibit visible region emission upon protonation, for the hybrid systems the fluorescence is manifested only for bases. The most remarkable observation is that the fluorescence of compound 5 can be switched on not only by means of organic or inorganic acids, but also through the formation of chelate complexes with such weak H-donors as water and primary alcohols. It was disclosed that water is present in the complex as a cluster comprising 8 interconnected H₂O molecules. Overall, the studied compounds demonstrate a previously unobserved type of dual mode optical response, H-sensing (emission enhancement in 5 and 6 on protonation) and π-sensing (emission quenching in 5H⁺ and 6H⁺ on coordination with π-donors). This work seems to be an important contribution to areas such as chemosensorics, the creation of new ligands, hydrogen transfer and some other phenomena representing different types of supramolecular interactions.

Synthesis and Anion Recognition Features of a Molecular Cage Containing Both Hydrogen Bond Donors and Acceptors

A molecular cage, macrobicycle 2, containing amide and pyrrole groups as hydrogen-bonding donors and imine groups as hydrogen-bonding acceptors has been synthesized. Compound 2 was found to recognize tetrahedral oxyanions with high affinities, such as H₂PO₄^-, HSO₄^-, SO₄^2-, and HP₂O₇^3-, as well as the spherical halide anions, in chloroform. A single-crystal X-ray diffraction analysis revealed that compound 2 formed a 1:1 complex with H₂PO₄^- in the solid state.

Gating the electron transfer at a monocopper centre through the supramolecular coordination of water molecules within a protein chamber mimic

Functionality of enzymes is strongly related to water dynamic processes.

Functionality of enzymes is strongly related to water dynamic processes. The control of the redox potential for metallo-enzymes is intimately linked to the mediation of water molecules in the first and second coordination spheres. Here, we report a unique example of supramolecular control of the redox properties of a biomimetic monocopper complex by water molecules. It is shown that the copper complex based on a calix[6]arene covalently capped with a tetradentate [tris(2-methylpyridyl)amine] (tmpa) core, embedding the metal ion in a hydrophobic cavity, can exist in three different states. The first system displays a totally irreversible redox behaviour. It corresponds to the reduction of the 5-coordinate mono-aqua-Cu^II complex, which is the thermodynamic species in the +II state. The second system is detected at a high redox potential. It is ascribed to an “empty cavity” or “water-free” state, where the Cu^I ion sits in a 4-coordinate trigonal environment provided by the tmpa cap. This complex is the thermodynamic species in the +I state under “dry conditions”. Surprisingly, a third redox system appears as the water concentration is increased. Under water-saturation conditions, it displays a pseudo-reversible behaviour at a low scan rate at the mid-point from the water-free and aqua species. This third system is not observed with the Cu-tmpa complex deprived of a cavity. In the calix[6]cavity environment, it is ascribed to a species where a pair of water molecules is hosted by the calixarene cavity. A molecular mechanism for the Cu^II/Cu^I redox process with an interplay of (H₂O)_x (x = 0, 1, 2) hosting is proposed on the basis of computational studies. Such an unusual behaviour is ascribed to the unexpected stabilization of the Cu^I state by inclusion of the pair of water molecules. This phenomenon strongly evidences the drastic influence of the interaction between water molecules and a hydrophobic cavity on controlling the thermodynamics and kinetics of the Cu^II/Cu^I electron transfer process.

Selective Anion Extraction and Recovery Using a FeII4 L4 Cage

Selective anion extraction is useful for the recovery and purification of valuable chemicals, and in the removal of pollutants from the environment. Here we report that Fe^II₄L₄ cage 1 is able to extract an equimolar amount of ReO₄⁻, a high‐value anion and a nonradioactive surrogate of TcO₄⁻, from water into nitromethane. Importantly, the extraction was efficiently performed even in the presence of 10 other common anions in water, highlighting the high selectivity of 1 for ReO₄⁻. The extracted guest could be released into water as the cage disassembled in ethyl acetate, and then 1 could be recycled by switching the solvent to acetonitrile. The versatile solubility of the cage also enabled complete extraction of ReO₄⁻ (as the tetrabutylammonium salt) from an organic phase into water by using the sulfate salt of 1 as the extractant.

Benzoins and cyclobenzoins in supramolecular and polymer chemistry

Benzoin condensation is one of the oldest rigorously described organic reactions, having been discovered in 1832 by Liebig and Wöhler. This Feature Article summarizes our work on cyclobenzoins: a class of macrocyclic compounds prepared by a benzoin cyclooligomerization of simple aromatic dialdehydes.

Hydrogen Peroxide Insular Dodecameric and Pentameric Clusters in Peroxosolvate Structures

Peroxosolvates of 2-aminonicotinic acid (I) and lidocaine N-oxide (II) including the largest insular hydrogen peroxide clusters were isolated and their crystal structures were determined by single-crystal X-ray diffraction. An unprecedented dodecameric hydrogen peroxide insular cluster was found in I. An unusual cross-like pentameric cluster was observed in the structure of II. The topology of the (H₂ O₂ )₁₂ assembly was never observed for small-molecule clusters. In I and II new double and triple cross-orientational disorders of H₂ O₂ were found. Cluster II is the first example of a peroxosolvate crystal structure containing H₂ O₂ molecules with a homoleptic hydrogen peroxide environment. In II, a hydrogen bond between an H₂ O₂ molecule and a peptide group -CONH⋅⋅⋅O₂ H₂ was observed for the first time.

Eight-coordinate fluoride in a silicate double-four-ring

Fluoride, nature's smallest anion, is capable of covalently coordinating to eight silicon atoms. The setting is a simple and common motif in zeolite chemistry: the box-shaped silicate double-four-ring (D4R). Fluoride seeks its center. It is the strain of box deformation that keeps fluoride in the middle of the box, and freezes what would be a transition state in its absence. Hypervalent bonding ensues. Fluoride's compactness works to its advantage in stabilizing the cage; chloride, bromide, and iodide do not bring about stabilization due to greater steric repulsion with the box frame. The combination of strain and hypervalent bonding, and the way they work in concert to yield this unusual case of multiple hypervalence, has potential for extension to a broader range of solid-state compounds.

Catching the chloride: searching for non-Hofmeister selectivity behavior in systematically varied polyamide macrocyclic receptors

Searching for regularities in the large set of structurally diverse macrocyclic probes allowed us to determine the structural requirements for the selective recognition of chloride over more basic anions such as H₂PO₄⁻ or RCO₂⁻ by a putative anion receptor.

Experimental Binding Energies in Supramolecular Complexes

On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.

Peripheral Templation Generates an M(II) 6 L4 Guest-Binding Capsule

Pseudo‐octahedral M^II₆L₄ capsules result from the subcomponent self‐assembly of 2‐formylphenanthroline, threefold‐symmetric triamines, and octahedral metal ions. Whereas neutral tetrahedral guests and most of the anions investigated were observed to bind within the central cavity, tetraphenylborate anions bound on the outside, with one phenyl ring pointing into the cavity. This binding configuration is promoted by the complementary arrangement of the phenyl rings of the intercalated guest between the phenanthroline units of the host. The peripherally bound, rapidly exchanging tetraphenylborate anions were found to template an otherwise inaccessible capsular structure in a manner usually associated with slow‐exchanging, centrally bound agents. Once formed, this cage was able to bind guests in its central cavity.

A double stranded metal-organic assembly accommodating a pair of water trimers in the host cavity and catalysing Glaser coupling

A supramolecular compound, catena-poly{[Cu2(1,3-μ2-(1a))2(μ2-ter)2(H2O)2]n·(6H2O)n} (1) has been synthesized using (1a) [(1a = N(1),N(3),N(5)-trimethyl-N(1),N(3),N(5)-tris((pyridin-4-yl)methyl)-1,3,5-benzene tricarboxamide] and terephthalate (ter) as the pillaring unit by self-assembly. The terephthalate units are connected by copper(II) ions forming a single strand, while a pair of such strands are then linked by (1a) via two pyridyl terminal arms bound to copper(II) nodes on either side forming a one-dimensional double stranded assembly propagating along the c axis. The compound crystallizes in the Fdd2 space group. The cavity created in the interior of this double strand assembly trap six water molecules and are stabilized by hydrogen bonding with the host. The arrangement of the pair of acyclic water trimers in isolated cavities of (1) is such that it resembles a closed-bracket-like formation. The Hirshfeld surface analysis of (1) reveals the presence of strong intermolecular hydrogen-bonding interactions between one-dimensional ladder-like units and with the water trimer in the host cavity. The copper(II)-containing coordination polymer also acts as an efficient catalyst for the Glaser-Hay homo-coupling reaction.

A nano-sized container for specific encapsulation of isolated water molecules

This calix[4]arene-based molecular box is able to encapsulate specifically two isolated water molecules in both non-protic and protic solvents.

A water molecule in the interior of a 1H-pyrazole Cu2+ metallocage

A pyrazole aza-macrocyclic Cu²⁺ metallocage shows the inclusion of a water molecule not hydrogen bonded with any acceptor or donor groups of the cage.

Stacking Interactions Drive Selective Self-Assembly and Self-Sorting of Pyrene-Based M(II)4L6 Architectures

Subcomponent self-assembly of two isomeric bis(3-aminophenyl)pyrenes, 2-formylpyridine and the metal ions Fe(II), Co(II), and Zn(II) led to the formation of two previously unidentified structure types: a C2-symmetric M(II)4L6 assembly with meridionally coordinated metal centers, and a C3-symmetric self-included M(II)4L6 assembly with facially coordinated metal centers. In both structures the meta linkages within the ligands facilitate π-stacking between the pyrene panels of the ligands. A C2h-symmetric M(II)2L2 box was also obtained, which was observed to selectively bind electron-deficient aromatic guests between two parallel pyrene subunits. Similar donor-acceptor interactions drove the selective self-assembly of a singular M(II)4L4L'2 architecture incorporating both a pyrene-containing diamine and an electron-deficient NDI-based diamine. This heteroleptic architecture was shown to be thermodynamically favored over the corresponding homoleptic M(II)4L6 and M(II)4L'6 complexes, which were nonetheless stable in each others' absence. By contrast, an isomeric pyrene-based diamine was observed to undergo narcissistic self-sorting in the presence of the NDI-based diamine.

Coordination diversity in hydrogen-bonded homoleptic fluoride-alcohol complexes modulates reactivity

The nucleophilic reactivity of fluoride ion is altered in the presence of hydrogen-bond donors, including alcohols. Relatively little is known about the coordination involved; to rectify this, the X-ray structures of fourteen novel fluoride-alcohol complexes with tetrabutylammonium as the counterion have been determined. The coordination number varies from two to four depending on the steric bulk of the alcohol and is closely linked to trends in reactivity. This diversity in coordination stoichiometry is unprecedented but significant, as it implies differences in the ability of the fluoride-alcohol complexes to dissociate in solution with release of a more active and/or selective fluoride source.

Mutual stabilisation between MII4L6 tetrahedra and MIIX42- metallate guests

A complex host-guest equilibrium employing metal ions incorporated into both the host and guest is discussed. MIIX42- metallate guests are shown to provide a good size and shape match for encapsulation within the M4L6 tetrahedral capsules, facilitating the generation of previously unreported Zn4L6 complexes. Displacement of the initial, primary template anion (ZnBr42-) by a secondary template anion (ClO4-) is shown to result in the formation of a pentagonal-prismatic Zn10L15 structure that incorporates both Br- and ClO4-. Furthermore, the formation of heterometallic complexes provides direct evidence for metal exchange between the guest and host complex.

A unique fluoride nanocontainer: porous molecular capsules can accommodate an unusually high number of "rather labile" fluoride anions

The present work refers to the challenging issue of fluoride anion recognition/binding in water by taking advantage of the unique possibilities offered by the porous molecular nanocontainers of the {Mo132} Keplerate type allowing the study of a variety of new phenomena. Reaction of the highly reactive carbonate-type capsule with aqueous HF results in the release of carbon dioxide and integration of an unprecedentedly large number of fluoride anions--partly as coordinated ligands at both the pentagonal units and the linkers, partly as a disordered water/fluoride assembly inside the cavity. The internal assembly and some of the fluoride ligands are easily released, which provides interesting options for future studies regarding coordination chemistry and catalysis under confined conditions.

Molecular recognition in chemical and biological systems

Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.

Open-cage fullerene with a stopper acts as a molecular vial for a single water molecule

An open-cage fullerene derivative with three carbonyl groups on the rim of the orifice reacts with o-diaminobenzene reversibly to form a tetrahydrofuran moiety above the orifice.

Arene platform based hexa-amide receptors for anion recognition: single crystal X-ray structural and thermodynamic studies

Compartmental recognition of [Cl₂(inf>O/inf>O)₂]²⁻ in the cavity of p-fluoro-phenyl substituted hexa-amide receptor.

Encapsulation of [X2(H2O)4]2- (X = F/Cl) clusters by pyridyl terminated tripodal amide receptor in aqueous medium: single crystal X-ray structural evidence

A new tris-amide receptor L based on 1,3,5-methyl substituted benzene platform and pyridyl as an attached unit is synthesized and explored towards anion recognition in aqueous environment. The presence of pyridyl terminal in L facilitates its aqueous solubility. The binding of halides and oxyanions towards L are examined by (1)H-NMR technique in solution and by single crystal X-ray crystallography in solid state studies. Crystallization of fluoride and chloride with L is carried out in acetone-water (1 : 1, v/v) binary solvent mixture that yields crystals for respective host-guest complexes, [L]2·[F2(H2O)4]·[TBA]2 (1) and [L]2·[Cl2(H2O)4]·[TBA]2 (2) suitable for single crystal X-ray diffraction studies. On the other hand, complexation of L with fluoride in dioxane-acetone (1 : 1, v/v) solvent mixture, results the formation of SiF6(2-) encapsulated complex, [L]2·[SiF6(H2O)2]·[TBA]2 (3). Crystallographic result shows the formation of [F2(H2O)4](2-) and [Cl2(H2O)4](2-) zipped 1D-polymeric tweezer-like assemblies of L in acetone-water (1 : 1, v/v) binary solvent mixture in complexes 1 and 2 respectively. Solution state (1)H-NMR studies in D2O-acetone-d6 (1 : 19, v/v) support 1 : 4 (host-guest) binding stoichiometry of F(-), Cl(-), Br(-), NO3(-), HSO4(-) and H2PO4(-) with L. Binding constants of these investigated anions with L by 1 : 1 binding model are calculated which show the following binding order: NO3(-) ≈ HSO4(-) > F(-) ≈ Cl(-) ≈ Br(-) > H2PO4(-). Further, solution state (19)F-NMR studies are also carried out to establish the F(-) binding with L in DMSO-d6.