Dramatic Enhancement of Binding Affinities Between Foldamer-Based Receptors and Anions by Intra-Receptor π-Stacking

As a synthetic model for intra-protein interactions that reinforce binding affinities between proteins and ligands, the energetic interplay of binding and folding was investigated using foldamer-based receptors capable of adopting helical structures. The receptors were designed to have identical hydrogen-bonding sites for anion binding but different aryl appendages that simply provide additional π-stacking within the helical backbones without direct interactions with the bound anions. In particular, the presence of electron-deficient aryl appendages led to dramatic enhancements in the association constant between the receptor and chloride or nitrate ions, by up to three orders of magnitude. Extended stacking within the receptor contributes to the stabilization of the entire folding structure of complexes, thereby enhancing binding affinities.     

Highly Effective Recognition of Carbohydrates by Phenanthroline‐Based Receptors: α‐ versus β‐Anomer Binding Preference

¹H NMR spectroscopic titrations in competitive and non‐competitive media, as well as binding studies in two‐phase systems, such as phase transfer of sugars from aqueous into organic solvents and dissolution of solid carbohydrates in apolar media revealed both highly effective recognition of neutral carbohydrates and interesting binding preferences of an acyclic phenanthroline‐based receptor 1 . Compared to the previously described acyclic receptors, compound 1 displays significantly higher binding affinities, the rare capability to extract sugars from water into non‐polar organic solutions and α‐ versus β‐anomer binding preference in the recognition of glycosides, which differs from those observed for other receptor systems. X‐ray crystallographic investigations revealed the presence of water molecules in the binding pocket of 1 that are engaged in the formation of hydrogen‐bonding motifs similar to those suggested by molecular modelling for the sugar OH groups in the receptor–sugar complexes. The molecular modelling calculations, synthesis, crystal structure and binding properties of 1 are described and compared with those of the previously described receptors.     

Carbohydrate–DNA Interactions at G‐Quadruplexes: Folding and Stability Changes by Attaching Sugars at the 5′‐End

Quadruplex DNA structures are attracting an enormous interest in many areas of chemistry, ranging from chemical biology, supramolecular chemistry to nanoscience. We have prepared carbohydrate–DNA conjugates containing the oligonucleotide sequences of G‐quadruplexes (thrombin binding aptamer (TBA) and human telomere (TEL)), measured their thermal stability and studied their structure in solution by using NMR and molecular dynamics. The solution structure of a fucose–TBA conjugate shows stacking interactions between the carbohydrate and the DNA G‐tetrad in addition to hydrogen bonding and hydrophobic contacts. We have also shown that attaching carbohydrates at the 5′‐end of a quadruplex telomeric sequence can alter its folding topology. These results suggest the possibility of modulating the folding of the G‐quadruplex by linking carbohydrates and have clear implications in molecular recognition and the design of new G‐quadruplex ligands.     

One‐pot Regioselective Synthesis of Novel 1‐N‐Methyl‐spiro[2,3′]oxindole‐spiro[3,3″]‐1″‐N‐arylpyrrolidine‐2″,5″‐dione‐4‐arylpyrrolidines through Multicomponent 1,3‐Dipolar Cycloaddition Reaction of Azomethine Ylide

An atom economic and facile synthesis of novel dispiro–oxindole–pyrrolidines has been achieved via a three‐component tandem cycloaddition of azomethine ylide generated in situ from isatin and sarcosine by decarboxylative condensation with N‐aryl‐3‐benzylidene‐pyrrolidine‐2,5‐dione derivatives as dipolarophiles. The salient features of synthetic procedure are characterized by the mild reaction conditions, high yields, high regioselectivity and stereoselectivity, one‐pot procedure, and operational simplicity. This regioselectivity was assumed to be under the influence of π–π stacking interactions between the aromatic rings of azomethine ylide and N‐aryl‐3‐benzylidene‐pyrrolidine‐2,5‐diones that further control the exo–endo selectivity of the reaction 1,3‐dipolar cycloaddition. The regiochemistry and structures of the cycloadducts were determined with spectroscopic data.     

Crystal Structure and Characterization of a Double‐helical‐chain Coordination Polymer Zinc Complex Constructed by Flexible Dicarboxylate Ligand 2‐Nitro‐benzene‐1,4‐di(oxyacetate) and Rigid 2,2′‐Bipyridine Ligand

A novel double‐helical‐chain coordination polymer [Zn(nbdoa)(2,2′‐bipy)(H₂O)]_n constructed by flexible 2‐nitro‐benzene‐1,4‐di(oxyacetate) ligand and rigid 2,2′‐bipyridine ligand was obtained by hydrothermal reaction. The crystal structure demonstrates that there is a double‐helical chain with an inner channel running parallel to the helix axis without any interpenetration, which is connected to network via π‐π stacking and hydrogen bond interactions. The thermal analysis shows that the infinite helical structure is stable up to 536 K. The luminescence property is investigated and the complex shows photoluminescence in the solid state at room temperature.     

(E)‐3‐{4‐[(7‐Chloroquinolin‐4‐yl)oxy]‐3‐methoxyphenyl}‐1‐(4‐methylphenyl)prop‐2‐en‐1‐one: a ladder‐like structure resulting solely from π–π stacking interactions

In the title compound, C₂₆H₂₀ClNO₃, the quinoline fragment is nearly orthogonal to the adjacent aryl ring, while the rest of the molecular skeleton is close to being planar. The crystal structure contains no hydrogen bonds of any sort, but there are two π–π stacking interactions present. One, involving the quinoline ring, links molecules related by inversion, while the other, involving the two nonfused aryl rings, links molecules related by translation, so together forming a ladder‐type arrangement     

Two‐Dimensional Crowding Uncovers a Hidden Conformation of α‐Synuclein

The intrinsically disordered protein (IDP), α‐synuclein (αS), is well‐known for phospholipid membrane binding‐coupled folding into tunable helical conformers. Here, using single‐molecule experiments in conjunction with ensemble assays and a theoretical model, we present a unique case demonstrating that the interaction–folding landscape of αS can be tuned by two‐dimensional (2D) crowding through simultaneous binding of a second protein on the bilayer surface. Unexpectedly, the experimental data show a clear deviation from a simple competitive inhibition model, but are consistent with a bimodal inhibition mechanism wherein membrane binding of a second protein (a membrane interacting chaperone, Hsp27, in this case) differentially inhibits two distinct modules of αS–membrane interaction. As a consequence, αS molecules are forced to access a hidden conformational state on the phospholipid bilayer in which only the higher‐affinity module remains membrane‐bound. Our results demonstrate that macromolecular crowding in two dimensions can play a significant role in shaping the conformational landscape of membrane‐binding IDPs with multiple binding modes.     

Induced‐Fit Binding of π‐Electron‐Donor Substrates to Macrocyclic Aromatic Ether Imide Sulfones: A Versatile Approach to Molecular Assembly

Novel macrocyclic receptors that bind electron‐donor aromatic substrates through π‐stacking donor–acceptor interactions are obtained by cycloimidisation of an amine‐functionalised aryl ether sulfone with pyromellitic and 1,4,5,8‐naphthalenetetracarboxylic dianhydrides. These macrocycles can form complexes with a wide variety of π‐donor substrates, including tetrathiafulvalene, naphthalene, anthracene, pyrene, perylene and functional derivatives of these polycyclic hydrocarbons. The resulting supramolecular assemblies range from simple 1:1 complexes to [2]‐ and [3]pseudorotaxanes and even (as a result of crystallographic disorder) an apparent polyrotaxane. Direct five‐component self‐assembly of a metal‐centred [3]pseudorotaxane is also observed on complexation of a macrocyclic ether imide with 8‐hydroxyquinoline in the presence of palladium(II) ions. Binding studies in solution were carried out by using ¹H NMR and UV/Vis spectroscopy, and the stoichiometries of binding were confirmed by Job plots based on the charge‐transfer absorption bands. The highest association constants were found for strong π‐donor guests with large surface areas, notably perylene and 1‐hydroxypyrene, for which K_a values of 1.4×10³ and 2.3×10³ M ^?1, respectively, were found. Single‐crystal X‐ray analyses of the receptors and their derived complexes reveal large induced‐fit distortions of the macrocyclic frameworks as a result of complexation. These structures provide compelling evidence for the existence of strong attractive forces between the electronically complementary aromatic π systems of host and guest.     

7,7,8,8‐Tetraaryl‐o‐quinodimethane Stabilized by Dibenzo Annulation: A Helical π‐Electron System That Exhibits Electrochromic and Unique Chiroptical Properties

When two benzene rings are fused to a tetraaryl‐o‐quinodimethane skeleton, sterically hindered helical molecules 1 acquire a high thermodynamic stability. Because the tetraarylbutadiene subunit contains electron‐donating alkoxy groups, 1 undergo reversible two‐electron oxidation to 2 ²⁺, which can be isolated as deeply colored stable salts. Intramolecular transfer of the point chirality (e.g., sec‐butyl) on the aryl groups to helicity induces a diastereomeric preference in dications 2 b ²⁺ and 2 c ²⁺, which represents an efficient method for enhancing circular‐dichroism signals. Thus, those redox pairs can serve as new electrochiroptical response systems. X‐ray analysis of dication 2 ²⁺ revealed π–π stacking interaction of the diarylmethylium moieties, which is also present in solution. The stacking geometry is the key contributor to the chirosolvatochromic response.     

(E)‐2‐(1,3‐Benzothiazol‐2‐yl)‐3‐(4‐fluorophenyl)acrylonitrile: a chain of π‐stacked hydrogen‐bonded rings

The title compound, C₁₆H₉FN₂S, crystallizes as a nonmerohedral twin with twin rotation about the reciprocal‐lattice vector [10]*. The molecules are nearly planar and the dihedral angle between the planes of the two aryl rings is only 4.4 (2)°. The molecules are linked by pairs of C—H...N hydrogen bonds to form cyclic centrosymmetric R₂²(18) dimers, which are linked into chains by an aromatic π–π stacking interaction. Comparisons are made with some related 3‐aryl‐2‐thienylacrylonitriles.     

Helical Folding of Conjugated Oligo(phenyleneethynylene): Chain‐Length Dependence,Solvent Effects,and Intermolecular Assembly

As a representative folding system that features a conjugated backbone, a series of monodispersed (o‐phenyleneethynylene)‐alt‐(p‐phenyleneethynylene) (PE) oligomers of varied chain length and different side chains were studied. Molecules with the same backbone but different side‐chain structures were shown to exhibit similar helical conformations in respectively suitable solvents. Specifically, oligomers with dodecyloxy side chains folded into the helical structure in apolar aliphatic solvents, whereas an analogous oligomer with tri(ethylene glycol) (Tg) side chains adopted the same conformation in polar solvents. The fact that the oligomers with the same backbone manifested a similar folded conformation independent of side chains and the nature of the solvent confirmed the concept that the driving force for folding was the intramolecular aromatic stacking and solvophobic interactions. Although all were capable of inducing folding, different solvents were shown to bestow slightly varied folding stability. The chain‐length dependence study revealed a nonlinear correlation between the folding stability with backbone chain length. A critical size of approximately 10 PE units was identified for the system, beyond which folding occurred. This observation corroborated the helical nature of the folded structure. Remarkably, based on the absorption and emission spectra, the effective conjugation length of the system extended more effectively under the folded state than under random conformations. Moreover, as evidenced by the optical spectra and dynamic light‐scattering studies, intermolecular association took place among the helical oligomers with Tg side chains in aqueous solution. The demonstrated ability of such a conjugated foldamer in self‐assembling into hierarchical supramolecular structures promises application potential for the system.     

Chloride‐Selective Electrodes Based on “Two‐Wall” Aryl‐Extended Calix[4]Pyrroles: Combining Hydrogen Bonds and Anion–π Interactions to Achieve Optimum Performance

The performance of chloride‐selective electrodes based on “two‐wall” aryl‐extended calix[4]pyrroles and multiwall carbon nanotubes is presented. The calix[4]pyrrole receptors bear two phenyl groups at opposite meso‐positions. When the meso‐phenyl groups are decorated with strong electron‐withdrawing substituents, attractive anion–π interactions may exist between the receptor’s aromatic walls and the sandwiched anion. These anion–π interactions are shown to significantly affect the selectivity of the electrodes. Calix[4]pyrrole, bearing a p‐nitro withdrawing group on each of the meso‐phenyl rings, afforded sensors that display anti‐Hofmeister behavior against the lipophilic salicylate and nitrate anions. Based on the experimental data, a series of principles that help in predicting the suitability of synthetic receptors for use as anion‐specific ionophores is discussed. Finally, the sensors deliver excellent results in the direct detection of chloride in bodily fluids.     

Synthesis,Structure, and Supramolecular Chemistry of Three Azide Manganese Complexes with 2, 6‐Bis(benzimidazol‐2‐yl)pyridine

Three azide complexes with the tridentate ligand 2, 6‐bis(benzimidazol‐2‐yl)pyridine (H₂BBIP) were synthesized and their complicated supramolecular interactions were investigated with single‐crystal X‐ray diffraction. Interestingly, the complexes are assembled by bifurcated hydrogen bonding, double helical π–π stacking, or anion–π stacking interactions of the benzimidazole rings by tuning the reaction conditions (temperature, ratio, solvent). Complex 1 is a mononuclear compound, namely, Mn(H₂BBIP)N₃(CH₃O) · CH₃OH. In its 3D supramolecular network, the nitrogen atom of the azide anion is acting as hydrogen bonding bifurcated acceptor. Complex 2 is a dinuclear compound, namely, Mn₂(H₂BBIP)₂(N₃)₂ · (H₂O)_0.5. The dinuclear unit is connected by intramolecular π–π stacking interactions. Furthermore, double helical π–π stacking interactions in the benzimidazole rings are observed. Complex 3 , Mn₂(H₂BBIP)₂(N₃)₂ · CH₃OH, can be formulated as a pseudopolymorph of complex 2 , which exhibits intramolecular π–π stacking interactions as well as anion–π interactions in the dinuclear unit.     

Construction of ZnII‐based rac‐Helical Chains Containing Semi‐rigid Dipolar Ligand 1,4‐Bis(benzimidazol‐1‐ylmethyl)benzene

A Zn^II compound based on the semi‐rigid dipolar ligand 1,4‐bis(benzimidazol‐1‐ylmethyl)benzene (L), {[Zn( L )₂Cl₂]·2DMF}_n ( 1 ) has been synthesized successfully under solvothermal conditions. X‐ray single crystal diffraction shows that the complex contains P‐helical and M‐helical chains with 2₁ screw axis but crystallizes as a racemate. Through π···π stacking interactions between two well‐overlapping benzimidazoleyl rings from two adjacent chains, the 3D racemic supramolecular network is assembled. Furthermore, the IR, TGA and luminescent properties are also investigated in this work.     

1,3‐Bis(4‐nitro­phenyl)­triazene

The structure of the title compound, C₁₂H₉N₅O₄, reveals an almost planar mol­ecule (r.m.s. deviation = 0.061 Å), in which the interplanar angle between the phenyl rings is 5.7 (1)° and the largest interplanar angle is that between the phenyl ring and the nitro group of one of the 4‐nitro­phenyl substituents [8.8 (3)°]. The observed mol­ecular conformation suggests a delocalization of π‐electrons extended over the diazo­amine group and the terminal aryl substituents. Intermolecular N—H⃛O interactions between the twofold screw‐related mol­ecules give rise to helical chains along the [010] direction. Intermolecular C—H⃛O interactions then generate sheets of mol­ecules in the (10) plane, and these sheets are held together by N⃛C and O⃛O π–π interactions.     

1,3‐Dipolar Cycloaddition Reactions Leading to the Synthesis of New 2,3,5‐Triaryl‐4H,2,3,3a,5,6,6a‐hexahydropyrrolo[3,4‐d]isoxazole‐4,6‐diones

Cycloaddition of C,N‐diphenylnitrones 1 to N‐aryl maleimides 2 afforded two diastereomeric isoxazolidines with high selectivity. The structure and steric configuration of the adducts have been assigned on the basis of ¹H NMR, ¹H NMR COSY, ¹³C NMR and IR spectroscopy. The π–π stacking interactions between maleimide's and nitrone's aromatic rings during the 1,3‐dipolar cycloaddition were assumed to control the exo–endo selectivity of the reaction. Thus, the exo–endo ratio depends upon the position of the substituent present on the C‐phenyl ring of the C,N‐diphenylnitrones.     

Bridge‐Clamp Bis(tetrazine)s with [N]8 π‐Stacking Interactions and Azido‐s‐Aryl Tetrazines: Two Classes of Doubly Clickable Tetrazines

Click chemistry at a tetrazine core is useful for bioorthogonal labeling and crosslinking. Introduced here are two new classes of doubly clickable s‐aryl tetrazines synthesized by Cu‐catalyzed cross‐coupling. Homocoupling of o‐brominated s‐aryl tetrazines leads to bis(tetrazine)s structurally characterized by tetrazine cores arranged face‐to‐face. [N]₈ π‐stacking interactions are essential to the conformation. Upon inverse electron demand Diels–Alder (iEDDA) cycloaddition, the bis(tetrazine)s produce a unique staple structure. The o‐azidation of s‐aryl tetrazines introduces a second proximal intermolecular clickable function that leads to double click chemistry opportunities. The stepwise introduction of fluorophores and then iEDDA cycloaddition, including bioconjugation to antibodies, was achieved on this class of tetrazines. This method extends to (thio)etherification, phosphination, trifluoromethylation and the introduction of various bioactive nitrogen‐based heterocycles.     

Highly Efficient Non‐Palladium‐Catalyzed Controlled Synthesis and X‐ray Analysis of Functionalized 1,2‐Diaryl‐, 1,2,3‐Triaryl‐, and 1,2,3,4‐Tetraarylbenzenes

A general, two‐step, highly efficient synthesis of 1,2‐diaryl‐, 1,2,3‐triaryl‐, and 1,2,3,4‐tetraarylbenzenes from simple stitching of α‐oxo‐ketene‐S,S‐acetals and active methylene compounds via a lactone intermediate is described. This procedure offers easy access to highly functionalized arylated benzenes that contain sterically demanding groups in good to excellent yields. The novelty of the procedure lies in the construction of aromatic compounds with the desired conformational flexibility along the molecular axis in a transition‐metal‐free environment through easily accessible precursors. Crystal analysis of these arylated benzene scaffolds showed that the peripheral aryl rings are arranged in a propeller‐like fashion with respect to the central benzene ring. Examination of the crystal packing in the structure of a 1,2,3,4‐tetraarylbenzene revealed an N???π interaction between molecules related by a two‐fold screw axis running in the direction of the a axis. Interestingly, the repeating array of N???π interactions around the axis of this 1,2,3,4‐tetraarylbenzene forces the molecules into a helical pattern.     

Triazine‐Carbon Nanotubes: New Platforms for the Design of Flavin Receptors

The synthesis of functionalised carbon nanotubes as receptors for riboflavin (RBF) is reported. Carbon nanotubes, both single‐walled and multi‐walled, have been functionalised with 1,3,5‐triazines and p‐tolyl chains by aryl radical addition under microwave irradiation and the derivatives have been fully characterised by using a range of techniques. The interactions between riboflavin and the hybrids were analysed by using fluorescence and UV/Vis spectroscopic techniques. The results show that the attached functional groups minimise the π‐π stacking interactions between riboflavin and the nanotube walls. Comparison of p‐tolyl groups with the triazine groups shows that the latter have stronger interactions with riboflavin because of the presence of hydrogen bonds. Moreover, the triazine derivatives follow the Stern–Volmer relationship and show a high association constant with riboflavin. In this way, artificial receptors in catalytic processes could be designed through specific control of the interaction between functionalised carbon nanotubes and riboflavin.     

Polymorphism of methyl 4‐amino‐3‐phenylisothiazole‐5‐carboxylate: an experimental and theoretical study

Being a close analogue of amflutizole, methyl 4‐amino‐3‐phenylisothiazole‐5‐carboxylate (C₁₁H₁₀N₂O₂S) was assumed to be capable of forming polymorphic structures. Noncentrosymmetric and centrosymmetric polymorphs have been obtained by crystallization from a series of more volatile solvents and from denser tetrachloromethane, respectively. Identical conformations of the molecule are found in both structures. The two polymorphs differ mainly in the intermolecular interactions formed by the amino group and in the type of stacking interactions between the π‐systems. The most effective method for revealing packing motifs in structures with intermolecular interactions of different types (hydrogen bonding, stacking, dispersion, etc.) is to study the pairwise interaction energies using quantum chemical calculations. Molecules form a column as the primary basic structural motif due to stacking interactions in both polymorphic structures under study. The character of a column (straight or zigzag) is determined by the orientations of the stacked molecules (in a `head‐to‐head' or `head‐to‐tail' manner). Columns bound by intermolecular N—H…O and N—H…N hydrogen bonds form a double column as the main structural motif in the noncentrosymmetric structure. Double columns in the noncentrosymmetric structure and columns in the centrosymmetric structure interact strongly within the ab crystallographic plane, forming a layer as a secondary basic structural motif. The noncentrosymmetric structure has a lower density and a lower (by 0.59 kJ mol^?1) lattice energy, calculated using periodic calculations, compared to the centrosymmetric structure.