Crystallographic and Theoretical Evidence of Anion–π and Hydrogen-Bonding Interactions in a Squaramide–Nitrate Salt

Chemically Fueled Communication Along a Scaffolded Nanoscale Array of Squaramides

Relaying conformational change over several nanometers is central to the function of allosterically regulated proteins. Replicating this mechanism artificially would provide important communication tools, but requires nanometer-sized molecules that reversibly switch between defined shapes in response to signaling molecules. In this work, 1.8 nm long rigid rod oligo(phenylene-ethynylene)s are scaffolds for switchable multi-squaramide hydrogen-bond relays. Each relay can adopt either a parallel or an antiparallel orientation relative to the scaffold; the preferred orientation is dictated by a director group at one end. An amine director responded to proton signals, with acid-base cycles producing multiple reversible changes in relay orientation that were reported by a terminal NH, which is 1.8 nm distant. Moreover, a chemical fuel acted as a dissipative signal. As the fuel was consumed, the relay reverted to its original orientation, illustrating how information from out-of-equilibrium molecular signals can be communicated to a distant site.

Squaramide-Based Self-Associating Amphiphiles for Anion Recognition

The synthesis and characterisation of two novel self-assembled amphiphiles (SSAs) SQS-1 and SQS-2 are reported. Both compounds, based on the squaramide motif, were fully soluble in a range of solvents and were shown to undergo self-assembly through a range of physical techniques. Self-assembly was shown to favour the formation of crystalline domains on the nanoscale but also fibrillar film formation, as suggested by SEM analysis. Moreover, both SQS-1 and SQS-2 were capable of anion recognition in DMSO solution as demonstrated using 1 H NMR and UV/Vis absorption spectroscopy, but displayed lower binding affinities for various anions when compared against other squaramide based receptors. In more competitive solvent mixtures SQS-1 gave rise to a colourimetric response in the presence of HPO42- that was clearly visible to the naked eye. We anticipate that the observed response is due to the basic nature of the HPO42- anion when compared against other biologically relevant anions.

Azacalix[3]triazines: A Substructure of Triazine-Based Graphitic Carbon Nitride Featuring Anion-π Interactions

Graphitic carbon nitride (GCN) has garnered broad research interest due to its unique catalytic properties. However, GCN, prepared by general methods, possesses myriad structural defects and it has been difficult to elucidate their intrinsic physical properties. We report the development of azacalix[3]triazines (AC3Ts), a substructure of triazine-based GCN (Tz-GCN). Despite the electron-deficient natures of triazine, AC3Ts capture protons as organic superbases. We reveal the unique anion-π interactions of AC3Ts that alters the ionization potentials of AC3Ts. To the best of our knowledge, these features have not yet been recognized for Tz-GCN. These unveiled features of AC3Ts are expected to expand the usage scope and possibilities for GCNs.

Construction of Aromatic Multilayered Structures Based on the Conformational Properties of N,N'-Dimethylated Squaramide

Squaramide is a highly rigid four-membered ring system bearing two carbonyl and two amino groups, and its derivatives have found applications in many fields. We synthesized several N,N'-dimethylated oligosquaramides linked via phenyl groups, and investigated their structures in the crystalline state and in solution. Compounds 1, 2 (bissquaramides), and 13 (trissquaramide) exist as folded structures in the crystalline state, in which the aromatic rings are located in a face-to-face position. In their multilayered structures, the benzene rings are more nearly parallel and are closer to each other, compared with those in N,N'-dimethylated oligoureas. Individual molecules of meta-connected compounds 2 and 13 show a helical structure with all-R or all-S axis chirality, but afford only racemic crystals. The NMR spectra indicated that these compounds retain well-ordered folded structures in solution. The unique steric and electronic properties of N,N'-dimethylated squaramide can provide access to novel functional aromatic multilayered and helical foldamers.

Highly Efficient, Tripodal Ion-Pair Receptors for Switching Selectivity between Acetates and Sulfates Using Solid-Liquid and Liquid-Liquid Extractions

A tripodal, squaramide-based ion-pair receptor 1 was synthesized in a modular fashion, and ¹H NMR and UV-vis studies revealed its ability to interact more efficiently with anions with the assistance of cations. The reference tripodal anion receptor 2, lacking a crown ether unit, was found to lose the enhancement in anion binding induced by presence of cations. Besides the ability to bind anions in enhanced manner by the “single armed” ion-pair receptor 3, the lack of multiple and prearranged binding sites resulted in its much lower affinity towards anions than in the case of tripodal receptors. Unlike with receptors 2 or 3, the high affinity of 1 towards salts opens up the possibility of extracting extremely hydrophilic sulfate anions from aqueous to organic phase. The disparity in receptor 1 binding modes towards monovalent anions and divalent sulfates assures its selectivity towards sulfates over other lipophilic salts upon liquid–liquid extraction (LLE) and enables the Hofmeister bias to be overcome. By changing the extraction conditions from LLE to SLE (solid–liquid extraction), a switch of selectivity from sulfates to acetates was achieved. X-ray measurements support the ability of anion binding by cooperation of the arms of receptor 1 together with simultaneous binding of cations.

Self-assembly of amphiphilic aryl-squaramides in water driven by dipolar π–π interactions

Amphiphilic aryl-squaramides self-assemble via unprecedented dipolar π–π interactions forming well-defined supramolecular aggregates and self-consistent hydrogels in water

Squaramide based ion pair receptors possessing ferrocene as a signaling unit

Ferrocene offers a convenient reporter in squaramide based ion pair sensors able to recognize anions more strongly in the presence of cations.

Synthesis, vibrational spectroscopy and X-ray structural characterization of novel NIR emitter squaramides

Two new 2-naphthyl squaramides, 3-methoxy -4-(2-naphtalenylamino)-3-cyclobutene-1,2-dione (SQ-NPh1) and bis-3,4-(2-naphtalenylamino)-3-cyclobutene-1,2-dione (SQ-NPh2) were synthesized via condensation reaction between the dimethylsquarate and 2-naphthylamine. The spectrometric characterization by ¹³C NMR confirmed the obtaining of the squaramide derivative and nor the squaraine analog. This hypothesis was corroborated by Raman and Infrared spectroscopy since the characteristic vibrational bands related to the oxocarbon portion of both structures have been assigned, such as the ones for SQ-NPh1 and SQ-NPh2. The single-crystal X-ray crystallography for SQ-NPh1 crystal structures have been solved and the structure of SQ-NPh2 have been refined using Powder Diffraction state-of-art. The SQ-NPh1 crystallizes in monoclinic system in P2/c space group. Both squaramides present absorption in the ultra-visible (220-370 nm) and fluorescent emission in the near-infrared (780-800 nm), besides they also presented high thermal stability (around 570 °C). Generally, only squaraines are reported as NIR emitters, this is the first description of NIR emission for squaramides, and since the synthesis of squaramides is very easy and the rational design of small-molecule NIR fluorophores is of high priority and great value, these results are very promising for the development of novel NIR fluorescent dyes.

Robust scalable synthesis of a bis-urea derivative forming thixotropic and cytocompatible supramolecular hydrogels

Synthetic hydrogels address a need for affordable, industrially scalable scaffolds for tissue engineering. Herein, a novel low molecular weight gelator is reported that forms self-healing supramolecular hydrogels. Its robust synthesis can be performed in a solvent-free manner using ball milling. Strikingly, encapsulated cells spread and proliferate without specific cell adhesion ligands in the nanofibrous material.

Recognition and Extraction of Sodium Chloride by a Squaramide-Based Ion Pair Receptor

We synthesized an ion pair receptor 1 consisting of a crown ether cation binding site and a squaramide anion binding domain and compared its binding properties to those of its analogous urea counterpart 2. We studied their salt binding properties using spectrophotometric and spectroscopic measurements in an acetonitrile solution and in acetonitrile/water mixtures. Apart from carboxylate anions, all of the anions tested were found to associate with receptor 1 and 2 more strongly in the presence of sodium cations. A homotopic anion receptor 3, lacking a crown ether unit, was unable to bind sodium salt more strongly than tetrabutylammonium salts. Solution and solid-state X-ray measurements revealed strong sodium chloride coordination to receptor 1, which is able to bind this salt even in the presence of 10% water. In contrast to the urea-based ion pair receptor 2 or anion receptor 3, ditopic receptor 1 is capable of extracting sodium chloride from aqueous media to the organic phase, as was evidenced unambiguously by ¹H nuclear magnetic resonance, mass spectrometry, and atomic absorption spectroscopy analyses.

Kinetic Analysis and Mechanism of the Hydrolytic Degradation of Squaramides and Squaramic Acids

The hydrolytic degradation of squaramides and squaramic acids, the product of partial hydrolysis of squaramides, has been evaluated by UV spectroscopy at 37 °C in the pH range 3-10. Under these conditions, the compounds are kinetically stable over long time periods (>100 days). At pH >10, the hydrolysis of the squaramate anions shows first-order dependence on both squaramate and OH^-. At the same temperature and [OH^-], the hydrolysis of squaramides usually displays biphasic spectral changes (A → B → C kinetic model) with formation of squaramates as detectable reaction intermediates. The measured rates for the first step (k₁ ≈ 10^-4 M^-1 s^-1) are 2-3 orders of magnitude faster than those for the second step (k₂ ≈ 10^-6 M^-1 s^-1). Experiments at different temperatures provide activation parameters with values of ΔH^⧧ ≈ 9-18 kcal mol^-1 and ΔS^⧧ ≈ -5 to -30 cal K^-1 mol^-1. DFT calculations show that the mechanism for the alkaline hydrolysis of squaramic acids is quite similar to that of amides.

Squaramides with cytotoxic activity against human gastric carcinoma cells HGC-27: synthesis and mechanism of action

A series of squaramates and squaramides have been synthesized and their cytotoxic activity has been investigated in different cancer cell lines.

Cell uptake and localization studies of squaramide based fluorescent probes

Cell internalization is a major issue in drug design. Although squaramide-based compounds are receiving much attention because of their interesting bioactivity, cell uptake and trafficking within cells of this type of compounds are still unknown. In order to monitor the cell internalization process of cyclosquaramide compounds we have prepared two fluorescent probes by covalently linking a fluorescent dye (BODIPY derivative or fluorescein) to a noncytotoxic cyclosquaramide framework. These two probes (C2-BDP and C2-FITC) rapidly internalize across live cell membranes through endocytic receptor-mediated mechanisms. Due to its higher fluorescence and photochemical stability, C2-BDP is a superior dye than C2-FITC. C2-BDP remains sequestered in late endosomes allowing their fast and selective imaging in various live cell types. Cyclosquaramide-cell membrane interactions facilitate cell uptake and have been investigated by binding studies in solution as well as in live cells. Cyclosquaramide 1 (C2-BDP) can be used as a highly fluorescent probe for the rapid and selective imaging of late endosomes in live cells.

Aromatic rings in chemical and biological recognition: energetics and structures

This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.

Squaramides: physical properties, synthesis and applications

Squaramides are remarkable four-membered ring systems derived from squaric acid that are able to form up to four hydrogen bonds. A high affinity for hydrogen bonding is driven through a concomitant increase in aromaticity of the ring. This hydrogen bonding and aromatic switching, in combination with structural rigidity, have been exploited in many of the applications of squaramides. Substituted squaramides can be accessed via modular synthesis under relatively mild or aqueous conditions, making them ideal units for bioconjugation and supramolecular chemistry. In this tutorial review the fundamental electronic and structural properties of squaramides are explored to rationalise the geometry, conformation, reactivity and biological activity.

N,N'-diarylsquaramides: general, high-yielding synthesis and applications in colorimetric anion sensing

Zinc trifluoromethanesulfonate promotes efficient condensations of anilines with squarate esters, providing access to symmetrical and unsymmetrical squaramides in high yields from readily available starting materials. Efficient access to electron-deficient diaryl squaramides has enabled a systematic investigation of the colorimetric anion-sensing behavior of a p-nitro-substituted squaramide. Its behavior differs in dramatic and unexpected ways from that of structurally similar p-nitroaniline-based ureas, an effect that highlights the remarkable differences in acidity between the squaramide and urea functional groups. Computational studies illustrating the enhanced hydrogen bond donor ability and acidity of squaramides in comparison to ureas are presented.

The squaramide versus urea contest for anion recognition

The interaction of a neutral squaramide-based receptor, equipped with two 4-nitrophenyl substituents (R(sq)), with halides and oxoanions has been studied in MeCN. UV/Vis and (1)H NMR spectroscopy titration experiments clearly indicated the formation of 1:1 hydrogen bonding [R(sq)X](+) complexes with all the investigated anions. X-ray diffraction studies on the chloride and bromide complex salts confirmed the 1:1 stoichiometry and indicated the establishment of bifurcated hydrogen-bond interactions between the squaramide-based receptor and the halide anion that involved both 1) amide N-H and 2) aryl proximate C-H fragments, for a total of four bonds. Probably due to the contribution of C-H fragments, complexes of R(sq) with halides are 1 to 2 orders of magnitude more stable than the corresponding ones with the analogous urea-based receptor that contains two 4-nitrophenyl substituents (R(ur)). In the case of oxoanions, R(sq) forms complexes, the stability of which decreases with the decreasing basicity of the anion (H(2)PO(4) (-)>NO(2) (-) approximately HSO(4) (-)>NO(3) (-)), and is comparable to that of complexes of the urea-based receptor R(ur). Such a behaviour is ascribed to the predominance of different contributions: electrostatic interaction for halides, acid-to-base 'frozen' proton transfer for oxoanions. Finally, with the strongly basic anions F(-) and CH(3)COO(-), R(sq) first gives genuine hydrogen-bond complexes of 1:1 stoichiometry; then, upon addition of a second anion equivalent, it undergoes deprotonation of one N--H fragment, with the simultaneous formation of the dianion hydrogen-bond complexes, [HF(2)](-) and [CH(3)COOHCH(3)COO](-), respectively. In the case of the urea-based derivative R(ur), deprotonation takes place with fluoride but not with acetate. The apparently higher Brønsted acidity of R(sq) with respect to R(ur) reflects the capability of the squaramide receptor to delocalise the negative charge formed on N--H deprotonation over the cyclobutene-1,2-dione ring and the entire molecular framework.