Search Results (16)

The cis- and trans-isomers of 6-(3-(3,4-dichlorophenyl)-1,2,4-oxadiazol-5-yl)cyclohex-3-ene-1-carboxylic acid (cis-A and trans-A) were obtained by the reaction of 3,4-dichloro-N′-hydroxybenzimidamide and cis-1,2,3,6-tetrahydrophthalic anhydride. Cocrystals of cis-A with appropriate solvents (cis-A‧½(1,2-DCE), cis-A‧½(1,2-DBE), and cis-A‧½C₆H₁₄) were grown from 1,2-dichloroethane (1,2-DCE), 1,2-dibromoethane (1,2-DBE), and a n-hexane/CHCl₃ mixture and then characterized by X-ray crystallography. In their structures, cis-A is self-assembled to give a hybrid 2D supramolecular organic framework (SOF) formed by the cooperative action of O–H⋯O hydrogen bonding, Cl⋯O halogen bonding, and π⋯π stacking. The self-assembled cis-A divides the space between the 2D SOF layers into infinite hollow tunnels incorporating solvent molecules. The energy contribution of each noncovalent interaction to the occurrence of the 2D SOF was verified by several theoretical approaches, including MEP and combined QTAIM and NCIplot analyses. The consideration of the theoretical data proved that hydrogen bonding (approx. −15.2 kcal/mol) is the most important interaction, followed by π⋯π stacking (approx. −11.1 kcal/mol); meanwhile, the contribution of halogen bonding (approx. −3.6 kcal/mol) is the smallest among these interactions. The structure of the isomeric compound trans-A does not exhibit a 2D SOF architecture. It is assembled by the combined action of hydrogen bonding and π⋯π stacking, without the involvement of halogen bonds. A comparison of the cis-A structures with that of trans-A indicated that halogen bonding, although it has the lowest energy in cis-A-based cocrystals, plays a significant role in the crystal design of the hybrid 2D SOF. The majority of the reported porous halogen-bonded organic frameworks were assembled via iodine and bromine-based contacts, while chlorine-based systems—which, in our case, are structure-directing—were unknown before this study. Full article

Structure and reversibility of cross-link junctions play pivotal roles in determining the nature of thermoreversible gelation and dynamic mechanical properties of the produced polymer networks. We attempt to theoretically explore new types of sol–gel transitions with mechanical sharpness by allowing cross-links to grow without upper bound. We consider thermoreversible gelation of the primary molecules R{A${}_f$} carrying the number f of low molecular weight functional groups (gelators) A. Gelators A are assumed to form supramolecular assemblies. Some examples are: telechelic polymers ($f=2$) carrying $\pi$–$\pi$ stacking benzene derivatives at their both ends, and trifunctional star molecules ($f=3$) bearing multiple hydrogen-bonding gelators. The sol–gel transition of the primary molecules becomes sharper with the cooperativity parameter of the stepwise linear growth of the cross-links. There is a polymerization transition (crossover without singularity) of the junctions in the postgel region after the gel point is passed. If the gelator A tends to form supramolecular rings competitively with linear chains, there is another phase transition in the deep postgel region where the average molecular weight of the rings becomes infinite (Bose–Einstein condensation of rings). As a typical example of binary cross-links where gelators A and B form mixed junctions, we specifically consider metal-coordinated binding of ligands A by metal ions B. Two types of multi-nuclear supramolecular complexes are studied: (i) linear stacking (ladder) of the sandwich A${}_2$B units, and (ii) linear train of egg-box A${}_4$B units. To find the strategy towards experimental realization of supramolecular cross-links, the average molecular weight, the gel fraction, the average length of the cross-link junctions are numerically calculated for all of these models as functions of the functionality f, the concentration of the solute molecules, and the temperature. Potential candidates for the realization of these new types of thermoreversible gelation are discussed. Full article

Two coordination compounds of Cu(II), namely, [Cu (phen)₂Cl](NO₃)·H₂O (compound 1) and [Cu₂(µ-Cl₂)Cl₂(Hdmpz)₄] (compound 2), where phen = 1,10-phenanthroline and Hdmpz = 3,5-dimethylpyrazole, were synthesized at room temperature and characterized using elemental analysis, TGA, spectroscopic techniques (FT-IR and electronic) and single-crystal X-ray diffraction studies. The cooperative anion–π/π–π/anion–π assemblies involving the coordinated phen, along with the uncoordinated nitrate moieties, played pivotal roles in the stabilization of the crystal structure of compound 1. Unconventional type I Cl⋯Cl interactions involving the coordinated Cl atoms provided reinforcement to the crystal structure of compound 2. We theoretically explored the supramolecular assemblies observed in the crystal structures of compounds 1 and 2 using DFT calculations, MEP surface analysis and combined NCI plot/QTAIM computational tools. Theoretical analysis revealed that the antiparallel π-stacking interactions in compound 1 and the N–H···Cl H-bonds in compound 2 were the strong structure-guiding non-covalent synthons which stabilized the compounds. In the anion–π/π–π/anion–π assembly observed in compound 1, the anion–π interaction reinforced the π-stacking by reducing the electrostatic repulsion between the metal-coordinated electron-deficient phen rings. Full article

Two new Ni(II) and Co(II) coordination compounds, viz., [Ni(H₂O)₅(DMAP)](IPhth)·2H₂O (1) and [Co(Hdmpz)₄(H₂O)₂]Cl₂ (2) (where DMAP = 4-dimethylaminopyridine, IPhth = Isophthalate, Hdmpz = 3,5-dimethylpyrazole),were synthesized and characterized using elemental analysis, TGA, spectroscopic (FTIR and electronic) and single-crystal X-ray diffraction techniques. Compound 1 crystallizes as a co-crystal hydrate of Ni(II), whereas compound 2 is a mononuclear compound of Co(II). The crystal structure analysis of compound 1 reveals the presence of various non-covalent interactions such as anion–π, π–π, C–H∙∙∙π, C–H∙∙∙C, etc., which stabilize the layered assembly of the compound. In compound 2, enclathration of counter chloride ions within the supramolecular trimeric host cavity plays a crucial role in the stabilization of the compound. The non-covalent interactions observed in the crystal structures were further studied theoretically, focusing on the cooperative π-stacking interactions between the DMAP and IPhth counter-ions in 1. To identify the non-covalent interactions of the compounds, Hirshfeld surfaces and their associated two-dimensional fingerprint regions were analyzed. Theoretical calculations confirm that H-bonding interactions combined with the π-stacking contacts are crucial synthons for the solid-state stability of compound 1. Full article

The exploration of the ionic liquids’ mechanism of action on nucleobase’s structure and properties is still limited. In this work, the binding model of the 1-alkyl-3-methylimidazolium bromide ([C_nmim]Br, n = 2, 4, 6, 8, 10) ionic liquids to the thymine (T) was studied in a water environment (PCM) and a microhydrated surroundings (PCM + wH₂O). Geometries of the mono-, di-, tri-, and tetra-ionic thymine (T-wH₂O-y[C_nmim]⁺-xBr⁻, w = 5~1 and x + y = 0~4) complexes were optimized at the M06-2X/6-311++G(2d, p) level. The IR and UV-Vis spectra, QTAIM, and NBO analysis for the most stable T-4H₂O-Br⁻-1, T-3H₂O-[C_nmim]⁺-Br⁻-1, T-2H₂O-[C_nmim]⁺-2Br⁻-1, and T-1H₂O-2[C_nmim]⁺-2Br⁻-1 hydrates were presented in great detail. The results show that the order of the arrangement stability of thymine with the cations (T-[C_nmim]⁺) by PCM is stacking > perpendicular > coplanar, and with the anion (T-Br⁻) is front > top. The stability order for the different microhydrates is following T-5H₂O-1 < T-4H₂O-Br⁻-1 < T-3H₂O-[C_nmim]⁺-Br⁻-1 < T-2H₂O-[C_nmim]⁺-2Br⁻-1 < T-1H₂O-2[C_nmim]⁺-2Br⁻-1. A good linear relationship between binding E_B values and the increasing number (x + y) of ions has been found, which indicates that the cooperativity of interactions for the H-bonding and π-π⁺ stacking is varying incrementally in the growing ionic clusters. The stacking model between thymine and [C_nmim]⁺ cations is accompanied by weaker hydrogen bonds which are always much less favorable than those in T-xBr⁻ complexes; the same trend holds when the clusters in size grow and the length of alkyl chains in the imidazolium cations increase. QTAIM and NBO analytical methods support the existence of mutually reinforcing hydrogen bonds and π-π cooperativity in the systems. Full article

In this work, an innovative nano-carbon material (N-CM) adsorbent was reported for exploring its adsorption behaviors toward cationic methylene blue (MB) and anionic reactive blue 19 (RB19) pollutants. The proposed N-CM was synthesized by a one-step solvothermal treatment of citric acid and zinc gluconate small precursors. N-CM consists of nanosheets that have an advantageous specific surface area, large sp²/sp³ hybridized domains, and abundant nitrogen/oxygen-containing surface functional groups. The synergistic effects of these features are conducive to the MB and RB19 adsorption. Different from anionic RB19 adsorption (79.54 mg/g) by the cooperative π-π stacking and hydrogen bonding, cationic MB adsorbed onto N-CM mainly by the electrostatic attraction at the natural pH solution (> pH_pzc), with an adsorption capacity up to 118.98 mg/g. Interestingly, both MB and RB19 adsorption conformed to the pseudo-second order kinetic (R² ≥ 0.995) and Langmuir isothermal (R² ≥ 0.990) models, accompanied by similar maximum monolayer adsorption capacities of 120.77 and 116.01 mg/g, respectively. Their adsorption processes exhibited spontaneously endothermic characteristics. Moreover, N-CM showed superior selective capability toward MB in different mixed dye systems, with high removal efficiencies of 73–89%. These results demonstrate that the high-performance carbon adsorbent prepared from small precursors via low-temperature carbonization shows great potentials in wastewater treatment. Full article

In comparison with the numerous studies that have centered on developing molecular frameworks for the functionalization of fluorescent materials, less research has addressed the influence of the side chains, despite such appendages contributing significantly to the properties and applications of fluorescent materials. In this work, a new series of cationic fluorescent probes with AIE characteristics have been developed, which exhibit unique sensitivity for charge-diffusion anions, namely HSO₃⁻, via the interactions of ions and the cooperation of the controllable hydrophobicity. The impact of the alkyl chain length attached at the cationic probes suggested that the fluorescent intensity and sensitivity of the probes could be partially enhanced by adjusting their aggregation tendency through the action of the hydrophobic effect under aqueous conditions. DLS and SEM images indicated that different particle sizes and new morphologies of the probes were formed in the anion-recognition-triggered self-assembly process, which could be attributed to the composite effect of electrostatic actions, Van der Waals forces and π-π stacking. Full article

This study expands and combines concepts from two of our earlier studies. One study reported the complementary halogen bonding and π-π charge transfer complexation observed between isomeric electron rich 4-N,N-dimethylaminophenylethynylpyridines and the electron poor halogen bond donor, 1-(3,5-dinitrophenylethynyl)-2,3,5,6-tetrafluoro-4-iodobenzene while the second study elaborated the ditopic halogen bonding of activated pyrimidines. Leveraging our understanding on the combination of these non-covalent interactions, we describe cocrystallization featuring ditopic halogen bonding and π-stacking. Specifically, red cocrystals are formed between the ditopic electron poor halogen bond donor 1-(3,5-dinitrophenylethynyl)-2,4,6-triflouro-3,5-diiodobenzene and each of electron rich pyrimidines 2- and 5-(4-N,N-dimethyl-aminophenylethynyl)pyrimidine. The X-ray single crystal structures of these cocrystals are described in terms of halogen bonding and electron donor-acceptor π-complexation. Computations confirm that the donor-acceptor π-stacking interactions are consistently stronger than the halogen bonding interactions and that there is cooperativity between π-stacking and halogen bonding in the crystals. Full article

In this paper, we report the development of the novel self-assembling systems based on oppositely charged Pillar[5]arenes and surfactants for encapsulation of diagnostic dye DAPI. For this purpose, the aggregation behavior of synthesized macrocycles and surfactants in the presence of Pillar[5]arenes functionalized by carboxy and ammonium terminal groups was studied. It has been demonstrated that by varying the molar ratio in Pillar[5]arene-surfactant systems, it is possible to obtain various types of supramolecular systems: host–guest complexes at equimolar ratio of Pillar[5]arene-surfactant and interpolyelectrolyte complexes (IPECs) are self-assembled materials formed in aqueous medium by two oppositely charged polyelectrolytes (macrocycle and surfactant micelles). It has been suggested that interaction of Pillar[5]arenes with surfactants is predominantly driven by cooperative electrostatic interactions. Synthesized stoichiometric and non-stoichiometric IPECs specifically interact with DAPI. UV-vis, luminescent spectroscopy and molecular docking data show the structural feature of dye-loaded IPEC and key role of the electrostatic, π–π-stacking, cation–π interactions in their formation. Such a strategy for the design of supramolecular Pillar[5]arene-surfactant systems will lead to a synergistic interaction of the two components and will allow specific interaction with the third component (drug or fluorescent tag), which will certainly be in demand in pharmaceuticals and biomedical diagnostics. Full article

We synthesized and studied the polymeric compound {[Cu₂(µ₄-EDTA)(Him)₂] 2H₂O}_n (1). The single-crystal structure is reported along with an in depth characterization of its thermal stability (TGA), spectral properties (FT-IR, Vis-UV and RSE), and magnetic behavior. The crystal consists of infinite 2D-networks built by centrosymmetric dinuclear motifs, constructed by means of a bridging anti,syn-carboxylate group from each asymmetric unit. Each layer guides Him ligands toward their external faces. They are connected by intermolecular (Him)N-H···O(carboxylate) bonds and antiparallel π–π stacking between symmetry related pairs of Him ligands, and then pillared in a 3D-network with parallel channels, where disordered water molecules are guested. About half of the labile water is lost from these channels over a wide temperature range (r.t. to 210 °C) before the other one, most strongly retained by the cooperating action of (water)O1-H(1A)···O(carboxylate) and (water) O1-H(1B)···π(Him) interactions. The latter is lost when organic ligands start to burn. ESR spectra and magnetic measurements indicated that symmetry related Cu(II) centers connected by the bridging carboxylate groups behave magnetically not equivalently, enabling an exchange interaction larger than their individual Zeeman energies. Full article

Herein, the X-ray powder diffraction (XRPD) crystal structure of a new Sildenafil cocrystal is reported, where resorcinol has been used as the coformer. The crystal structure has been solved by means of direct space methods used in combination with density functional theory (DFT) calculations. In the structure, the Sildenafil and resorcinol molecules form cooperative hydrogen bond (HB) and π-stacking interactions that have been analyzed using DFT calculations, the molecular electrostatic potential (MEP) surface, and noncovalent interaction plot (NCI plot). The formation of O–H⋯N H-bonds between resorcinol and Sildenafil increases the dipole moment and enhances the antiparallel π-stacking interaction. Full article

The success of innovative drugs depends on an interdisciplinary and holistic approach to their design and development. The supramolecular architecture of living systems is controlled by non-covalent interactions to a very large extent. The latter are prone to extensive cooperation and like a virtuoso play a symphony of life. Thus, the design of effective ligands should be based on thorough knowledge on the interactions at either a molecular or high topological level. In this work, we emphasize the importance of supramolecular structure and ligand-based design keeping the potential of supramolecular H-bonding synthons in focus. In this respect, the relevance of supramolecular chemistry for advanced therapies is appreciated and undisputable. It has developed tools, such as Hirshfeld surface analysis, using a huge data on supramolecular interactions in over one million structures which are deposited in the Cambridge Structure Database (CSD). In particular, molecular interaction surfaces are useful for identification of macromolecular active sites followed by in silico docking experiments. Ornithine-derived compounds are a new, promising class of multi-targeting ligands for innovative therapeutics and cosmeceuticals. In this work, we present the synthesis together with the molecular and supramolecular structure of a novel ornithine derivative, namely N-α,N-δ)-dibenzoyl-(α)-hydroxymethylornithine, 1. It was investigated by modern experimental and in silico methods in detail. The incorporation of an aromatic system into the ornithine core induces stacking interactions, which are vital in biological processes. In particular, rare C=O^…π intercontacts have been identified in 1. Supramolecular interactions were analyzed in all structures of ornithine derivatives deposited in the CSD. The influence of substituent was assessed by the Hirshfeld surface analysis. It revealed that the crystal packing is stabilized mainly by H^…O, O^…H, C^…H, Cl (Br, F)^…H and O^…O interactions. Additionally, π^…π, C-H^…π and N-O^…π interactions were also observed. All relevant H-bond energies were calculated using the Lippincott and Schroeder H-bond model. A library of synthons is provided. In addition, the large synthons (Long-Range Synthon Aufbau Module) were considered. The DFT optimization either in vacuo or in solutio yields very similar molecular species. The major difference with the relevant crystal structure was related to the conformation of terminal benzoyl C15-C20 ring. Furthermore, in silico prediction of the extensive physicochemical ADME profile (absorption, distribution, metabolism and excretion) related to the drug-likeness and medicinal chemistry friendliness revealed that a novel ornithine derivative 1 has the potential to be a new drug candidate. It has shown good in silico absorption and very low toxicity. Full article

In this paper, the columnar supramolecular aggregates of photosensitive star-shaped azobenzenes with benzene-1,3,5-tricarboxamide core and azobenzene arms are analyzed theoretically by applying a combination of computer simulation techniques. Without a light stimulus, the azobenzene arms adopt the trans-state and build one-dimensional columns of stacked molecules during the first stage of the noncovalent association. These columnar aggregates represent the structural elements of more complex experimentally observed morphologies—fibers, spheres, gels, and others. Here, we determine the most favorable mutual orientations of the trans-stars in the stack in terms of (i) the $\pi$ – $\pi$ distance between the cores lengthwise the aggregate, (ii) the lateral displacements due to slippage and (iii) the rotation promoting the helical twist and chirality of the aggregate. To this end, we calculate the binding energy diagrams using density functional theory. The model predictions are further compared with available experimental data. The intermolecular forces responsible for the stability of the stacks in crystals are quantified using Hirshfeld surface analysis. Finally, to characterize the self-assembly mechanism of the stars in solution, we calculate the hydrogen bond lengths, the normalized dipole moments and the binding energies as functions of the columnar length. For this, molecular dynamics trajectories are analyzed. Finally, we conclude about the cooperative nature of the self-assembly of star-shaped azobenzenes with benzene-1,3,5-tricarboxamide core in aqueous solution. Full article

New Fe(III) compounds from qsal ligand, [Fe(qsal)₂](CH₃OSO₃) (1) and [Fe(qsal)₂](CH₃SO₃)·CH₃OH (3), along with known compound, [Fe(qsal)₂](CF₃SO₃) (2), were obtained as large well-shaped crystals (Hqsal = N-(8-quinolyl)salicylaldimine). The compounds 1 and 2 were in the low-spin (LS) state at 300 K and exhibited a cooperative spin crossover (SCO) transition with a thermal hysteresis loop at higher temperatures, whereas 3 was in the high-spin (HS) state below 300 K. The optical conductivity spectra for 1 and 3 were calculated from the single-crystal reflection spectra, which were, to the best of our knowledge, the first optical conductivity spectra of SCO compounds. The absorption bands for the LS and HS [Fe(qsal)₂] cations were assigned by time-dependent density functional theory calculations. The crystal structures of 1 and 2 consisted of a common one-dimensional (1D) array of the [Fe(qsal)₂] cation, whereas that of 3 had an unusual 1D arrangement by π-stacking interactions which has never been reported. The crystal structures in the high-temperature phases for 1 and 2 indicate that large structural changes were triggered by the motion of counter anions. The comparison of the crystal structures of the known [Fe(qsal)₂] compounds suggests the significant role of a large non-spherical counter-anion or solvate molecule for the total lattice energy gain in the crystal of a charged complex. Full article

The acylation of unsymmetrical N-benzylbispidinols in aromatic solvents without an external base led to the formation of supramolecular gels, which possess different thicknesses and degrees of stability depending on the substituents in para-positions of the benzylic group as well as on the nature of the acylating agent and of the solvent used. Structural features of the native gels as well as of their dried forms were studied by complementary techniques including Fourier-transform infrared (FTIR) and attenuated total reflection (ATR) spectroscopy, atomic force microscopy (AFM), transmission electron microscopy (TEM), scanning electron microscopy (SEM), and small-angle X-ray scattering and diffraction (SAXS). Structures of the key crystalline compounds were established by X-ray diffraction. An analysis of the obtained data allowed speculation on the crucial structural and condition factors that governed the gel formation. The most important factors were as follows: (i) absence of base, either external or internal; (ii) presence of HCl; (iii) presence of carbonyl and hydroxyl groups to allow hydrogen bonding; and (iv) presence of two (hetero)aromatic rings at both sides of the molecule. The hydrogen bonding involving amide carbonyl, hydroxyl at position 9, and, very probably, ammonium N-H⁺ and Cl⁻ anion appears to be responsible for the formation of infinite molecular chains required for the first step of gel formation. Subsequent lateral cooperation of molecular chains into fibers occurred, presumably, due to the aromatic π−π-stacking interactions. Supercritical carbon dioxide drying of the organogels gave rise to aerogels with morphologies different from that of air-dried samples. Full article