Cyclic Hexamer Research Articles

Like-likes-Like: Cooperative Hydrogen Bonding Overcomes Coulomb Repulsion in Cationic Clusters with Net Charges up to Q=+6e.

Quantum chemical calculations have been employed to study kinetically stable cationic clusters, wherein the monovalent cations are trapped by hydrogen bonding despite strongly repulsive electrostatic forces. We calculated linear and cyclic clusters of the hydroxy‐functionalized cation N‐(3‐hydroxypropyl) pyridinium, commonly used as cation in ionic liquids. The largest kinetically stable cluster was a cyclic hexamer that very much resembles the structural motifs of molecular clusters, as known for water and alcohols. Surprisingly, strong cooperative hydrogen bonds overcome electrostatic repulsion and result in cationic clusters with a high net charge up to Q=+6e. The structural, spectroscopic, and electronic signatures of the cationic and related molecular clusters of 3‐phenyl‐1‐propanol could be correlated to NBO parameters, supporting the existence of “anti‐electrostatic” hydrogen bonds (AEHB), as recently suggested by Weinhold. We also showed that dispersion forces enhance the cationic cluster formation and compensate the electrostatic repulsion of one additional positive charge.

Controlled Synthesis of Organic Frameworks of Pillar[6]Arene By Electrochemical Oxidation

Recently, the novel synthesis of supramolecular 2D sheet materials composed of a pillar[6]arene (a cyclic hexamer of p-arylenemethylene), driven by charge-transfer (CT) interaction between its hydroquinone form and its benzoquinone form was reported [1]. When the hydroquinone form of pillar[6]arene was oxidized with an oxidant in a methanol solution, a generated partially oxidized benzoquinone form underwent CT complex formation with its pristine form to 2D-assemble with a hexagonal packing, followed by further assembly to form fibrils. In order to control the size and shape of the material, we investigated the electrochemical oxidation of a pillar[6]arene, and resulted in the successful formation of uniform hexagonal cylinder structures on an electrode surface (Figure 1) [2]. [1] T. Ogoshi, K. Yoshikoshi, R. Sueto, H. Nishihara, T. Yamagishi, Angew. Chem. Int. Ed. 2015, 54, 6466-6469. [2] C. Tsuneishi, Y. Koizumi, R. Sueto, H. Nishiyama, K. Yasuhara, T. Yamagishi, T. Ogoshi, I. Tomita, S. Inagi, Chem. Commun. 2017, 53, 7454-7456. Figure 1

Ice-like Cyclic Water Hexamer Trapped within a Halide Encapsulated Hexameric Neutral Receptor Core: First Crystallographic Evidence of a Water Cluster Confined within a Receptor-Anion Capsular Assembly

Over the past few decades, the tren [tris(2-aminoethyl)amine] skeleton has materialized as one of the supreme anion binding building blocks demonstrating a strong interplay among topology, complementarity, cooperativity, and coordination. However, anion recognition by modest tren-based unsubstituted aromatic urea has been underexplored, mainly due to the deficiency of π-acidic or electron-withdrawing aryl terminals. This report establishes an infrequent hexameric neutral receptor-anion-water molecular self-assembly, where a conformationally flexible C3v-symmetric halide (F–/Cl–) encapsulated electron-rich naphthyl group containing N-bridged tripodal urea receptor effectively entraps a chair-shaped ice-like neutral cyclic water hexamer within the hexameric cavity of a neutral receptor-halide host–guest assembly.

Cyclic (H2O)6confined hexameric host–guest assemblies and aerial CO2fixation by electron-rich neutral urea/thiourea scaffolds

Neutral capsular assemblies of electron-rich tris-urea/thiourea receptors are formedviacyclic (H2O)6trapping or atmospheric CO2fixation.

Auxetics and Other Systems of Anomalous Characteristics

Auxetics and Other Systems of Anomalous Characteristics

Single-Acetylene Linked Porphyrin Nanorings.

The synthesis of ethyne-linked porphyrin nanorings has been achieved by template-directed Sonogashira coupling. The cyclic hexamer and octamer are predicted by density functional theory to adopt low symmetry conformations, due to dihedral twists between neighboring porphyrin units, but their symmetries are effectively D6h and D8h, respectively, in solution by 1H NMR. The fluorescence spectra indicate that the singlet excited states of these nanorings are highly delocalized.

Effect of Alkyl Substituents on 2D and 1D Self-assembly and Photovoltaic Properties of Hydrogen-bonded Oligothiophene Rosettes

Hydrogen-bonding oligothiophene bearing octyl chains self-assembles into extended nanorods via the formation of cyclic hexamer. The nanorods can function as an electron-donating materials for electron-accepting PC71BM in bulk-heterojunction solar cells.

Unexpected Interactions between Alkyl Straps and Pyridine Ligands in Sulfur-Strapped Porphyrin Nanorings

Strapped or “basket-handle” porphyrins have been investigated previously as hemoglobin mimics and catalysts. The facial selectivity of their interactions with axial ligands is a sensitive test for noncovalent bonding. Here the binding of pyridyl ligands to zinc porphyrins with thioester-linked alkyl straps is investigated in solution by NMR spectroscopy and UV–vis titration, and in the solid state by X-ray crystallography. We expected that coordination of the axial ligand would occur on the less hindered face of the porphyrin, away from the strap. Surprisingly, attractive interactions between the strap and the ligand direct axial coordination to the strapped face of the porphyrin, except when the strap is short and tight. The strapped porphyrins were incorporated into π-conjugated cyclic porphyrin hexamers using template-directed synthesis. The strap and the sulfur substituents are located either inside or outside the porphyrin nanoring, depending on the length of the strap. Six-porphyrin nanorings with outwardly pointing sulfur anchors were prepared for exploring quantum interference effects in single-molecule charge transport.

Hydrogen bonding characterization in water and small molecules.

The prototypical hydrogen bond in water dimer and hydrogen bonds in the protonated water dimer, in other small molecules, in water cyclic clusters, and in ice, covering a wide range of bond strengths, are theoretically investigated by first-principles calculations based on density functional theory, considering not only a standard generalized gradient approximation functional but also, for the water dimer, hybrid and van der Waals corrected functionals. We compute structural, energetic, and electrostatic (induced molecular dipole moments) properties. In particular, hydrogen bonds are characterized in terms of differential electron density distributions and profiles, and of the shifts of the centres of maximally localized Wannier functions. The information from the latter quantities can be conveyed to a single geometric bonding parameter that appears to be correlated with the Mayer bond order parameter and can be taken as an estimate of the covalent contribution to the hydrogen bond. By considering the water trimer, the cyclic water hexamer, and the hexagonal phase of ice, we also elucidate the importance of cooperative/anticooperative effects in hydrogen-bonding formation.

Nanoclusters of Cyanuric Acid

In this article, the self-assembly of cyanuric acid (CA) molecules into nano-structures is examined. Equilibrium geometry of CA is planar and it belongs to the D 3h point group. It is shown that CA clusters form three dimensional bowls and balls. Cyclic pentamer (5-bowl) is the basic motif responsible for these non-planar geometries. It is also shown that the cyclic hexamer based clusters can be non-planar if they contain a 5-bowl. A unified criterion for the formation of bowls and balls from basic molecular building blocks emerges from this study. The role of symmetry in supramolecular self-assembly is also clearly evident from the present study. This article demonstrates that clusters of cyanuric acid with complementary hydrogen bonding interaction sites could result in the formation of bowls and balls in addition to the well - known planar sheet structures.

Coming full circle: constructing a [Gd6] wheel dimer by dimer and the importance of spin topology.

The syntheses, structures, magnetic and thermodynamic properties of three related triethanolamine-based GdIII complexes are described. The smallest, a dimer ([Gd2]), can be viewed as the subunit from which the two larger complexes, a linear tetramer ([Gd2]2) and a cyclic hexamer ([Gd2]3), are composed by further deprotonation of the triethanolamine ligand. In all cases, nearest neighbour magnetic ions are weakly correlated by antiferromagnetic isotropic exchange, whose strength does not change significantly from one complex to another; J ranging from -0.10 to -0.13 cm-1. Therefore, rather than the strength of the coupling, it is the spin topology that is the dominant factor in determining the differences between the physical properties - specifically, the nuclearity and the transition from open (dimer and tetramer) to cyclic (hexamer) boundary conditions. Indeed the hexanuclear wheel reaches the continuum limit of classical Heisenberg spin chains. In terms of the magnetocaloric properties, the smaller the nuclearity, the larger the magnetic entropy and adiabatic temperature changes.

Synthesis and Self-Assembly of Cyclic 2,7-Anthrylene Ethynylene 1,3-Phenylene Ethynylene Trimer with a Planar Conformation.

Cyclic arylene ethynylene hexamer 1, composed of alternating 2,7-anthrylene ethynylene units and meta-phenylene ethynylene units, was synthesized. It shows C3 symmetry and possesses a flat and rigid conformation with a large equilateral triangle-like cavity. Macrocycle 1 self-associates through π-π stacking interactions between the anthracene-containing macrocyclic aromatic cores with indefinite-association constant KE =6980 m-1 in CDCl3 at 303 K. Macrocycle 1 also self-assembles into π-stacked nanofibers in the drop-cast film.

Reactions between arylhydrazinium chlorides and 2-chloroquinoline-3-carbaldehydes: molecular and supramolecular structures of a hydrazone, a 4,9-dihydro-1H-pyrazolo[3,4-b]quinoline and two 1H-pyrazolo[3,4-b]quinolines

Hydrazone derivatives exhibit a wide range of biological activities, while pyrazolo[3,4-b]quinoline derivatives, on the other hand, exhibit both antimicrobial and antiviral activity, so that all new derivatives in these chemical classes are potentially of value. Dry grinding of a mixture of 2-chloroquinoline-3-carbaldehyde and 4-methylphenylhydrazinium chloride gives (E)-1-[(2-chloroquinolin-3-yl)methylidene]-2-(4-methylphenyl)hydrazine, C17H14ClN3, (I), while the same regents in methanol in the presence of sodium cyanoborohydride give 1-(4-methylphenyl)-4,9-dihydro-1H-pyrazolo[3,4-b]quinoline, C17H15N3, (II). The reactions between phenylhydrazinium chloride and either 2-chloroquinoline-3-carbaldehyde or 2-chloro-6-methylquinoline-3-carbaldehyde give, respectively, 1-phenyl-1H-pyrazolo[3,4-b]quinoline, C16H11N3, (III), which crystallizes in the space group Pbcn as a nonmerohedral twin having Z' = 3, or 6-methyl-1-phenyl-1H-pyrazolo[3,4-b]quinoline, C17H13N3, (IV), which crystallizes in the space group R\overline{3}. The molecules of compound (I) are linked into sheets by a combination of N-H...N and C-H...π(arene) hydrogen bonds, and the molecules of compound (II) are linked by a combination of N-H...N and C-H...π(arene) hydrogen bonds to form a chain of rings. In the structure of compound (III), one of the three independent molecules forms chains generated by C-H...π(arene) hydrogen bonds, with a second type of molecule linked to the chains by a second C-H...π(arene) hydrogen bond and the third type of molecule linked to the chain by multiple π-π stacking interactions. A single C-H...π(arene) hydrogen bond links the molecules of compound (IV) into cyclic centrosymmetric hexamers having \overline{3} (S6) symmetry, which are themselves linked into a three-dimensional array by π-π stacking interactions.

Theoretical study of graphite intercalated with water cyclic hexamers

Water-treated graphite has attracted attention as a possible room-temperature superconductor. In this work, we use density functional theory to calculate the structural and electronic properties of crystal graphite intercalated with cyclic water hexamers. We treat two different stackings of this system. In the first, we consider an AB stacking which is typical of graphite. In the second, we consider two configurations of an AA stacking which is typical of the superconducting graphite intercalation compounds. All three of the configurations studied are stable and in all three cases, we found the system to be a semimetal. Certain impurities or hydrostatic pressure might change the system into a metal, which seems more suitable for studying its behaviour as a superconductor. This is the first work that considers a crystal structure in the problem of water-treated graphite.

Tailoring Poisson's ratio by introducing auxetic layers

AbstractMonte Carlo simulations in the isobaric–isothermal ensemble with variable shape of the periodic box are used to study elastic properties of two‐dimensional (2D) model systems of hard discs with parallel layers of hard cyclic hexamers. Both the particles in their pure phases form elastically isotropic crystals. However, the crystal of discs shows positive and that of hexamers – negative Poisson's ratio (PR). The studied systems with layers are of low symmetry. Hence, a general analytic formula for the orientational dependence of PR in 2D systems is applied to such systems. It is shown that, by changing parameters of the particles and their relative concentration, as well as orientation of the layers, one can obtain systems which are non‐auxetic (their PR is positive), auxetic (their PR is negative), or partially auxetic ones (their PR is negative for some directions and positive for other ones). If the disks and hexamers are interpreted as small molecules, the obtained results indicate that by introducing auxetic nano‐layers one can strongly modify PR of crystals or even thin layers.The periodic box withparticles can be thought of as a model of a thin layer or as a model crystalline structure with parallel horizontal layers built of four hard cyclic hexamer rows in the hard disc system.

Supramolecular macrocycles reversibly assembled by Te(…)O chalcogen bonding.

Organic molecules with heavy main-group elements frequently form supramolecular links to electron-rich centres. One particular case of such interactions is halogen bonding. Most studies of this phenomenon have been concerned with either dimers or infinitely extended structures (polymers and lattices) but well-defined cyclic structures remain elusive. Here we present oligomeric aggregates of heterocycles that are linked by chalcogen-centered interactions and behave as genuine macrocyclic species. The molecules of 3-methyl-5-phenyl-1,2-tellurazole 2-oxide assemble a variety of supramolecular aggregates that includes cyclic tetramers and hexamers, as well as a helical polymer. In all these aggregates, the building blocks are connected by Te…O–N bridges. Nuclear magnetic resonance spectroscopic experiments demonstrate that the two types of annular aggregates are persistent in solution. These self-assembled structures form coordination complexes with transition-metal ions, act as fullerene receptors and host small molecules in a crystal.

Self-Assembly of 4-(Diethylboryl)pyridine: Crystal Structures of the Cyclic Pentamer and Hexamer and Their Solvent-Dependent Selective Crystallization.

Two distinct oligomeric structures were obtained by the self-assembly of 4-(diethylboryl)pyridine (1). In the (1)H NMR spectrum of 1 in CDCl3, at least two sets of signals were observed for the pyridyl α- and β-hydrogen atoms. ESI-MS, VPO, and TLC analysis revealed that 1 assembles mainly into a mixture of cyclic pentamers and hexamers in solution via intermolecular boron-nitrogen coordination bonds. Crystallization of 1 in THF by vapor diffusion of EtOH or in CHCl3 afforded the cyclic hexamer incorporating one THF molecule (16·THF) or 1.5 mol equiv of chloroform molecule (16·CHCl3), respectively. Similarly, a solution of 1 in a mixture of benzene and hexane furnished the cyclic pentamer bearing two benzene molecules (15·C6H6). It seems that the solvent differences affected the crystallization of the two distinct cyclic oligomers of 1, either of which was cocrystallized predominantly with the solvent molecule. Thermogravimetric analysis of the crystals and NMR studies of the solution revealed that the noncovalent interactions between the host and guest are not strong enough to hold the guest molecule in the cavity.

Periodic Functionalization of Surface-Confined Pores in a Two-Dimensional Porous Network Using a Tailored Molecular Building Block

We present here the periodic functionalization of a two-dimensional (2D) porous molecular network using a tailored molecular building block. For this purpose, a dehydrobenzo[12]annulene (DBA) derivative, 1-isoDBA, having an isophthalic acid unit connected by an azobenzene linker to a C12 alkyl chain and five C14 chains, was designed and synthesized. After the optimization of monolayer preparation conditions at the 1,2,4-trichlorobezene (TCB)/graphite interface, scanning tunneling microscopy (STM) observation of the self-assembled monolayer of 1-isoDBA revealed the formation of extended domains of a porous honeycomb-type molecular network, which consists of periodically located nanowells each functionalized by a cyclic hexamer of hydrogen-bonded isophthalic acid units and those without functional groups. This result demonstrates that the present strategy based on precise molecular design is a viable route to site-specific functionalization of surface-confined nanowells. The nanowells of different size can be used for guest coadsorption of different guests, coronene COR and hexakis[4-(phenylethynyl)phenylethynyl]benzene HPEPEB, whose size and shape match the respective nanowells. STM observation of a ternary mixture (1-isoDBA/COR/HPEPEB) at the TCB/graphite interface revealed the site-selective immobilization of the two different guest molecules at the respective nanowells, producing a highly ordered three-component 2D structure.

Molecular and supramolecular chemistry of rosette nanotubes

Synthetic strategies used to tune the properties of a class of supramolecular 1D nanostructures, the rosette nanotubes, are reviewed herein.

Structural properties of high-energy N12C6 molecules: Cyclic hexamers of NCN

Molecules with high nitrogen content are of interest for their potential as high-energy materials. However, many molecules with 100% nitrogen content are unstable and dissociate with low barriers, which limits practical applications. In the present study, cyclic hexamers of the basic unit NCN (70% nitrogen by mass) are studied to determine the structural features and bonding characteristics that lead to more stable molecules. Double- and triple-bonded NCN units are compared to determine which form of NCN contributes the greater stability. Theoretical calculations using density functional theory and couple-cluster theory are carried out on a series of N12C6 molecules to determine trends in stability. Energetic and structural trends, as well as differences between DFT and coupled-cluster theory, are calculated and discussed.