Cyclic Hexamer Research Articles

Thermodynamics of forming water clusters at various temperatures and pressures by Gaussian-2, Gaussian-3, complete basis set-QB3, and complete basis set-APNO model chemistries; implications for atmospheric chemistry.

The Gaussian-2, Gaussian-3, complete basis set- (CBS-) QB3, and CBS-APNO methods have been used to calculate Delta H degrees and Delta G degrees values for neutral clusters of water, (H(2)O)(n), where n = 2-6. The structures are similar to those determined from experiment and from previous high-level calculations. The thermodynamic calculations by the G2, G3, and CBS-APNO methods compare well against the estimated MP2(CBS) limit. The cyclic pentamer and hexamer structures release the most heat per hydrogen bond formed of any of the clusters. While the cage and prism forms of the hexamer are the lowest energy structures at very low temperatures, as temperature is increased the cyclic structure is favored. The free energies of cluster formation at different temperatures reveal interesting insights, the most striking being that the cyclic trimer, cyclic tetramer, and cyclic pentamer, like the dimer, should be detectable in the lower troposphere. We predict water dimer concentrations of 9 x 10(14) molecules/cm(3), water trimer concentrations of 2.6 x 10(12) molecules/cm(3), tetramer concentrations of approximately 5.8 x 10(11) molecules/cm(3), and pentamer concentrations of approximately 3.5 x 10(10) molecules/cm(3) in saturated air at 298 K. These results have important implications for understanding the gas-phase chemistry of the lower troposphere.

An Efficient Synthesis of Tetraoxaquaterene Derivatives Starting from 2,2-Difurylpropane

Four non-symmetric tetraoxaquaterenes (5, 6, 8, and 9) and two cyclic hexamers 11 and 13 were efficiently prepared via the condensation reaction of furyl precursors 3 and 4 with various ketones, catalysed by 90.5% sulfuric acid.

Synthesis of cyclic hexameric porphyrin arrays. Anchors for surface immobilization and columnar self-assembly.

To investigate new architectures for the self-assembly of multiporphyrin arrays, a one-flask synthesis of a shape-persistent cyclic hexameric array of porphyrins was exploited to prepare six derivatives bearing diverse pendant groups. The new arrays contain 6-12 carboxylic acid groups, 12 amidino groups, 6 thiol groups, or 6 thiol groups and 6 carboxylic acid groups in protected form (S-acetylthio, TMS-ethyl, TMS-ethoxycarbonyl). The arrays contain alternating Zn and free base (Fb) porphyrins or all Zn porphyrins. The one-flask synthesis entails a template-directed, Pd-mediated coupling of a p/p'-substituted diethynyl Zn porphyrin and a m/m'-substituted diiodo Fb porphyrin. The porphyrin building blocks (trans-A(2)B(2), trans-AB(2)C) contain the protected pendant groups at nonlinking meso positions. A self-assembled monolayer (SAM) of a Zn(3)Fb(3) cyclic hexamer containing one thiol group on each porphyrin was prepared on a gold electrode and the surface-immobilized architecture was examined electrochemically. Together, the work reported herein provides cyclic hexameric porphyrin arrays for studies of self-assembly in solution or on surfaces.

Theoretical Study of the Lowest Energy Structure of the Water Undecamer

Density functional calculations and ab initio calculations have been carried out to study the lowest energy structure of the water (<TEX>$H_2O)_{11}$</TEX>. Among five structures suggested by four different groups, the lowest energy structure is found to have the skeletal structure of Prism56 (Pr56-24) that a cyclic pentamer and a cyclic hexamer are fused into a prism-shape with 16 hydrogen-bonds (HBs).

Cyclic Water Hexamers and Decamers in a Porous Lanthanide−Organic Framework: Correlation between Some Physical Properties and Crystal Structure

Erbium fumarate [Er2(fum)3(H2O)4]·8H2O, 1, (fum = fumarate dianion) crystallizes at room temperature in a silica gel column. The structure is three-dimensional and consists of layers of erbium fumarate pillared by fumarate dianions acting in the bis-chelating mode. The layers contain arrays of erbium cations bridged by fumarate dianions acting in the bis-bidentate bridging mode. The relatively large channels formed in the direction of the a and c axes are filled by water molecules that form a hydrogen bonded layer, comprising cyclic hexamers with both boat and chair conformations and cyclic decamers with boat−chair−boat conformation. The water molecules are reversibly removed at 90 °C. The evacuated metal−organic framework, 2, is stable up to 400 °C. Both compounds 1 and 2 exhibit weak antiferromagnetic interactions.

In vitro and in vivo efficacy of α-cyclodextrin for treatment of experimental cryptosporidiosis

The efficacy of α-cyclodextrin against infection by Cryptosporidium parvum was evaluated using in vitro and in vivo models . Cyclodextrins are water-soluble cyclic hexamers of glucose units with hydrophobic cavities capable of solubilizing lipophiles and are widely used as drug excipients in the pharmaceutical industry. The viability of purified C. parvum oocysts, exposed for 30, 60, 90, 120 min and 24 h to different concentrations of α-cyclodextrin (2.5, 5, 7.5, 10, 12.5 and 15%), was evaluated by inclusion or exclusion of two fluorogenic vital dyes and by an excystation technique. Preventive and curative efficacies against cryptosporidial infections, at different doses (2.5 and 5%) and regimes of administration of α-cyclodextrin, were determined in an experimental neonatal mice model. Results of the viability assay showed a decrease in oocyst viability that was associated with an increase in exposure time, for each of the concentrations used. Moreover, a high proportion of nonviable oocysts (81%) was observed when C. parvum oocysts were exposed to α-cyclodextrin (2.5%) for 24 h. The intensity of infection, determined 7 days post-inoculation by examination of intestinal homogenates, was significantly lower ( P<0.05) than in the control litters, for all the assays carried out with α-cyclodextrin. Only 38.8% of the animals became infected when the α-cyclodextrin solution (5%) was administered 2 h before inoculated oocysts, and every 24 h at 1 and 2 days post-inoculation.

Supramolecular variations on a molecular theme: the structural diversity of phosphazenes (RNH)6P3N3 in the solid state

Herein, we introduce an extremely ‘soft’ tecton, which interacts via ‘soft’ synthons displaying an unprecedented variety of supramolecular architectures in the solid state. Hexakis(organoamino) cyclotriphosphazene derivatives, (RNH)6P3N3, contain a polar core comprising an equatorial belt of three ring nitrogen atoms and six NH functions which is sandwiched between hemispheres of lipophilic substituents R. A range of derivatives equipped with hydrocarbon side chains were synthesised and structurally characterised including R = tert-butyl (1), cyclohexyl (2), iso-propyl (3), benzyl (4), 2-phenylethyl (5), iso-butyl (6), phenyl (7), p-tolyl (8), n-propyl (9), allyl (10), propargyl (11) and methyl (12). The study shows that subtle modifications of the lipophilic periphery lead to considerable changes in the solid-state aggregation pattern. With the exception of 1 all solid-state structures show intermolecular NH⋯N bonding with motifs containing one, two, three and four H-bridges. Supramolecular architectures include monomer (1), dimer (2), cyclic hexamer (3), zigzag chain (4, 6), linear chain (5·thf, 7, 8), double chain (9), graphite-type sheet (10), rectangular grid (11) and hexagonal close-packed sheet (12). The structural variety is due to easy rotation around exocyclic P–N bonds, which allows variable directionalities of all six N–H bonds. M.O. calculations on the gas phase dimer of (H2N)6P3N3 mirror the H-bridging motifs observed in crystal structures of (RNH)6P3N3 derivatives.

Hexameric macroring of gable-porphyrins as a light-harvesting antenna mimic.

Construction of a self-assembled supramolecular macroring that has distances and orientations of porphyrin dimer units in close analogy to those of the natural light-harvesting complexes was achieved. In natural light-harvesting complexes, bacteriochlorophyll-a's are arranged in macroring structures by coordination from imidazolyl side chains. A structural determination of a light-harvesting antenna complex (LH2) elucidated the arrangement of 18 bacteriochlorophyll-a's in a slipped-cofacial way with C9 symmetry in B850 in 1995. To obtain such an elegant macroring architecture as an artificial light-harvesting complex, we connected slipped-cofacial dimers of imidazolylporphyrins in a gable-porphyrin orientation. The introduction of zinc assembled by coordination porphyrins with originally a broad molecular weight distribution (MWD). When coordination bonds were cleaved and reorganized under high dilution conditions using chloroform/methanol solution, the MWD was perfectly converged. This crop gave particle images of a uniform height by atomic force microscopy measurements. Further purification was successfully achieved by gel permeation chromatography, and the first eluting component gave a diameter corresponding to the cyclic hexamer of gable-porphyrins from a small-angle X-ray scattering measurement with synchrotron radiation. In summary, porphyrin assemblies in a macroring arrangement were constructed using the gable-porphyrin motif, and their photophysical properties are highly interesting.

Changes of Silica Species in Sodium Chloride Solution by Fast Atom Bombardment Mass Spectrometry: Silicate Complex Substituted by Sodium Ion

Abstract The types of chemical species of silicate complex ion exchanged with sodium ions (silicate–Na+ complex) with increasing concentration of sodium chloride (NaCl) and their numbers of chemical species of silicate–Na+ complexes formed were examined. Silicate–Na+ complexes in several concentrations of NaCl were identified by fast atom bombardment mass spectrometry (FAB-MS). The basic structures of silicate species are not complexes with Na+, such as the dimer, trimer, cyclic tetramer, linear tetramer, cyclic pentamer, linear pentamer, cyclic hexamer and linear hexamer, were identified. When the peak intensity ratios of silicate–Na+ complexes were plotted against the concentration of NaCl, the changes with increasing concentration of NaCl were mainly classified into two patterns. One is the linear silicate–Na+ complex pattern (dimer–Na+ complex, trimer–Na+ complex and linear tetramer–Na+ complex), and the other is the cyclic silicate–Na+ complex pattern (cyclic tetramer–Na+ complex and cyclic pentamer–...

Folded Structure of a Cyclic Hexamer of 4-(Methylamino)benzoic Acid in the Crystal

A cyclic hexamer of 4-(methylamino)benzoic acid was crystallized from dichloromethane-ethyl acetate to give colorless prisms, which belonged to space group P1 with a = 12.441(1)A, b = 16.003(1)A, c = 11.7479(9)A α = 94.421(7)°, β = 117.911(5)°, γ = 100.205(7)°, V = 1999.5(3)A3, and Z = 2. The compound adopted a folded conformation with all six N-methylamides having a cis (E) conformation; four intermolecular CH/n contacts were observed in the crystal.

The bicyclic n,n'-diacylaminal: a new motif for molecular self-assembly.

A cage-shaped N,N'-diacylaminal crystallizes from some aromatic solvents as "supramolecular chair cyclohexanes", squat cylindrical hexamers with approximate D3d symmetry containing two arene molecules, and from other aromatic and nonaromatic solvents as infinite tapes. A homologous diacylaminal crystallizes only as an infinite tape. The hexamers represent the first examples of cyclic hexamers held together by %@mt;sys@%%@bold@%R%@rsf@%%@sx@%2%@be@%2%@sxx@%%@fn;(;vis;full;auto@%8%@fnx;);vis;full@%-type%@mx@% hydrogen bonds in which the hydrogen-bonded atoms are not coplanar. The diacylaminal represents a new supramolecular synthon, one perhaps more suited to the design of three-dimensional architectures.

Supramolecular polymer chemistry: self-assembling dendrimers using the DDA.AAD (GC-like) hydrogen bonding motif.

Heterocyclic unit 2 containing complementary donor-donor-acceptor (DDA) and acceptor-acceptor-donor (AAD) hydrogen bonding arrays at an angle of about 60 degrees was designed to self-assemble into a hexamer. To investigate whether this unit could self-assemble dendrimers, the 2,8-diamino-2-N-ethylpyrimido-(4,5-b)(1,8)naphthyridine-3H-4-one subunit was synthesized with a first (2a), second (2b), and third generation (2c) Fréchet-type dendron attached to the 8-amino group. The synthesis of 2a-c was accomplished in 11 steps beginning with 2,6-diaminopyridine and the corresponding dendron bromide. Studies using (1)H NMR, size exclusion chromatography (SEC), and dynamic light scattering (DLS) support the cooperative formation of cyclic hexamers in apolar solvents. The stability of the self-assembled dendrimers is dependent on the size of the attached dendron, and mixing studies with 2a-c indicate their usefulness in constructing dynamic combinatorial libraries.

Efficient Synthesis of Benzene‐Centered Cyclic Porphyrin Hexamers.

Abstract Palladium- and cobalt-catalyzed trimerization of diphenylethynyl-bridged diporphyrin gave benzene-centered cyclic porphyrin hexamers.

Synthesis and structural characterization of new stiff rod oligomeric domains by X-ray crystallography and NMR.

The monomers N,N'-dibenzylbenzene-1,4-diamine (1), N,N'-dibenzylnaphthalene-1,5-diamine (2), and N,N'-dibenzylanthracene-1,9-diamine (3) were reacted with phosgene in the presence of a base to produce the corresponding N,N'-dibenzyl-1,4-bis(chlorocarbonylamino)benzene (4), N,N'-dibenzyl-1,5-bis(chlorocarbonylamino)naphthalene (5), and N,N'-dibenzyl-9,10-bis(chlorocarbonylamino)anthracene (6). These monomers were used to create zigzag type stacks, in a stepwise fashion, of trimers and 9-mers of either 1,4-diureidobenzenes ((Phe)K(3) and (Phe)K(9)) or 1,5-diureidonaphthalenes ((Nap)K(3) and (Nap)K(9)). A byproduct in the formation of (Phe)K(9) was a cyclic hexamer (Phe)K(6). NMR gave evidence of the structure in solution while X-ray crystallographic information was obtained for 5, 6, (Nap)K(3), and the cyclic (Phe)K(6).

Water diffusion and clustering on Pd(111).

The adsorption, diffusion, and clustering of water molecules on a Pd(111) surface were studied by scanning tunneling microscopy. At 40 kelvin, low-coverage water adsorbs in the form of isolated molecules, which diffuse by hopping to nearest neighbor sites. Upon collision, they form first dimers, then trimers, tetramers, and so on. The mobility of these species increased by several orders of magnitude when dimers, trimers, and tetramers formed, and decreased again when the cluster contained five or more molecules. Cyclic hexamers were found to be particularly stable. They grow with further exposure to form a commensurate hexagonal honeycomb structure relative to the Pd(111) substrate. These observations illustrate the change in relative strength between intermolecular hydrogen bonds and molecule-substrate bonds as a function of water cluster size, the key property that determines the wetting properties of materials.

Efficient synthesis of benzene-centered cyclic porphyrin hexamers

Palladium- and cobalt-catalyzed trimerization of diphenylethynyl-bridged diporphyrin gave benzene-centered cyclic porphyrin hexamers.

M-Diethynylbenzene macrocycles: syntheses and self-association behavior in solution.

m-Diethynylbenzene macrocycles (DBMs), buta-1,3-diyne-bridged [4(n)]metacyclophanes, have been synthesized and their self-association behaviors in solution were investigated. Cyclic tetramers, hexamers, and octamers of DBMs having exo-annular octyl, hexadecyl, and 3,6,9-trioxadecyl ester groups were prepared by intermolecular oxidative coupling of dimer units or intramolecular cyclization of the corresponding open-chain oligomers. The aggregation properties were investigated by two methods, the (1)H NMR spectra and the vapor pressure osmometry (VPO). Although some discrepancies were observed between the association constants obtained from the two methods, the qualitative view was consistent with each other. The analysis of self-aggregation by VPO revealed unique aggregation behavior of DBMs in acetone and toluene, which was not elucidated by the NMR method. Namely, the association constants for infinite association are several times larger than the dimerization constant, suggesting that the aggregation is enhanced by the formation of dimers (a nucleation mechanism). In polar solvents, DBMs aggregate more strongly than in chloroform due to the solvophobic interactions between the macrocyclic framework and the solvents. Moreover, DBMs self-associate in aromatic solvents such as toluene and o-xylene more readily than in chloroform. In particular, the hexameric DBM having a large macrocyclic cavity exhibits extremely large association constants in aromatic solvents. By comparing the aggregation properties of DBMs with the corresponding acyclic oligomers, the effect of the macrocyclic structure on the aggregation propensity was clarified. Finally, it turned out that DBMs tend to aggregate more readily than the corresponding phenylacetylene macrocycles, acetylene-bridged [2(n)]metacyclophanes, owing to the withdrawal of the electron density from the aromatic rings by the butadiyne linkages which facilitates pi-pi stacking interactions.

Formation of the cyclic ice hexamer via excitation of vibrational molecular modes by the scanning tunneling microscope

Starting from water monomers adsorbed on Cu(111), we have induced the formation of small ice clusters via the tip of a low temperature scanning tunnelling microscope. We show that diffusion, formation, and structural changes of clusters are induced by electrons coupling to vibrational modes of the molecule. The manipulation transfers enough energy into the system to induce stable clusters both two-dimensional and three-dimensional ones, including the important cyclic hexamer. Only the three-dimensional clusters develop a localized gap around the Fermi energy of ≈76 meV, which varies for different positions on a cluster.

Infrared spectroscopy of ethanol clusters in ethanol–hexane binary solutions

Temperature and concentration dependent infrared spectra were recorded for binary solutions of ethanol–hexane, ethanol–carbon tetrachloride, and ethanol–cyclopentane. The temperature range covered was 198 K to 298 K; concentrations ranged from 0.45 mole percent to 4.0 mole percent ethanol. Changes in the OH stretch frequency are consistent with the formation of ethanol clusters (EtOH)n, where n ranges from 2 to 6. The geometry, OH stretch frequency and proton chemical shift for 14 different ethanol clusters ranging from monomer to hexamer in cyclic and linear arrangements were investigated using density functional methods (B3LYP/6-31+G*). These clusters include both gauche and anticonformers of the monomer unit. The OH stretch frequency calculations were compared to experimental Fourier transform infrared measurements made as a function of concentration and temperature for dilute ethanol in hexane binary mixtures. Analysis of the O–H stretch frequency data (3100 to 3700 cm−1) indicate the presence of small clusters of ethanol. The data indicate that at the lower temperatures the clusters are primarily cyclic tetramers, pentamers, and hexamers. This infrared data is in excellent agreement with recent concentration and temperature dependent nuclear magnetic resonance chemical shift investigations that indicate a dramatic change in cluster size with concentration and temperature.

Molecular Architecture with Nucleobases, Metal Ions and Water Molecules: Mixed Adenine, Hypoxanthine Quartet Containing trans -(NH 3 ) 2 Pt II and Ag + and Harboring a Water Hexamer in Its Chair Conformation

The formation and X-ray crystal structure of a molecular rectangle of 14.25(2) Å ‐ 10.36(2) Å, comprised of two neutral 9-methyladenine (9-MeA) and two anionic 9-methylhypoxanthinate (9-MeHx) model nucleobases as well as two trans -(NH 3 ) 2 Pt II and two Ag + entities, and further cross-linked intermolecularly by Ag + ions, is described: trans -[{(NH 3 ) 2 Pt(9-MeA)(9-MeHx)Ag(NO 3 ) (H 2 O)} 2 Ag](NO 3 ) 3 6H 2 O ( 4 ). The water molecules are located between adjacent purine quartets and adopt a cyclic water hexamer structure in a chair conformation. In addition, the X-ray crystal structure of the precursor of 4 , trans -[(NH 3 ) 2 Pt(9-MeA)(9-MeHxH)](NO 3 ) 2 H 2 O ( 2 ), is reported. 4 is discussed in terms of its relationship to proposals in the literature concerning possible structures of metalated forms of purine quartets.