Cyclic Hexamer Research Articles

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.

Scanning tunnelling microscopy investigation of water in submonolayer coverage on Ag(1 1 1)

Water adsorbed at 70 K on Ag(1 1 1) is investigated by low-temperature scanning tunnelling microscopy. At half a bilayer, the H 2O molecules form simultaneously hydrogen-bonded networks of different dimensionalities. An apparently zero-dimensional structure is a cyclic hexamer with molecules adsorbed in on-top positions. A one-dimensional amorphous structure forms at the upper step edge. At the lower step edge a two-dimensional bilayer grows on which a second layer nucleates heterogeneously.

Intermolecular bond length of ice on Ag(111).

Water adsorbed in submonolayer coverage on Ag(111) at 70 K forms hydrogen-bonded networks. High resolution images in combination with calculation reveal that single protrusions represent a cyclic water hexamer with the intermolecular bond stretched to the silver lattice constant of 0.29 nm. Scanning tunneling spectroscopy indicates that the bond length within the two-dimensional hydrogen-bonded water layer is shortened. The spectra contain further information about the vibrational modes of water molecules.

Novel water clusters in the crystalline state: structures of a symmetrical, cyclic hexamer and an 'opened-cube' octamer.

Six- and eight-membered hydrogen-bonded water clusters of novel structure types have been found in crystalline hydrates.

Hydrogen bonds in crystals of HO-(N∩N′)M(CO)3L complexes: chains, dimers and an unexpected hexamer

Complexes of the type [HO-(N∩N′)]M(CO)3L (M = Cr, Mo, W; L = CO, CNtBu) have been prepared and characterised and their crystal structures have been determined by X-ray crystallography. The aggregation of the complexes in the solid state follows general patterns due to the formation of multiple hydrogen bonds giving infinite chains, dimers and a cyclic hexamer. The hydrogen bonding in the solid state is also detected and analysed by IR spectroscopy and corroborated by DFT calculations.

Solid state structures of homo- and hetero-bimetallic alkali metal complexes containing the dianion of (S)-N-(α-methylbenzyl)allylamine

Dilithiation of the chiral amine (S)-N-(α-methylbenzyl)allylamine in the absence of a coordinating Lewis donor results in formation of crystals of a cyclic hexamer, {[(S)-α-(PhC(H)Me)(CH2CHCHLi)N]Li}6, 1, (rhombohedral, R3) while the addition of tmeda (N,N,N′,N′-tetramethylethylenediamine) leads to deaggregation and formation of the dimer, {[(S)-α-(PhC(H)Me)(CH2CHCHLi)N]Li·(tmeda)2}2, 2 (monoclinic, P21). Reaction with nBuLi followed by nBuNa leads to crystals of a cyclic mixed metal tetramer coordinated with thf, {[(S)-α-(PhC(H)Me)(CH2CHCHNa)N]Li·(thf)}4, 3 (orthorhombic, P212121). The three bimetallic complexes have been characterised by single crystal X-ray diffraction, NMR and elemental analysis. The allyl moieties in all three complexes retain the bonding pattern expected in an N-allylamine (–N(M)—CH2–C(H)C(H)M′, M = Li, M′ = Li or Na) rather than forming a delocalised dianion or an enamide. The anionic amido N and the terminal vinylic C centres form multiple short bonds to all metal centres which in turn form short interactions with all atoms in the allyl groups, and in 1 with the closest Ph carbons.

Observation of the cyclic water hexamer in solid parahydrogen

We present infrared (IR) absorption spectra of cryogenic parahydrogen solids doped with small water clusters. We observe a sequence of peaks shifted to the red by ≈15 cm−1 from the absorptions of cyclic water clusters in liquid helium droplets [K. Nauta and R. E. Miller, Science 287, 293 (2000)]; this sequence includes the peak due to the cyclic isomer of the water hexamer: cyc-(H2O)6. We believe this is only the second spectroscopic observation of isolated cyc-(H2O)6, and the first report of the IR spectrum of the isolated cluster in the solid phase.

Rational syntheses of cyclic hexameric porphyrin arrays for studies of self-assembling light-harvesting systems.

Two new cyclic hexameric arrays of porphyrins have been prepared in a rational, convergent manner. The porphyrins in each cyclic hexamer are joined by diphenylethyne linkers affording a wheel-like array with a diameter of approximately 35 A. One array is comprised of five zinc (Zn) porphyrins and one free base (Fb) porphyrin (cyclo-Zn(5)FbU) while the other is comprised of an alternating sequence of two Zn porphyrins and one Fb porphyrin (cyclo-Zn(2)FbZn(2)FbU). The prior synthesis employed a one-flask template-directed process and afforded alternating Zn and Fb porphyrins or all Zn porphyrins. More diverse metalation patterns are attractive for manipulating the flow of excited-state energy in the arrays. The rational synthesis of each array employed three Pd-mediated coupling reactions with four tetraarylporphyrin building blocks bearing diethynyl, diiodo, bromo/iodo, or iodo/ethynyl groups. The final ring closure yielding the cyclic hexamer was achieved by reaction of a porphyrin pentamer + porphyrin monomer or the joining of two porphyrin trimers. In the presence of a tripyridyl template, the yields of the 5 + 1 and 3 + 3 reactions ranged from 10 to 13%. The 5 + 1 reaction in the absence of the template proceeded in 3.5% yield, thereby establishing the structure-directed contribution to cyclic hexamer formation. The 3 + 3 route relied on successive ethyne + iodo/bromo coupling reactions. One template-directed route to cyclo-Zn(2)FbZn(2)FbU employed a magnesium porphyrin, affording cyclo-Zn(2)FbZn(2)MgU from which magnesium was selectively removed. The arrays exhibit absorption spectra that are nearly the sum of the spectra of the component parts, indicating weak electronic coupling. Fluorescence spectroscopy showed that the quantum yield of energy transfer in toluene at room temperature from the Zn porphyrins to the Fb porphyrin(s) was 60% in cyclo-Zn(5)FbU and 90% in cyclo-Zn(2)FbZn(2)FbU. Two dipyridyl-substituted porphyrins, a Zn tetraarylporphyrin and a Fb oxaporphyrin, have been synthesized for use as guests in the cyclic hexamers, affording self-assembled arrays for light-harvesting studies.

A Monolithiated and Its Related 1,3-Dilithiated Benzylsilane: Syntheses and Crystal Structures

The monolithiated (aminomethyl)benzylsilane Me2Si[CHLi(C6H5)](CH2NC5H10) (3) and the corresponding 1,3-dilithiated compound Me2Si[CHLi(o-C6H4Li)](CH2NC5H10) (4) (CH2NC5H10 = piperidinomethyl), metalated at the benzyl position and at the ortho position of the phenyl ring, were obtained by successive deprotonation of Me2Si[CH2(C6H5)](CH2NC5H10) (1). Monolithiated 3, an internally coordinated cyclic tetramer, and 1,3-dilithiated 4, an internally coordinated cyclic hexamer, were structurally characterized by single-crystal X-ray diffraction methods.

Synthesis of expanded calix[ n]pyrroles and their furan or thiophene analogues

meso-Dialkylporphyrinogen-like mixed cyclic oligomers containing furans, pyrroles and thiophenes have been synthesized by ‘3+1’, ‘3+2’ and ‘3+ketone’ approaches. Condensation of 2,5-bis[1-methyl-1(1 H-pyrrol-2-yl)-ethyl]furan with 2,5-bis[(α-hydroxy-α,α-dimethyl)furan or 2,5-bis[(α-hydroxy-α,α-dimethyl)thiophene resulted in the formation of the mixture of cyclic tetramer, cyclic octamer and cyclic hexamer possessing different numbers of furans (thiophenes) and pyrroles. The major product was found to be the cyclic tetramer in ‘3+1’ condensation while cyclic pentamer was the major product in ‘3+2’ condensation. Appreciable amounts of cyclic decamer was isolated in ‘3+2’ condensation. The formation of furan–pyrrole alternating cyclic hexamer in ‘3+1’ condensation indicates acid-catalyzed, reversible cleavage of the starting material during the reaction. In the same analogy, cyclic dodecamer was synthesized by ‘4+2’ approach. Synthesis of cyclic dodecamer and cyclic pentadecamer was also achieved by condensing 2,5-bis[1-methyl-1(1 H-pyrrol-2-yl)-ethyl]furan with ketones. The effect of catalysts, temperature, templates, solvent and concentration was examined and no appreciable changes in the product distribution were found.

Cyclic homooligomers from sugar amino acids: synthesis, conformational analysis, and significance.

Sugar amino acids (SAAs) were designed as new building blocks carrying an amino group and a carboxyl group on a carbohydrate scaffold. By exploiting standard solid- and solution-phase coupling procedures, linear and cyclic homooligomers containing glucosyluronic acid methylamine (Gum) were synthesized. We achieved a high yield and a very short coupling time for the oligomerization and cyclization of sequences encompassing two, three, four, and six Gum units. The synthesis of cyclic oligomers containing only SAAs as repetitive units has not been reported before. The conformational preferences in aqueous solution of the cyclic derivatives and their applications as potential host molecules are described herein. Benzoic acid and p-nitrophenol were chosen as model guest molecules to study the formation of cyclodextrin-like inclusion complexes. The complexation behavior of the cyclic hexamer was proved from three different points of view: chemical shifts, longitudinal relaxations (T(1)), and diffusion coefficients. All of them showed different values for host and guest molecules measured independently and in the presence of each other.

Supramolecular assemblies between macrocyclic porphyrin hexamers and star-shaped porphyrin arrays.

The syntheses of eight new star-shaped D(3)-symmetric arrays in which three 15-(pyrid-4-yl)porphyrin subunits are attached to the 1, 3, and 5 positions of a benzene core through linkers consisting of collinear repetitive phenylethynyl units have been carried out using Pd(0)-catalyzed coupling reactions. By the same procedure, an analogous 10-(4-pyridin-yl)porphyrin hexamer in which all positions of the benzene core are substituted has been obtained. Likewise, the preparation of suitably sized cyclic porphyrin hexamers, in which all six or at least three alternate porphyrin rings are complexed with Zn(II) ions, is described in detail. In solution, such cyclic porphyrin hexamers form supramolecular assemblies with the star-shaped polyporphyrins in which the latter are held in the interior of the macrocycle through coordination of the apical pyridine rings with the Zn(II) ions. The suggested structures are supported by (1)H NMR spectroscopic and MALDI-TOF mass spectrometric measurements. They agree with the high values of the binding constants of the corresponding supramolecules, which range between K = 1.1 x 10(10) and 1.4 x10(9) M(-1).

Structures, energies, and vibrational spectra of water undecamer and dodecamer: An ab initio study

Ab initio calculations have been carried out to study the water clusters of undecamer [(H2O)11] and dodecamer [(H2O)12]. At the level of Møller–Plesset second-order perturbation theory using TZ2P++ basis set, the lowest-energy conformer of the undecamer has the skeletal structure of Prism56 that a cyclic pentamer and a cyclic hexamer are fused into a prism shape with 16 hydrogen bonds (HBs). In this case, there are quite a number of nearly isoenergetic conformers with different hydrogen orientations. Among these, more stable conformers tend to have dangling H atoms separated (i.e., less clustered). The lowest energy conformer of the undecamer is different in hydrogen orientation from any previously suggested structure (including the ones obtained from various minimization algorithms). A second lowest energy skeletal structure is of Prism56B that a cyclic pentamer and an open-book hexamer are fused into a prism shape with 17 HBs. The most stable dodecamer is a fused cubic or tetragonal prism skeletal structure (Prism444) with 20 HBs. The lowest energy structure among these skeletal conformers has HB orientations with opposite helicities between adjacent tetragonal rings. The second lowest-energy skeletal structure is the hexagonal prism structure (Prism66) with 18 HBs fused by two cyclic water hexamers. The OH stretching vibrational spectra and electronic properties of several low energy conformers of (H2O)11,12 are also reported.

Extended Silapericyclynes

Abstract The synthesis of medium to large-membered cyclic silicon-butadiyne compounds (‘extended silapericyclynes’) was accomplished by the reaction of dilithiobutadiyne with dichlorodiisopropylsilane. The cyclic tetramer, pentamer, hexamer, and heptamer were obtained in 8%, 5%, 4%, and 2% yields, respectively. The structure of the tetramer was determined, and column-like packing was observed. The UV spectra of all compounds are also shown.

Cover Picture

The cover picture shows the reaction between zinc oxide (upper right) and the α-amino acid isovaline, whose formula is depicted in front of a fragment of the Murchison meteorite (upper left). One of the products of this reaction is an unprecedented, cyclic zinc isovalinato hexamer. The occurrence of amino acids, for example isovaline, in certain primitive meteorites gives rise to the assumption that metal amino acidates may already have formed on early Earth some 4×109 years ago. At higher temperatures, solid metal amino acidates decompose to yield large numbers of organic compounds. In prebiotic times, the necessary thermal energy could have been provided by volcanic activities and meteorite impacts. These points are discussed in more detail by Strasdeit et al. on p. 1133 ff. (We thank J. Hurley for the permission to use the picture of the Murchison fragment.)

Role of the (O‒H)6 Synthon in the Construction of Organic Inclusion Compounds

The racemic diol 5 crystallises from ethanol in the orthorhombic space group Cmca (a 19.05, b 14.93, c 10.12 Å) as the cocrystalline solid 5°C2H5OH. In contrast, the racemic diol 6 crystallises from benzene in the cubic space group Ia3 (a 19.85 Å) as a clathrate compound. The principal supramolecular synthon involved in both cases is a cyclic hexamer of hydrogen bonded hydroxy groups, (O-H)6. While the former cycle is almost planar, rather uncommonly the latter is cyclohexane-like in geometry. A major function of the (O-H)6 cycle is to allow efficient packing between opposite enantiomers within the crystal lattice.

Determination of the changes of the basic structures of silica species in dependence on the concentration of sodium chloride by FAB-MS

The chemical species of silica in NaCl solutions of different concentrations were identified by FAB-MS (fast atom bombardment mass spectrometry). The basic structures of silica species, such as cyclic pentamer (Si5 (OH)9O6-), linear pentamer (Sis(OH)11O5-), cyclic hexamer (Si6(OH)9O8-, Si6(OH)11O7-) and linear hexamer (Si6(OH)14 O6-), were identified, in addition to dimer (Si2(OH)5O2-), trimer (Si3(OH)7O3-) and cyclic tetramer (Si4(OH)7O5-). The patterns of changes of the peak intensities of the silicate complexes relative to the dimer with increasing NaCl concentration were classified into two types: that represented by linear silicate complexes and the other by cyclic silicate complexes. The differences in the type of chemical species and their changes according to the NaCl concentration reflect the number of bonds necessary for polymerization and hydrolysis of the silica complexes. The differences between the linear and the cyclic silicate type have some implications on the dissolution mechanism of silicate complexes, the hydration of the molecules and the equilibrium between solubility, hydrolysis, polymerization and the salting-out effect in NaCl solution.

Sulfone-linked paracyclophanes via macrocyclic aromatic thioethers: synthetic and structural investigations.

Reaction of 4,4'-sulfonylbis(benzenethiol) with 4,4'-dichlorodiphenylsulfone under pseudo-high-dilution conditions leads to macrocyclic thioethersulfones [-S-Ar-SO2-Ar-]n (Ar = 1,4-phenylene). These include a highly strained [1+1] cyclodimer (n = 2), a cyclotrimer resulting from thioetherexchange reactions, and a [2+2] cyclotetramer which can adopt two entirely different conformations in the crystalline state, one having molecular D2d ("tennis-ball-seam") symmetry. The same type of reaction is successful using 4,4'-thiobis(benzenethiol) instead of 4,4'-sulfonylbis(benzenethiol) and affords macrocycles with a higher ratio of thioether to sulfone linkages. Exhaustive oxidation of macrocyclic thioethersulfones with hydrogen peroxide affords a series of sulfone-linked paracyclophanes, [-Ar-SO2-]4, [-Ar-SO2-]6, [-Ar-SO2-]8 and [-Ar-SO2-]12. Single crystal X-ray analysis reveals [Ar-SO2-]4 to be a near-perfect square box, whilst the cyclic hexamer [-Ar-SO2-]6 adopts a much more irregular conformation. and [-Ar-SO2-]8 displays a "double-box" structure clearly related to that of [Ar-SO2-]4.

Aggregation of water molecules: Atmospheric implications

The equilibrium constants for water oligomers ranging from dimers to cyclic hexamers are determined using Wertheim’s theory of associating systems. In the present model for water, the pair potential has a spherical hard core, and tetrahedral hydrogen bonds which are represented by an energy parameter and an interaction volume. On the basis of the present theory, one predicts that in earth’s troposphere, water dimers and perhaps trimers may contribute to the absorption of solar radiation, but concentrations of higher oligomers are too low to influence the optical properties of the earth’s atmosphere.

Cyclic Polylactones and their Cyclic Polyorthoester Valence Tautomers: Potential Ionophores

The geometries and energies of the cyclic hexamer ( 9) of glycolic acid, and its polycyclic orthoester valence tautomer ( 10) have been studied by ab initio molecular orbital calculations at the HF/6-31G ∗ and MP2//HF/6-31G ∗ levels of theory. Both molecules are preorganised to bind metal ions in both endohedral and exohedral modes. The binding of 9 and 10 with Li +, Na +, K +, Be 2+, Mg 2+, B 3+ and Al 3+ have been examined, and the energies and geometries of the resulting complexes are discussed.