Hydrogen bonding hexamers

It was demonstrated that hydrogen bonded hexamers ( rosettes ) can be formed not only in the crystalline state but also in apolar solvents and that various well-defined self-assembled species can be obtained from building blocks in which melamine and barbiturate/cyanurate fragments are covalently attached in an appropriate way to a molecular skeleton.279... 

Fig. 6. Hexa-host strategy Close connection between (a) a hydrogen-bonded hexamer unit typical of phenolic hosts (hydroquinone, Dianin s compound cf. Fig. 4) and (b) of a hexasubstituted benzene analogue (follow up the shaded hexagons) (c) characteristic constitution of hexa-host molecules and (d) host-guest packing of a representative clathrate inclusion compound (dioxane clathrate of I3a, 1 1 dioxane molecules hatched)...

The dicarboxyazobenzene nnits are connected via metfl-phenylene linkers at the ends of C12 chains. The length of the unfunctionalized chains is set to C14 based on molecular modeling to fit with the functionalized chains for making the interdigitated alkyl chain linkage. Indeed, STM observation showed that by self-assanbly of DBA-AB at the 1-octanoic acid/HOPG interface, a honeycomb network was formed wherein six azobenzene units were visualized as spoke-like features. This indicates the formation of hydrogen-bonded hexamers of the isophthalic acid parts of the molecules. 

In another example of catalysis by the hydrogen-bonded hexamers, Shimizu et al. prepared Teflon-footed resorcin[4]arenes [56] (i.e., resorcin[4]arenes with per-fluorinated side chains) that form hexameric capsules in wet fluorous solvents. These capsules, several years later, were used to accelerate a Diels-Alder reaction in abiphasic system [56b]. 

Studies have indicated that the association of HF in the gas phase leads predominantly to dimers or hexamers with small amounts of tetramers. Hydrogen bonding in liquids such as sulfuric and phosphoric acids is responsible for them being viscous liquids that have high boiling points. 

Insulin therefore consists of two peptide chains that are connected by two disulfide bonds, since the C-peptide is cleaved off. There are some species-specific differences in the amino acid sequence of the hormone. X-ray diffraction studies have shown that insulin occurs as a hexameric protein containing two Zn atoms. The dimers are first held by four hydrogen bonds and a hydrophobic bond along the sequence in the form of an antiparallel P sheet. The dimers then bind by interaction of the B -Ala, B -Leu, and B -Val residues. The core of the hexamer contains water. 

Comparative Aspects of Polyphenol Metabolism - Proanthocyanidins and the complex esters of gallic and hexahydroxydiphenic acid show many structural similarities as plant metaijol i tes. The shape and size of the ester (5) is thus very similar to that of a proanthocyanidin hexamer (1, n = 4). The most striking feature of both structures however s the manner in which free phenolic groups are distributed over the surface of the molecule providing a structure with the inbuilt capacity for multidentate attachment to other species by hydrogen bonding. 

Figure 13.3 Proton ordering in hydrogen bonding, illustrating favorable (Grotthuss-like) ordering in a chain (above) or cyclic hexamer (a), contrasted with the unfavorable isomer (b), one of many similar that cannot survive thermodynamically. All clusters are ice rule-compliant (cf. Sidebar 5.18).

Figure 3. The shape and size of the cavity/channel of Dianin s compound, (a) The cage formed by two sets of hexamers. (b) The top or bottom half of the cage, hexamers are held together by hydrogen bonds, (c) Schematic illustration of the cage/channel. The stacking is along the c axis. (Reproduced with permission from D. D. MacNicol in Inclusion Compounds, Vol. 2, J. L. Atwood, J. E. D. Davies, and D. D. MacNicol, Eds., Academic Press, New York, 1984, p. 1.)...

Computer simulation studies by Stillinger and Rahman (1974) suggest that the pentamer is the most likely structure to spontaneously arise in water at many temperatures, followed in frequency by hexamers, and squares. In a review of water, Frank (1970) noted that closed rings of bonds are always more stable than the most stable open chains of the same cluster number, due to the extra energy of the hydrogen bond. Through molecular dynamics studies of many five-molecule clusters, Plummer and Chen (1987) argued that the cyclic pentamer that comprises many hydrate cavities is the only stable five-member cluster above 230 K. 

Resorcarene hexamers bridged either by 24 Cu(II) ions or 12 Ga(III) ions have also been prepared.36 37 These compounds are closely analogous to hydrogen-bonded resorcarene and pyrogallolarene hexamers (indeed the metal-bridged compounds can be prepared by substitution of 2H+ for Cu2+) and we will look at these systems as a whole in Section 10.6.3. 

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