Cavity-forming structures

These few examples exhibit cavity-forming structures, making them suitable for receptor library developments. 

O2. Methane and H2S (radii 2.18 and 2.29 A, respectively), while still small enough to fit within the 5 cavities, form structure 1 hydrates. Helium, hydrogen and neon are small enough to diffuse through the... 

Figure 14.11 Crystal structure of HPF6.6H2O showing the cavity formed by 24 H2O molecules disposed with their O atoms at the vertices of a truncated octahedron, The PFe octahedra occupy centre and comers of the cubic unit cell, i.c. one PFr, at the centre of each cavily. ...

According to these authors all gas hydrates crystallize in either of two cubic structures (I and II) in which the hydrated molecules are situated in cavities formed by a framework of water molecules linked together by hydrogen bonds. The numbers and sizes of the cavities differ for the two structures, but in both the water molecules are tetrahedrally coordinated as in ordinary ice. Apparently gas hydrates are clathrate compounds. 

Fig. 1. The crystal structure of a hydroquinone clathrate according to Palin and Powell. 8 The balls inside the transparent spheres represent argon atoms encaged in the cavities formed by the two interpenetrating lattices, (photograph kindly supplied by Dr. Powell).

Zinc phosphite compounds, Zn(H2P03)2-3I I20 and Zn3Na2(HP03)4, have also been characterized in the solid state and revealed structures in contrast with those observed for the phosphates. The tendency to form structures with open cavities is greater due to the reduced bridging ability of the phosphite donor ligand.421... 

In the quantum mechanical continuum model, the solute is embedded in a cavity while the solvent, treated as a continuous medium having the same dielectric constant as the bulk liquid, is incorporated in the solute Hamiltonian as a perturbation. In this reaction field approach, which has its origin in Onsager s work, the bulk medium is polarized by the solute molecules and subsequently back-polarizes the solute, etc. The continuum approach has been criticized for its neglect of the molecular structure of the solvent. Also, the higher-order moments of the charge distribution, which in general are not included in the calculations, may have important effects on the results. Another important limitation of the early implementations of this method was the lack of a realistic representation of the cavity form and size in relation to the shape of the solute. 

In general, heterogeneities in structural materials are often the source of mechanical failure, but specific types also provide ways to disperse energy without failure. For example, some silks, at a microscopic and macroscopic level, are able to form structures such as spherulite inclusions that will develop into elongated cavities in the solid fibers (Akai, 1998 Frische et al., 1998 Robson, 1999 Tanaka et al., 2001). Interestingly, Isobe et al. (2000), in a significant but largely overlooked paper, showed that synthetic A/ i 4o produced spherulites that had the essential features of Alzheimer s amyloid senile plaques (Kaminsky et al., 2006). 

The simplest of structures is the rock salt structure, depicted in Figure 2.2a. Magnesium oxide is considered to be the simplest oxide for a number of reasons. It is an ionic oxide with a 6 6 octahedral coordination and it has a very simple structure — the cubic NaCl structure. The structure is generally described as a cubic close packing (ABC-type packing) of oxygen atoms in the (111) direction forming octahedral cavities. This structure is exhibited by other alkaline earth metal oxides such as BaO, CaO, and monoxides of 3d transition metals as well as lanthanides and actinides such as TiO, NiO, EuO, and NpO. 

The ditrigonal cavity formed by six corner sharing silica tetrahedra (Fig. 3.10) has a diameter of 0.26 nm and is bordered by six sets of lone-pair electron orbitals emanating from the surrounding ring of oxygen atoms. These structural features - as is pointed out by Sposito (1984) - qualifies the ditrigonal cavity as a soft Lewis base capable to complex water molecules (and possibly other neutral dipolar molecules). 

Lipid transfer peptides and proteins occur in eukaryotic and prokaryotic cells. In vitro they possess the ability to transfer phospholipids between lipid membranes. Plant lipid transfer peptides are unspecific in their substrate selectivity. They bind phosphatidylcholine, phosphatidylethanolamine, phosphatidylinositol, and glycolipids. Some of these peptides have shown antifungal activity in vitro The sequences of lipid transfer proteins and peptides contain 91-95 amino acids, are basic, and have eight cysteine residues forming four disulfide bonds. They do not contain tryptophan residues. About 40% of the sequence adopts a helical structure with helices linked via disulfide bonds. The tertiary structure comprises four a-helices. The three-dimensional structure of a lipid transfer peptide from H. vulgare in complex with palmitate has been solved by NMR. In this structure the fatty acid is caged in a hydrophobic cavity formed by the helices. 

Fig. 4 Stereo views (in transparent, space-filling models) of selected hydrophobic interactions in the Fab-peptide and -pentasaccharide complexes. A Trp P3 buried in the hydrophobic cavity formed by CDR L3, His H58 and Trp H47. B Interactions of the side chain of Met P5 with Trp H33. C and D Interactions of the peptide and pentasaccharide, respectively, with His L27D and Tyr L32 (the pocket which accommodates the GlcNAc D methyl group). In (C) the hydrogen bond between the Asp P2 side chain and His L27D NE2 is also shown. A corresponding hydrogen bond between Rha Al 3-OH and His L27D NE2, shown in (D), represents an element of structural mimicry. Reproduced from [80]. 2003 by The National Academy of Sciences of the USA...

Figure 4.4 (a) View of the alpha (grc) cavity bicapped in the c-axis direction by wbc cavities forming pockets accessible though eight-rings on opposite sides of each alpha cavity. The three unique T-atoms in the structure are... 

Cadmium cyanide, CdCCN), is analogous to Si02 with respect to the AB2 composition, the tetrahedral confiugration of A, the bridging behavior of B between a pair of A atoms, and the ability to build a three-dimensional framework in which cavities of molecular scale are formed. Cadmium caynide itself crystallizes in a cubic system of the anticuprite type, in which two identical fr-cristobalite-like frameworks interpenetrate each other without any cross-connection the cavity formed in one framework is filled by the other. When we replace one of the frameworks by appropriate guest molecules such as those of CCl, CCl CH, etc., we may obtain a novel clathrate structure with an adamantane-like cavity, as shown in Fig. 1 [1], Our results including those recently obtained are summarized in Table 1. 

In zeolite synthesis, large cations such as tetramethylammonium (NMe4" ) and tetrapropylammonium (N(C3H7)4" ) can be used as a template around which the aluminosilicate framework crystallizes with large cavities to accommodate the ion. On subsequent heating the cation is pyrolysed, but the structure retains the cavities. Such structures formed around a single molecule template, with pore sizes between 200 and 2000 pm, are known as microporous. 

The important structural feature of zeolites, which can be exploited for various uses, is the network of linked cavities forming a system of channels throughout the structure. These cavities are of molecular dimensions and can adsorb species small enough to gain access to them. A controlling factor in whether molecules can be adsorbed in the cavities is the size of the window or port into the channel, thus the... 

Applying the previous picture this would imply a noteworthy difference in stability between the two triple ions resulting in an ionic recombination process between a triple ion and simple ion. Such a difference in stability would be very plausible judging from the important difference in size and shape of the two ions which would make the triple anion more stable as a structure where the two plcrate ions penetrate along "threefold axes" in two cavities formed by the alkyl-limbs. Applying eq. 

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