Cavity dimer

For simplicity, we restrict ourselves to a one-component dimerizing fluid, o + o 02, and define the one-particle cavity functions / = 0,1, for bonded and unbonded species as follows... 

The phenyl ether oxygen atoms allow the two borazaphenanthrene rings to pivot with respect to each other, therefore this dimeric boronic acid anhydride can potentially exist in two isomeric forms, either face-to-face or helical (Fig. 18). In the face-to-face form the boron atoms of the bis(borazaphe-nanthrene) moieties have syn-orientation, while they have approximate anti-orientation in the helical form. Compound 68 has been characterized by X-ray crystallography in the helical form [109]. The dimensions of the cavity can be described by the transannular C C contacts between the carbon atoms in 2-position of the phenyl ether units, which have values of 5.12 and 6.21 A. 

Matsue et al. [43] attempted to study the molecular rocket reaction in a ruthenocene-/ -cyclodextrin inclusion compound using the I00Ru y, p) "raTc reaction. They noticed a parallel relationship between chemical processes and nuclear-recoil-induced processes in the non-included ruthenocene compound, as shown in Fig. 9. In the nuclear-recoil-induced processes no dimerization can be observed because of the extremely low concentration of the product, whereas in the chemical processes dimerization is possible, as demonstrated by Apostolidis et al. [48]. When ruthenocene included in /J-cyclodextrin is irradiated with y-rays, a part of the ruthenocene molecule is converted to [TcCp2-] which escapes from the jS-cyclodextrin cavity. The [TcCp2] rocket thus produced can attack neighboring inclusion compounds so as to extract the enclosed ruthenocene molecules and abstract H or Cp (Cp cyclopentadienyl radical). This process is shown schematically in Fig. 10. 

Rhodopsin is a seven ot-helix trans-membrane protein and visual pigment of the vertebrate rod photoreceptor cells that mediate dim light vision. In this photoreceptor, retinal is the chromophore bound by opsin protein, covalently linked to Lys296 by a Schiff base linkage. Kpega et al.64 have studied NMR spectra of Schiff bases being derivatives of all-frans retinal and amino-p-cyclodextrins as a model of rhodopsin, where p-cyclodextrin plays a role of a binding pocket. On the basis of analysis of the chemical shift differences for the model compound in the presence and in the absence of adamantane carboxylate, it has been shown that the derivative of 3-amino-p-cyclodextrin forms dimer in water and retinoid is inserted into p-cyclodextrin cavity [31]. 

Co-facial dimers consist of two simple macrocyclic systems connected by linkages such that the respective cyclic portions are constrained to stack one above the other. Such molecules define three cavities two within the macrocyclic subunits and a third between these subunits. 

Fujita and coworkers have also reported the encapsulation of multimeric porphyrin assemblies in the box-shaped cavities of ternary Pd6 coordination cages. Two types of cofacial porphine dimers A and B could be stabilized (133). In the smaller [Pd6(L14)2(L15)6]12+ cage 29, whose diameter is 10.4 A (Fig. 21), two porphyrin molecules can be stackedo directly on top of each other with an interplane distance of 3.4 A. In the larger cage 30, an additional molecule of L14 is intercalated between the two porphyrin bases. All complexes were found to be water-soluble in contrast to other 7i-stacked porphyrin dimers. The encapsulation... 

The CoA binding tunnel provides access to the internal cavity. B. Molecular surface representation of the CHS-CoA complex oriented as shown in (A). In the -bottom panel, the two CHS monomers are separated and rotated slightly to highlight the flat dimerization interface along with the methionine side chain and dyad related hole in the backside of the CHS active site. 

Figure 2. Left Family of softball" monomers 4-7. Different spacers between the centerpiece and the glycoluril binding sites permit assembly of dimers with cavity volumes between 186 A3 and 313 A3. Right Computer-minimized...

The future prospects for the capsule project emerge from these considerations. Further increasing the size of the capsule and building chemical functionalities into the inner cavity would allow a closer emulation the functions of enzymes, especially those that require cofactors in order to catalyze chemical transformations. Another important aspect is to design capsules that can combine stereospecificity and catalysis - that is accelerate stereoselective transformations. Capsules that reversibly dimerize in water would probably contribute a lot more to our understanding of non-covalent forces and solvent effects in this most biorelevant medium. So far, water solubility and assembly have not been achieved with hydrogen-bonded capsules. 

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