Folded molecules

The chain direction within the crystal is along the short dimension of the crystal, indicating that the molecule folds back and forth, fire hose fashion, with successive layers of folded molecules accounting for the lateral growth of the platelets. 

Among the variety of nitrogen-containing fulvalenes emerging from types 7-14, X-ray structural determinations have been performed on about 20 representative examples. Tire first crystal structure determination was carried out by application of the folding-molecule method on 3,3 -diphenyl-l,l -bi-isoindolylidene 64 (R = FI) (71CB3108). Tire dimeric isoindolenine system... 

Figure 5.13 The RNA of bacteriophage MS2. The molecule is single stranded but there are extensive regions of complementary bases, so that pairing within the strand leads to the secondary structure shown. Note that the start sites for three coding regions are in the same part of the folded molecule.

If pseudo association exists in a substance, there are at least two types of molecules, namely simple and complex. I say at least two types because it cannot be assumed that all complexes are of equal size. But as a first step I have assumed only two types, i.e., simple molecules and n-fold molecules. For a really scientific treatment, of course, it would be necessary to assume all values of n as possible and to seek the law of distribution for these values. 

Protein folding is a complex, trial and error process that can sometimes result in improperly folded molecules. These misfolded proteins are usu ally tagged and degraded within the cell (see p. 441). However, this qual ity control system is not perfect, and intracellular or extracellular aggregates of misfolded proteins can accumulate, particularly as individ uals age. Deposits of these misfolded proteins are associated with a number of diseases including amyloidoses. 

Cells of mycoplasmas sometimes grow as filaments but are often spherical and as small as 0.3 micrometer (pm) in diameter. Their outer surface consists of a thin cell membrane about 8 nanometers (nm) thick. This membrane encloses the cytoplasm, a fluid material containing many dissolved substances as well as sub-microscopic particles. At the center of each cell is a single, highly folded molecule of DNA, which constitutes the bacterial chromosome. Besides the DNA there may be, in a small spherical mycoplasma, about 1000 particles 20 nm in diameter, the ribosomes. These ribosomes are the centers of protein synthesis. Included in the cytoplasm are many different kinds of... 

The sequences of all three pieces of RNA in the E. coli ribosomes are known as are those from many other species. These include eukaryotic mitochondrial, plas-tid, and cytosolic rRNA. From the sequences alone, it was clear that these long molecules could fold into a complex series of hairpin loops resembling those in tRNA. For example, the 16S rRNA of E. coli can fold as in Fig. 29-2A and eukaryotic 18S RNA in a similar way (Fig. 29-4).38/39/67 69 The actual secondary structures of 16S and 18S RNAs, within the folded molecules revealed by X-ray crystallography, are very similar to that shown in Fig. 29-2A. Ribosomal RNAs undergo many posttranscriptional alterations. Methylation of 2 -hydroxyls and of the nucleic acid bases as well as conversion to pseudouridines (pp. 1638-1641) predominate over 200 modifications, principally in functionally important locations that have been found in human rRNA.69a... 

Fig. 5.A4. The structure of haemoglobin and its iron porphyrin prosthetic group. This diagram is highly simplified and the dotted line indicates the overall shape of the folded molecule and the zones of the a helical structure within the molecule are also shown...

Schmuck, C. (2000) Self-folding molecules A well defined, stable loop formed by a carboxylate-guanidinium zwitterion in DMSO, J. Org. Chem. 65, 2432-2437. 

The ketone had to be protected before epoxidation (avoiding the Baeyer-Villiger reaction ) and epoxidation then occurred on the outside of the folded molecule 47. 

Reagents, whether electrophilic or nucleophilic, prefer to approach the outside or exo face of folded molecules. These are cis -fused four-, five-, or six-membered rings. If a substituent is needed on the inside or endo face, it must be added first, that is disconnected second 54, as in the synthesis of the ketone 54. If there is only one substituent and it is endo, R2 can be H. 

Folded molecules in lamellas crystallized from molten polymers. J. Appl. Phys. 33, 642-643 (1962). 

As discussed earlier, solid polymers can be distinguished into amorphous and the semicrystalline categories. Amorphous solid polymers are either in the glassy state, or - with chain cross linking - in the rubbery state. The usual model of the macromolecule in the amorphous state is the "random coil". Also in polymer melts the "random coil" is the usual model. The fact, however, that melts of semi-crystalline molecules, although very viscous, show rapid crystallisation when cooled, might be an indication that the conformation of a polymer molecule in such a melt is more nearly an irregularly folded molecule than it is a completely random coil. 

It is now generally accepted that the morphology of a polymer depends on the contributions of three different macro-conformations (a) the random coil or irregularly folded molecule as found in the glassy state, (b) the folded chain, as found in lamellar structures and (c) the extended chain. The fringed micelle (d) may be seen as mixture of (a), (b) and (c) (see Fig. 2.12) with paracrystallinity as an extreme. 

Finally, a second hydroboration with 9-BBN occurs regiospecifically and on the outside of the folded molecule. This reaction adds the last two centres making five in all. 

Treatment of the other product, the keto-tosylate, with base leads to an intramolecular enolate alkylation—a cyclization on the inside of the folded molecule that actually closes a four-membered ring. The reaction is easily seen in conformational terms and the product cannot readily be drawn in conventional diagrams. 

---