Conformer pendant group

Our procedure depends on a new computer program, RAMM (RAndom Molecular Mechanics), which is applicable to any kind of biomolecule. It is described in detail elsewhere (KoS r, T./ Petrak, F. Galova, Z. TvaroSka, I. Carbohvdr. Res.. in Press). Only the basic characteristics of RAMM and its application to conformational analysis of disaccharides are discussed here, concentrating on the effect of the orientations of pendant groups on the energy values at the various < ) and f torsion angles. 

To simplify the problem for this demonstration, we assume that all bond lengths, bond angles and the other torsion angles are fixed. With only three staggered minima for each of the pendant groups, the number of possible conformations is still 3 (59,049) for each 0 and f. It is therefore almost impossible to analyze all possible conformations, and a major objective of our methodology was to surmount this difficulty. 

This table shows that there are substantial changes in the orientations of the pendant groups to accoirqpany the changes in energy. Also, the optimal orientations are not generally similar for the two linkage conformations. 

These results indicate that the random walk procedure is an efficient tool to improve the performance of the molecular mechanics methods and to provide a better description of oligosaccharide conformations. While Figures 3 and 4 illustrate the effects of changes in the pendant group orientations, in normal use the entire structure would be optimized after the random walk procedure had detennined low-energy positions for the pendant groups. 

The ease in going from one conformer to the other decreases as the pendant groups increase in size and in secondary bonding. Thus, PMMA is hard at room temperature because... 

Which protein would be more apt to be present in a helical conformation (a) a linear polyamide with small pendant groups or (b) a linear polyamide with bulky pendant groups ... 

The intramolecular mobility, which yields many other conformations between these two extremes, is the basis for viscoelasticity in polymers. Pendant groups, such as the methyl group in isobutane, and lower temperatures decrease the mobility of model compounds such as ethane as well as the polymer chains of polyethylene. 

Commercial PAN is normally produced as an atactic polymer with strong hydrogen-bonded intermolecular forces. Because of repulsion between cyano pendant groups and intermolecular hydrogen bonds, the molecule assumes a crystallizable rodlike conformation. The hydrogen bonds between the rodlike chains create bundles of these chains. PAN may be spun into strong fibers. It has a Tg of 104 C... 

The beta arrangement, or pleated sheet conformation (see Figure 14.2), is predominant when small pendant groups are present in the chain, as in silk fibroin. The silk fibroins, which are spun by various species of silkworms, are monofilament polypeptides with extensive secondary interchain bonding. The crystalline portion of the fibroin is a polymer of a hexapeptide. The... 

The clustering of the apolar pendant groups, which has been clearly revealed by nmr spectroscopy, places rather strong constraints on the type of conformation that the hydrophobic PEI derivatives can assume in aqueous solution. We have built a three-dimensional model that illustrates one type of conformation consonant with these constraints. A photograph of this model giving a full view of a large segment of polymer is displayed in Fig. 11. 

The concept of photostimulated phase separation can be applied to construct chemical-induced phase transition systems, which change the conformation reversibly in response to special chemicals. For the systems, host molecules are used as the receptor groups instead of photoisomerizable chromophores. Host molecules, such as crown ethers or cyclodextrins, are known to change the property by capturing guest chemicals in their cavity [16]. We employed benzo[l 8]crown-6 as the receptor molecule and incorporated it into the pendant groups of PNIPAM. 

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