Bonding in Individual Chains

The three-dimensional character of molecules is expressed by its stereochemistry. By looking at the stereochemistry of a molecule, the spatial relationships between atoms on one carbon and the atoms on an adjacent carbon can be examined. Since rotation can occur around carbon-carbon single bonds in open chain molecules, the atoms on adjacent carbons can assume different spatial relationships with respect to each other. The different arrangements that atoms can assume as a result of a rotation about a single bond are called conformations. A specific conformation is called a conformer. While individual isomers can be isolated, conformers cannot since interconversion, by rotation, is too rapid. 

The three distribution functions for the three possible directions in space must be interdependent when the number of bonds N is small. For N = 1, for example. Lx + lJ + Lz = must hold, where b is the bond length. The three components of the overall distribution function become less dependent on each other with increasing number of bonds in the chain molecule. If is very large, and L is simultaneously much smaller than the square of the length of the fully stretched chain molecule, then the components can be considered to be independent of each other. The total probability is simply the product of the individual probabilities, i.e.,... 

NH—CH(R)—CO-grouping is the amino acid residue, in which R is the side chain characteristic for the individual amino acid. Conventionally, the peptide bonds in the chain are written, as shown here, in the —CO—NH— direction. The amino acid residues are designated with a three-later symbol, the peptide bond usually with a hyphen. Thus, the segment —alanyl-glycyl— of a peptide chain appears as -Ala-Gly- or AlaGly. The same amino acids at the amino terminus of a peptide chain and at the carboxyl end, respectively, are written as... 

PROPERTIES OF SPECIAL INTEREST Two crystalline forms of polyglycine, I and II, have been observed. Form I is thought to have a /3 structure where the individual chains exist in a helical conformation and form sheets stabilized by hydrogen bonds. The individual chains in form II also have a helical conformation but are packed in a hexagonal lattice with a three-dimensional array of hydrogen bonds. ... 

Optimal diffusion constants for overall anisotropic rigid body reorientation of enkephalin were computed by least-squares fitting of the observed spin-lattice relaxation times of proton-bearing carbons (Somorjal and Deslaurlers, 1976). Correlation times for Internal motion about Individual C-C bonds In side chains were estimated according to methods described by Deslaurlers and Somorjal (1976). 

In thermoplastic polymers the bonds between individual chains are secondary and the amount of free volume is sufficient for local chain motion. In thermosetting polymers interchain interactions between cross-linked sites are also secondary bonds and motion of these segments is similar. A mechanism of switching often used to describe the nature of motion in a viscous liquid is sometimes used to describe these local atomic movements in polymers. As illustrated in Fig. 11.1(a), the atoms in a liquid can change... 

Based on the above, the longitudinal modulus Ej of individual aromatic chains should scale as chains with coaxial single bonds > chains with noncoaxial bonds in bridge > chains with single-atom swivels > chains with flexible multiple-atom bridges. 

Secondary bonds are considerably weaker than the primary covalent bonds. When a linear or branched polymer is heated, the dissociation energies of the secondary bonds are exceeded long before the primary covalent bonds are broken, freeing up the individual chains to flow under stress. When the material is cooled, the secondary bonds reform. Thus, linear and branched polymers are generally thermoplastic. On the other hand, cross-links contain primary covalent bonds like those that bond the atoms in the main chains. When a cross-linked polymer is heated sufficiently, these primary covalent bonds fail randomly, and the material degrades. Therefore, cross-linked polymers are thermosets. There are a few exceptions such as cellulose and polyacrylonitrile. Though linear, these polymers are not thermoplastic because the extensive secondary bonds make up for in quantity what they lack in quahty. 

Similarly, polymers dissolve when a solvent penetrates the mass and replaces the interchain secondary bonds with chain-solvent secondary bonds, separating the individual chains. This cannot happen when the chains are held together by primary covalent cross-links. Thus, linear and branched polymers dissolve in appropriate solvents, whereas cross-linked polymers are insoluble, although they may be swelled considerably by absorbed solvent. 

Pleated p sheet (Section 27.19) Type of protein secondary structure characterized by hydrogen bonds between NH and C=0 groups of adjacent parallel peptide chains. The individual chains are in an extended zigzag conformation. 

If the protein of interest is a heteromultimer (composed of more than one type of polypeptide chain), then the protein must be dissociated and its component polypeptide subunits must be separated from one another and sequenced individually. Subunit associations in multimeric proteins are typically maintained solely by noncovalent forces, and therefore most multimeric proteins can usually be dissociated by exposure to pEI extremes, 8 M urea, 6 M guanidinium hydrochloride, or high salt concentrations. (All of these treatments disrupt polar interactions such as hydrogen bonds both within the protein molecule and between the protein and the aqueous solvent.) Once dissociated, the individual polypeptides can be isolated from one another on the basis of differences in size and/or charge. Occasionally, heteromultimers are linked together by interchain S—S bridges. In such instances, these cross-links must be cleaved prior to dissociation and isolation of the individual chains. The methods described under step 2 are applicable for this purpose. 

Nylon fibers are semicrystalline, that is, they consist of crystallites separated by amorphous regions. Hydrogen bonding is an important secondary valence interaction in nylon-6 and nylon-6,6. Individual chains in the microcrystalline regions of nylons are held together by hydrogen bonds. Nylons are resistant to aqueous alkali but deteriorate more readily on exposure to mineral acids. 

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