Intramolecular hydrogen randomization

Many synthetic water-soluble polymers are easily analyzed by GPC. These include polyacrylamide,130 sodium poly(styrenesulfonate),131 and poly (2-vinyl pyridine).132 An important issue in aqueous GPC of synthetic polymers is the effect of solvent conditions on hydrodynamic volume and therefore retention. Ion inclusion and ion exclusion effects may also be important. In one interesting case, samples of polyacrylamide in which the amide side chain was partially hydrolyzed to generate a random copolymer of acrylic acid and acrylamide exhibited pH-dependent GPC fractionation.130 At a pH so low that the side chain would be expected to be protonated, hydrolyzed samples eluted later than untreated samples, perhaps suggesting intramolecular hydrogen bonding. At neutral pH, the hydrolyzed samples eluted earlier than untreated samples, an effect that was ascribed to enlargement... 

The essence of this model for the second virial coefficient is that an excluded volume is defined by surface contact between solute molecules. As such, the model is more appropriate for molecules with a rigid structure than for those with more diffuse structures. For example, protein molecules are held in compact forms by disulfide bridges and intramolecular hydrogen bonds by contrast, a randomly coiled molecule has a constantly changing outline and imbibes solvent into the domain of the coil to give it a very soft surface. The present model, therefore, is much more appropriate for the globular protein than for the latter. Example 3.3 applies the excluded-volume interpretation of B to an aqueous protein solution. 

Secondary protein structures are the local regular and random conformations assumed by sections of the peptide chains found in the structures of peptides and proteins. The main regular conformations found in the secondary structures of proteins are the a-helix, the fl-pleated sheet and the triple helix (Figure 1.8). These and other random conformations are believed to be mainly due to intramolecular hydrogen bonding between different sections of the peptide chain. 

In solvents having unusually strong hydrogen-bonding ability the intramolecular hydrogen bonds of the helices are no longer stable and the conformation of the polypeptides is that of a random coil. Doty et al. (1956) found that in dichloroacetic acid [i ] = 2.78 X 10 the exponent... 

The interpretation of chemical shift effects induced by pressure in proteins is still in its infancy, although at least some of the changes can be consistently interpreted in structural terms, e.g the change of the H -chemical shifts could be associated with the change of the length of intramolecular hydrogen bond under pressure. Arnold et al. reported a data basis for the chemical shift changes with pressure for random-coil peptides. 

At least two other secondary structures are observed with peptides a P pleated sheet and a random coil. Poly(aspartic) acid, mentioned previously, forms a random coil structure. A random coil, as its name implies, does not assume a regular structure such as the a-helix because hydrogen bonds are not easily formed. Rotation about the / and ( ) angles (see 126) leads to a random orientation of the various amino acid residues. The -pleated sheet, on the other hand, does involve intramolecular hydrogen bonding. In other words, there are hydrogen bonds between two different peptide chains rather than within a single peptide chain. 

Hydrogen-bonded conformers are often very pH-dependent, because H ions protonate the exposed electronegative atoms (for example, the carboxyl oxygens in a peptide), robbing those atoms of the opportunity to form intramolecular hydrogen bonds. Without the stabilizing influence of the hydrogen bonds, these molecules form disordered structures called random coils at low pH. 

Messenger RNA (mRNA)—very little intramolecular hydrogen bonding and the molecule is in a fairly random coil... 

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