Chain conformation disordered conformations

Polymers showing crystalline mesomorphic modifications, characterized by chains in disordered conformations, are exceptions to the equivalence principle. Examples of these cases are shown in Section 2.6. 

The observed chemical shifts imply that while the signals of the (l->3)-P-linked backbone were completely suppressed in the gel-state due to the rigid helical conformation and the resulting restriction of the motion, (l- 6)-linked side-chains preserved disordered conformation and in this manner their NMR signals became visible in the gel-state spectrum due to the almost complete loss of the major component - the backbone carbons signals. Since the signals of the side-chain residues were fully observed in the gel-state, there appears to be no specific role for (1- 6)-linked units in gel formation. Therefore the gelation fenomenon may be discussed solely in terms of mutual association of (1—>3)-linked chains. 

Chain Conformation—Disordered. An area of current interest is application of vibrational spectroscopy, particnlarly Raman, for analysis of disordered chains which may include pol5uners in solntion, melt, or the solid state. These chains lack long-range order but may contain short ordered sequences. In addition, these disordered chains may adopt a specific conformational distribution. 

The quantitative determination of phospholipid acyl chain conformational disorder in hydrated systems of dipalmitoylphosphatidylcholine (DPPC), dipalmitoylphosphatidylethanolamlne (DPPE), mixtures containing DPPC and cholesterol, and mixtures of DPPC and Gramicidin D has been made using FT-IR. The... 

Figure 14a. Although our values are not in quantitative agreement with the experimental values (see Ref. 50 for a discussion), they faithfully reproduce the well-known observation that the disorder increases from the tops of the chains toward the middle of the bilayer, with a more pronounced increase in the last few carbons of the chain. The. S cd represent different types of disorder, including chain conformational defects and whole molecule wobbling [67].

In order to examine whether this sequence gave a fold similar to the template, the corresponding peptide was synthesized and its structure experimentally determined by NMR methods. The result is shown in Figure 17.15 and compared to the design target whose main chain conformation is identical to that of the Zif 268 template. The folds are remarkably similar even though there are some differences in the loop region between the two p strands. The core of the molecule, which comprises seven hydrophobic side chains, is well-ordered whereas the termini are disordered. The root mean square deviation of the main chain atoms are 2.0 A for residues 3 to 26 and 1.0 A for residues 8 to 26. 

Here, the second term describes the change of the hopping amplitudes due to the displacement of the atoms parallel to the chain [cf. Eq. (3.5)] and the third term is a random contribution resulting from the conformational disorder (chain twists). While the lattice displacements u are dynamic variables, the fluctuations dl +t due to disorder are assumed to be frozen ( quenched disorder). 

Figure 3-7. A simplified picture of a //wi-v-polyacelylcne chain with conformational disorder the right part of the chain is rotated with respect to its left part over the angle .

As an example of the second case, we may have conformationally disordered chains, but long-range order in the positions of the chain axes (condis crystals [5]). Fiber spectrum features are the occurrence of sharp reflections on the equator only and diffuse reflections on the other layer lines. 

A conformationally disordered mesomorphic form is present, for instance, in the high-temperature phase I of PTFE. In this form, a long-range 3-D order is present only in the periodic pseudohexagonal placement of the chain axes [49]. In fact intramolecular helix reversals would produce the conformational disorder [50-52] and a complete intermolecular rotational disorder would be also present [49, 52,53]. 

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