Ordered conformers

Polymers can be crystalline, but may not be easy to crystallize. Computational studies can be used to predict whether a polymer is likely to crystallize readily. One reason polymers fail to crystallize is that there may be many conformers with similar energies and thus little thermodynamic driving force toward an ordered conformation. Calculations of possible conformations of a short oligomer can be used to determine the difference in energy between the most stable conformer and other low-energy conformers. 

Microbial polysaccharides in solution lose their ordered conformation on heating. The temperature at which the polymer melts to a disordered state is known as the melting temperature (Tm) and is determined by a variety of factors ... 

To be successful in these applications, it is important that materials can self-assemble into precisely defined structures. Peptide-based polymers have many advantages over conventional synthetic polymers since they are able to hierarchically assemble into stable, ordered conformations [4]. Depending on the substituents of the amino acid side chain, polypeptides are able to adopt a multitude of... 

Figure 2 compares the conformational transition curves of wild-type yeast glucan (branch frequency = 0.20) and PGG (branch frequency = 0.50). Wild-type yeast glucan required approximately 0.1M NaOH to disrupt the triple helical conformation, whereas this transition is observed at approximately 0.04 M NaOH with PGG. This trend is consistent with the observation that curdlan, an entirely linear p-D(l-3)-linked glucan, requires approximately 0.25M NaOH to disrupt the ordered conformation (76). Hence, it is concluded that the highly branched PGG molecules only form weak inter-chain associations resulting in the formation of predominantly single-helical zones. 

When dissolved in more saline waters, xanthan gum produces a higher apparent viscosity than the same concentration of polyacrylamide (292). Prehydration of xanthan in fresh water followed by dilution in the saline injection water has been reported to provide higher viscosity than direct polymer dissolution in the same injection water. Optical rotation and intrinsic viscosity dependence on temperature indicate xanthan exists in a more ordered conformation in brine than in fresh water (293). 

Xanthan is reported to undergo a chiroptically detected temperature or salt-driven conformational change from an ordered conformation at high salt and low temperature to a disordered conformation either associated with lowering the salt concentration, or with increasing the temperature (2-5). The primary structure of xanthan has been known for about a decade (6,7), but different structures have been suggested both for the ordered and disordered conformation. Some workers (8-13) conclude that the ordered conformation is double-stranded or double-helix, whereas others (14-17) claim that a single stranded description can account for the observed data under... 

Ordered conformation. Figure 1. shows representative electron micrographs of samples A, B, C, and D vacuum dried from xanthan solutions under ordering conditions as specified in the legend. Xanthan samples A -D appear as unbranched, uniformly thick, convoluted chains. The contour length varies from molecule to molecule as expected for a polydisperse polymer. The electron micrographic... 

Grasdalen, H. and Smidsrod, O. (1981) Iodide-specific formation of K-carrageenan single helices-1-127 NMR spectroscopic evidence for selective site binding of iodide anions in the ordered conformations. Macromolecules, 14, 1842-1845. 

The reaction system, 2A = B = > C, has been studied in a constant volume, batch reactor with the tabulated results. Assuming the orders conform to the stoichiometry, find the specific rates. 

Ab initio molecular dynamics simulation of a triflic acid monohydrate crystal. The intermediate state (right) with two delocalized protons is 0.3 eV higher in energy than the ordered conformation of the native crystal (left). 

Mg (but not Na" ") results in a structure that is equivalent to the 30-nm compact fiber in the extent of condensation [49]. Finally, the independent and critical function of core histone N-termini in chromatin condensation was demonstrated by showing that nucleosomal filaments reconstituted from core histones lacking their N-terminal domains are unable to condense into folded structures upon an increase of Mg " ", despite the presence of properly bound histone H5 ([50,51], see also Ref. [52] for the discussion of the special role of H3 and H4 tails). Thus, the presence of HI is not a sine-qua-non condition for salt-induced chromatin folding, which can proceed in Hi s absence and is an intrinsic property of filaments consisting of spaced core particles. A key question is how many of the features of the native 30-nm compact fiber are due to the presence of histone HI From the available data it seems that HI may influence the intrinsic folding pathway of the chromatin filament by stabilizing a single ordered conformation. This property can have much to do with the cooperativity of HI interactions within chromatin but also with the way HI is bound to the nucleosome and with the efifect it exerts on the path of linker DNA. 

Its aqueous solutions are not only viscous but become gels over the temperature range 20 - 90 C. The course of sol-gel transition as a function of temperature monitored by optical rotation (25) suggests the conversion of a conformationally mobile random coil in the sol state to a rigid ordered conformation in the gel state. The midpoint of transition is approximately around 45 C. Only oriented, noncrystalline fibers could be prepared, the best of them at 45 C. 

A better knowledge of force constants, the use of more detailed physical models, and the availability of large computers and of new methods of calculation has permitted the prediction, within close approximation, of the frequencies and, to a lesser degree, the intensities of absorptions of stereoregular polymers in ordered conformations (helix, zigzag, etc.). In this way data on molec-... 

The H-bonds between the paired bases and the Van der Waals attractive forces that hold the staked base-pairs, aligned one pair on top of the other, are disrupted. The ordered conformation breaks and the double helix dissociates into random, disordered coils. The viscosity of the solution drops sharply. 

Direct experimental evidence for the existence of an ordered conformation of sugar nucleotides in solutions has been reported by Hirano,344 who observed characteristic optical-rotatory changes for a series of these compounds upon transition from water to concentrated urea solutions. The structural requirements for such an ordered conformation are still not clear. However, data at this point, based on indirect kinetic evidence from hydrogenation and hydroxylamin-olysis reactions (see Section IV, p. 360), seem to accord with the hypothetical model just described. Further studies on the conformations of sugar nucleotides in solution are highly desirable. 

Hjerde, T., Smidsrad, O., Christensen, B.E. (1998b). Acid hydrolysis of k- and i-carra-geenan in the disordered and ordered conformations characterization of partially hydrolyzed samples and single-stranded oligomers released from the ordered structures. Macromolecules, 31, 1842-1851. 

It has been shown142 that, for long-chain polymers in an ordered conformation, the calculation of the normal modes is reduced by symmetry arguments to the determination of the vibrations of the repeat unit. The vibrations in a chemical unit are related to those in adjacent units by the secular equation through a phase angle 6, so that the form of the secular equation used in the previous calculations29-30 was... 

---