Conformations types

The sedimentation coefficient provides a useful indicator of polysaccharide conformation and flexibility in solution, particiflarly if the dependence of on Mw is known [62]. There are two levels of approach (i) a general level in which we are delineating between overall conformation types (coil, rod, sphere) (ii) a more detailed representation where we are trying to specify particle aspect ratios in the case of rigid structures or persistence lengths for linear, flexible structures. 

Fig. 8 The Haug triangle. The three extremes of conformation compact sphere, random coil and rigid rod) are placed at the apices of a triangle. The conformation of a given macromolecule is represented by a locus along the sides of the triangle between these extremes. Knowledge of the power law exponents (see text) can help to give us an idea of the conformation type. From [61]...

Once a general conformation type or preliminary classification has been established it is possible to use sedimentation data to obtain more detailed information about polysaccharide conformation. For example, the low value of ks/[v 0 25 found for the bacterial polysaccharide xylinan has been considered to be due to asymmetry [115]. If we then assume a rigid structure the approximate theory of Rowe [36,37] can be applied in terms of a prolate ellipsoid of revolution to estimate the aspect ratio p L/d for a rod, where L is the rod length and d is its diameter) 80. 

Fig. 9 Conformation zoning of polysaccharide, a Conformation zones b Empirical plots for various polysaccharides of known conformation type used to form the zone plot. Measurement of s, ks and Ml for a target polysaccharide will then help define its conformation zone or type. Redrawn and based on [112,113]...

The exact nature of the lesion in DNA is unknown, and so is the type of DNA that is attacked. Recent X-ray crystallographic studies, as well as other physicochemical studies, have made it clear that DNA is not simply a polynucleotide, folded as Watson and Crick (106) proposed. There are three main conformational types of DNA they each keep the hydrogen-bonded bases in the center of the helix, but may tilt them by a "propellor twist," may slide them from the center of the helix in the plane of the base pairs, and may vary the amount of rotation from one base pair to the next up the helical axes. 

In B-DNA the major groove is deep and wide and the minor groove is narrower and shallow in A-DNA the major groove is deeper in Z-DNA only the minor groove remains. So there are different possiblities for accommodating a bulky PAH group for each conformational type of DNA. 

Experimentally based intuitive arguments have been presented to arrive at a regional rule for optical activity of d-d transitions of conformational isomers of octahedral metal complexes. Conformational preferences for chelate rings formed by 1,3-pn in its octahedral mono, bis, and tris metal complexes have been studied by calculation of the conformational energies. In all cases, the chair conformation was found to be the most stable. The lowest energy pathway for converting from one chair configuration into another has a barrier to activation of about 7 kcal mol Conformational types of metal-edta complexes have been studied. ... 

Disubstitution (A and B H), on the other hand, destabilized intermediate conformations 460 and 462, causing then to be nonplanar and so facilitating their closure to a heterocycle (459). 165.167.174.2°8.395. .402 Cyclic forms 459 seem to exist only in cases where their valence isomeric cis dienones possess no stable planar conformation type of 460 or 462,164 but... 

Draw Haworth- and conformation-type formulas for each of the following ... 

According to Venkatachalam P-turns are classified into conformational types depending on the values of four backbone torsional angles (< >,VP1,2, P2) (Table... 

An elegant synthesis of inherently chiral calix[4]arenes 75 in the 1,3-altemate conformation (type AABB) was recently described by Gutsche et al.136 It consists of the ring opening aminolysis of calix anhydride 74, which is available from the corresponding 1,3-altemate tetraacid 73 by reaction with oxalyl chloride in yields up to 60%. 

Aaij and Borst (1972) have also demonstrated the separation of closed circular DNA double helices from their linear counterparts in polyacrylamide gels, and have found that log-linear calibrations of molecular weight against relative mobility can be set up. A conspectus of the differences in electrophoretic behaviour between three conformational types - linear single-stranded, linear double-stranded and circular double-stranded - is available from the curve relating... 

Helical structures also are encountered in proteins. Three conformational types characterize their secondary structure the a-structure (helix), the P-helix is a right-handed screw with 3.6 amino acids forming one turn — its pitch height is 540 pm. 

Figure 5 Far ultraviolet region of the CD spectra of (a) YINLIYRLRY-NH2 (compound 58, solid line) and YINLITRQRY-NH2 (compound 11, dashed line) in methanol and (b) INPIYRLRY-NH2 (compound 66) as a function of solvent. Solid lines correspond to 10 mM peptide in 10 mM sodium phosphate buffer, pH 7.5, and dashed lines correspond to 10 mM peptide in methanol. The CD spectrum in aqueous buffer correspond to a mixture of predominantly unfolded conformers. Type C spectra are observed in methanol, corresponding to the presence of predominantly helical conformers. (Reproduced from J. Med. Chem. 1995 38, 1150-1157.)...

Photoisomerizations of eyelohexa-2,4-dienones to bicyclo[3.1.0]hexe-nones must be reekoned with if the dieneketene substitution pattern affects the population of the idealized conformation types (see Scheme 17), to the benefit of A or D. The electronic structure of a dieneketene in its grovmd state resembles electronically excited conjugated trienes" ). 

FIGURE 6-3 Components Requiring Evidence of Conformity Type-Approval... 

Often the chemist may prefer to use experimental evidence gained principally from dynamic NMR studies to limit this vast calculated total picture. Usually, even with most efficient slowing of conformational processes on the NMR timescale, only one or two sets of signals are observed, so each cycloalkane can be considered in terms of one or two conformational types, with different positions that a CH2 group can occupy within each type. Calculations may show slightly less stable local minima nearby, but the simplification subsumes these by treating the conformational type as a dynamic equilibrium fast on the NMR timescale. 

---