Conformation wheel

Besides these qualitative nomenclatural systems, quantitative systems are available to describe the ring. shape, or puckering. Two puckering parameters. suffice for five-membered rings, where three are needed for pyranoses. For furanoses, the phase angle 4> is related to where the ring is most puckered, and specifically points to a position on the conformational wheel. The information on extent of deviation from planarity is furnished by the amplitude. 

Figure 39-15. The leucine zipper motif. A shows a helical wheel analysis of a carboxyl terminal portion of the DNA binding protein C/EBP. The amino acid sequence is displayed end-to-end down the axis of a schematic a-helix. The helical wheel consists of seven spokes that correspond to the seven amino acids that comprise every two turns of the a-helix. Note that leucine residues (L) occur at every seventh position. Other proteins with "leucine zippers" have a similar helical wheel pattern. B is a schematic model of the DNA binding domain of C/EBP. Two identical C/EBP polypeptide chains are held in dimer formation by the leucine zipper domain of each polypeptide (denoted by the rectangles and attached ovals). This association is apparently required to hold the DNA binding domains of each polypeptide (the shaded rectangles) in the proper conformation for DNA binding. (Courtesy ofS McKnight)...

Fig. 13. Conformational map of C-6-unsubstituted septanosides. Left A pseudorotational wheel of septanose conformations. Solid ovals mark conformations of P-septanosides, dashed ovals a-septanosides. Right Septanosides and the conformers that have been observed for them.

Again it was surprising that enantioseparation by HPLC was successful because the conformational flexibility of the wheel and the thread entail reduced structural dissymmetry of the enantiomers compared with more rigid molecules. For the rotaxanes 80m and 100 separation factors a were found to be 1.48 and 1.69, respectively. The circular dichrogram of the cycloenantiomeric [ljrotaxane 100 is given in Figure 50. 

Figure 10. Top view and side view of the minimal energy conformations of the stopper-wheel complexes with trityl phenolate (left) and 3,5-di-f-butyl phenolate (right) as obtained from a 3000 step Monte Carlo conformational search with the AMBER force field. The arrows show the most favorable attack paths for the electrophile. (E+= approaching electrophile)...

This expansion contains only seven terms. This expression means that only seven conformational energy values have to be determined for retaining all the main features of potential energy surface of pyrocatechin. These seven conformations have to be conveniently chosen in order to avoid linear dependency. In particular, the 90 , 90 and 90 , -90 conformations have to be considered in order to take accurately into account the cog wheel effect. This particularity is often forgotten by the spectroscopists when they determine the V/i term, i.e, the Aff of the potential energy function (111). 

Fnrther, if in all para-snbstitnted phenols the CO stretching vibration is mainly localized on these two fnndamental modes, in some ortho- and meta-phenols it appears coupled with the mode corresponding to the fnndamental three of benzene whose displacements resemble a distortion towards a Catherine wheel type of strnctnre. Snch vibration appears to be rather sensitive to the position (i.e. either cis or tram) of the X atom, being almost independent of its natnre. In all tram ortho- and meto-snbstitnted phenols, it is placed at slightly lower wavennmbers and characterized by a consistently larger IR intensity compared to the cis conformers. Consider the following example. For all tram m-XCeHjOH, it is centred at ca 1322 cm (81-83 kmmoC ) and bine shifts to ca 1334 cm (2-7 kmmoG ) for the cis conformer. In tram ortto-snbstitnted forms, it is found at 1316-1317 cm (73-78 kmmoC ), while in the cis forms it is at 1323-1324 cm- (21-28 kmmor ). 

A very important aspect of solid-state NMR studies of uniaxiaUy oriented peptides is the possibility to directly determine the conformation of the protein in the bilayer. The PISA wheels 2 for regular secondary structures, which may be considered a direct NMR mapping of the so-called helical wheels, help interpreting the experimental spectra. More recently, Opella and co-workers have suggested to exclusively use the effective dipolar couplings in the analysis of such spectra to alleviate uncertainties from small residue/structure-specific variations in the chemical shifts. 

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