Right-handed helix

A peptoid pentamer of five poro-substituted (S)-N-(l-phenylethyl)glycine monomers, which exhibits the characteristic a-helix-like CD spectrum described above, was further analyzed by 2D-NMR [42]. Although this pentamer has a dynamic structure and adopts a family of conformations in methanol solution, 50-60% of the population exists as a right-handed helical conformer, containing all cis-amide bonds (in agreement with modeling studies [3]), with about three residues per turn and a pitch of 6 A. Minor families of conformational isomers arise from cis/trans-amide bond isomerization. Since many peptoid sequences with chiral aromatic side chains share similar CD characteristics with this helical pentamer, the type of CD spectrum described above can be considered to be indicative of the formation of this class of peptoid helix in general. 

The structures shown in Fig. 4-1 are for B-form DNA, the usual form of the molecule in solution. Different double-helical DNA structures can be formed by rotating various bonds that connect the structure. These are termed different conformations. The A and B conformations are both right-handed helices that differ in pitch (how much the helix rises per turn) and other molecular properties. Z-DNA is a left-handed helical form of DNA in which the phosphate backbones of the two antiparallel DNA strands are still arranged in a helix but with a more irregular appearance. The conformation of DNA (A, B, or Z) depends on the temperature and salt concentration as well as the base composition of the DNA. Z-DNA appears to be favored in certain regions of DNA in which the sequence is rich in G and C base pairs. 

In the resolution of racemates having a C2 axis and two aromatic groups using (+)-l, the more retained enantiomers have P-helicity with respect to their aromatic groups if one looks at the molecules from the direction perpendicular to a C2 axis (Figure 3.8). This could suggest that (+)-l has P-helicity that is, a right-handed helical conformation.45... 

Figure 5.8 Electron micrographs of (a) right-handed helices and tubules from A-dodeca-5,7-diyne-D-galactonamide (10) and (b) braided fibers from A-dodeca-5,7-diyne-L-arabonamide (11). Reprinted with permission from Ref. 47. Copyright 1994 by the American Chemical Society.

Figure 5.21 Transmission electron micrographs showing right-handed helical ribbons of L-Glu-Bis-3 (37) in aqueous environment. Reprinted with permission from Ref. 97. Copyright 2002 by Elsevier Science.

The second issue is how to explain the observation of both left- and right-handed helices in the phosphonate material. While Thomas et al. found both helical senses in the early stages of formation of DCggPC tubules, they found both helical senses even in the equilibrium state of the phosphonate. In the previous section, we attributed their results on tubule formation kinetics to a biased chiral symmetry-breaking in which the molecular packing has two possible states which are approximately mirror images of each other. The... 

Figure 6.9 Schematic representation of hierarchical self-assembly process for chiral phthalocya-nine 64. Phthalocyanine molecules self-assembly into helical columns with right-handed screw sense (left). These right-handed helices subsequently aggregate to give left-handed super-helices.

Figure 7.9 Different handedness of packing of right-handed helices with different pitch-to-diameter ratios. Right-handed helices with p/d < n interact to give right-handed superhelix, while when p/d > it, superhelix is left-handed. (Reprinted with permission of Wiley-VCH from Chemistry—A European Journal, Vol. 6, p. 3249 ad ff., copyright 2000.)...

Fig. 11. Drawing of a typical a-helix, residues 40-51 of the carp muscle calciumbinding protein. The helical hydrogen bonds are shown as dotted lines and the main chain bonds are solid. The arrow represents the right-handed helical path of the backbone. The direction of view is from the solvent, so that the side groups on the front side of the helix are predominantly hydrophilic and those in the back are predominantly hydrophobic.

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