Pucker, 3 -endo

It can be seen that alkylation has changed the sugar-base conformation (distant from the site of alkylation) from anti (as in deoxyadenosine and in B-DNA) to syn (as in alkylated deoxyadenosine and in some bases in Z-DNA). The sugar puckers are either C2 -endo or C3 -endo. A second structural feature of great interest in these crystals is that the more planar anthracene portion of the PAH is stacked between adenine residues of other molecules throughout the crystal. The highly buckled region of the PAH does not take part... 

The differing conformations of the ribose have been named with respect to that ring atom which puckers out of the plane given by the other ring atoms. The most prominent conformations are Cy-endo in B-helices and Cy-endo in A-helices. At room temperature both conformers are in a dynamic equilibrium. Intermediates between Cy-endo and Cy-endo are found in several (time-averaged) structures obtained from X-ray crystallography or NMR. When changing the pucker phase... 

In the light of the appreciable puckering found in the seven-membered ring of [16], Childs (1984) recalculated the expected chemical shifts for the exo and endo H(8) protons of [12]. He calculated the difference in chemical shift (A6) to be 6.9 ppm which is in good agreement with the observed AS - 5.86 ppm. However, his calculations revealed that both the exo and endo protons are shielded. This surprising result is opposed to the accepted intuitive view that in an aromatic/homoaromatic system protons with the H(8)(exo) orientation should be deshielded and those with the H(8)(cndo) orientation shielded. This result closely parallels the analogous calculated data for the homocyclopropenyl cation [2] (Schindler, 1987). 

Balasubramanian et concluded that the Pro ring has two typical puckered conformations (1) conformation A characterized by negative values of %1 (Cq-exo) (found in residues having a-helix-type torsion angles) and (2) conformation B characterized by positive (C7-endo) (found in residues having collagen-type torsion angles). 

X-Ray diffraction analyses of vincristine methiodide (39) and vinzoli-dine 1-naphthalene sulfonate (40) provide atomic coordinates of compounds that are either modified in the velbanamine portion (alkylation at N-6, Fig. 3) or in the vindoline portion (a spiro-fused oxazolidinedione at C-3 and C-23, Fig. 4). These structures show a chair-boat conformation for ring C with C-8 exhibiting an endo pucker. Ring D is clearly in a chair conformation, but, in contrast to the conclusions drawn from C-NMR studies, the N-6 -C-7 bond is axial relative to the piperidine ring. 

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