Geometry secondary amides

Primary amides and secondary amides, and a few lactams, display a band or bands in the region of 1650-1515 cm 1 caused primarily by NH2 or NH bending, the amide II band. This absorption involves coupling between N—H bending and other fundamental vibrations and requires a trans geometry. 

Unfortunately, none of the analogs 34, 35, 37, or (A-unsubstituted secondary amide) 36, which would mimic a rranj -olefin geometry) showed any appreciable tubulin-polymerizing or antiproliferative activity, despite the fact that preliminary NMR studies with compound (34) in DMSO/water indicate that the preferred conformation about the 12/13 A-methyl amide bond is indeed cis, that is, the methyl group and the carbonyl oxygen are located on the same side of the partial C-N double bond (cis/trans-mtio 4/l 34 may thus be considered a direct structural mimetic of Epo D). The underlying reasons for the lack of biological activity of... 

The oxindole construction mentioned above is a variation of an oxindole synthesis developed by Jones. An application of this method to the synthesis of horsfi-line is outlined in Eq. (11) [21], It is notable that whereas the cyclization of 37 is quite efficient, attempts to cyclize amide 38 gave only reduction of the aryl bromide. This is a common problem in radical cyclizations involving secondary amides as the ii-geometry of the amide precludes cyclization. This general problem was first... 

If the allenic Claisen substrate is derived from a secondary allenyl alcohol, e.g., 7, the relative configuration of the diastereomeric alcohol determines the geometries of the double bonds of the diene part, and the absolute configuration of the stereocenter at C-2 of the product depends on the absolute configuration of the substrate by 1,4-chirality transfer, provided the rearrangement takes place via a chairlike transition state. Chair transition state A, with the substitutuent R1 equatorial, seems to be preferred because of 1,3-diaxial interactions of R1 with the amide group in transition state B660. 

The order or sequence of individual amino acid residues along the peptide chain defines the covalent structure of the molecule. It is also called primary structure in order to make a clear distinction from the three dimensional geometry in peptides and proteins. The latter is generated by non-covalent forces such as hydrogen bonds between amide groups secondary structure) and combination of polar and non-polar interactions and of disulfide bridges which result in chain folding tertiary structure). 

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