Geometry primary 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. 

In order to construct crystals of this required structure type, we applied some empirical rules of packing. We avoided the use of carboxylic acids or primary amides, since molecules containing these functional groups generally pack in centrosymmetric or Mfifi / -centrosymmetric structures. Instead, we selected ester moieties as X and Y, because in many crystals bearing these functional groups an attractive interaction between carbonyls and phenyls of adjacent molecules has been observed which would juxtapose the double bonds, in our case, at the correct distance and in the required geometry (Scheme 3). ° Non-equivalence between the two reactive sites was... 

Side chain introduction by carbopalladation has been utilized in a total synthesis of an-thramycin methyl ether (32) (Scheme Heck reaction of the alkenyl triflate 30 with acrylamide installs the necessary three-carbon chain in moderate yield. The desired alkene geometry and oxidation state are observed in the dienamide 31 with no need for protection of the primary amide. The organopalladium precursor can also be part of the side chain being introduced as illustrated in a synthesis of prostaglandin E2 33. ... 

The presence of pyridine exhibited interference in amide-to-amide hydrogen bonds in the majority of the cases analysed. In the case of primary amides, the pyridine interrupted one of the amide synthons (I or II). The survival probability of synthon I was found to be greater compared with synthon n. The molecular geometry was also found... 

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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