Peptide unit partial double bond character

Peptides and proteins are composed of amino acids polymerized together through the formation of peptide (amide) bonds. The peptide bonded polymer that forms the backbone of polypeptide structure is called the a-chain. The peptide bonds of the a-chain are rigid planar units formed by the reaction of the oc-amino group of one amino acid with the a-carboxyl group of another (Figure 1.1). The peptide bond possesses no rotational freedom due to the partial double bond character of the carbonyl-amino amide bond. The bonds around the oc-carbon atom, however, are true single bonds with considerable freedom of movement. 

The observed lengths in nanometers determined by X-ray diffraction measurements are given in Fig. 2-5 (top). The partial double-bond character of the C-N bond has important consequences. The peptide unit is nearly planar as is indicated by the dashed parallelogram in Fig. 2-5. 

Although the peptide unit is mostly considered to be plane (co = 1 °) because of the partial double bond character of the amide bond, careful analyse by means of X-ray revealed deviaticms of torsion angles from planarity of up to 10°. 

An amide (peptide) bond connects two amino acid residues. The amide unit is quite interesting in that it is essentially planar. Structure 125 shows an amide bond fragment and the electrons are delocalized as shown by the two resonance structm-es, 125A and 125B. This delocalization leads to the C-N unit having partial double-bond character, which is normal for the C-N unit in simple amides such as acetamide (ethanamide see Chapter 16, Section 16.7, and Chapter 20, Section 20.6). This phenomenon is observed in the infrared spectrum of primary and secondary amides, which exhibit two absorptions (1640 cm"i [C-0 stretch] and 1650-1515 cm [imine N-H bend of NH2 or NH] for the amide I and amide II bands see Chapter 14, Section 14.3.4). 

One should note the difference between amino acid residues which refers to —NH—CHR—CO and peptide units which refers to —CHR—CO—NH— (Fig. 2.2). The peptide unit corresponds to the properties of the peptide bond it has a partial double-bond character because of the existence of two resonance forms (Fig. 2.3a) which strongly restricts the possibility of rotation around the C—N bond. Consequently, this group is generally planar however, deviations from planarity of the peptide bond have been observed. An evaluation of conformational energy calculations indicated deviation of only 1-3° in low energy minima of Gly-Gly, but as much as 10° in Gly-Pro (Zimmerman and Scheraga, 1976). 

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