Peptide bond double-bond character

The amide bond that links different amino acids together in peptides is no different from any other amide bond (Section 24.3). Amide nitrogens are non-basic because their unshared electron pair is delocalized by interaction with the carbonyl group. This overlap of the nitrogen p orbital with the p orbitals of the carbonyl group imparts a certain amount of double-bond character to the... 

Although peptides are written as if a single bond finked die a-carboxyl and a-nitrogen atoms, this bond in fact exhibits partial double-bond character ... 

The partial double-bond character of the bond that links the carbonyl carbon and the nitrogen of a peptide renders four atoms of the peptide bond coplanar and restricts the number of possible peptide conformations. 

A protein s secondary structure arises from the formation of intra- and inter-molecular hydrogen bonds. All carboxyl group oxygens and amine hydrogens of a polypeptide participate in H-bonding. Protein secondary structure also derives from the fact that although all C-N bonds in peptides have some double bond character and cannot rotate, rotation about the Co-N and Ca-C bonds is possible and is... 

A peptide chain consists of a succession of -C(=0)-N-C - atoms that are coplanar, with the C-N bond being shorter than that of a normal amide. There is a partial sharing of the 7t-electrons between the C=0 and the C-N bond, giving the latter double-bond character (-40%), so that it is unable to rotate freely. The NH-proton and the oxygen atom are in the same plane but in a trans relationship (Figure 6.24). 

The torsion angle co, which is common to peptides and nonpeptidic amides, always prefers a planar over a nonplanar conformation due to the partial double-bond character of the amide bond (Fig. 6.3, right). Thus, a peptide bond resembles an amide bond in conformational and electronic terms [2] [3], However, peptides differ from amides in that both the carbonyl C-atom and the amido N-atom are nearly always bound to an sp3-hybridized C-atom. As a result, the trans-conformer (a>=180°) is consistently preferred over the cw-conformer, the energy difference usually being ca. 90 kJ mol 1 (Fig. 6.3). The relationship between the partial double-bond character of the amide bond (Fig. 6.3, right) and hydrolysis will be considered in Sect. 6.3. 

Such a difference in partial double-bond character has implications for the mechanism, and, hence, the reaction rate, of acid-catalyzed hydrolysis (Fig. 6.15). In delocalized peptide bonds (Fig. 6.15,a), protonation involves the carbonyl O-atom with its partial negative charge. In non-delocalized peptide bonds (Fig. 6.15,b), protonation involves the N-atom, which is rendered more basic by the lack of delocalization [73],... 

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. 

The partial double bond character of a peptide bond has its greatest effect in which structure of an enzyme ... 

The geometry of the amide bond helps determine the overall shape of a peptide or protein. The nitrogen of an amide is sp2 hybridized, so the electron pair on the nitrogen is in a p orbital that can overlap with the pi bond of the carbonyl group. The nitrogen is planar, and there is considerable double-bond character to the bond connecting it to the carbonyl carbon. In other words, the structure on the right makes an important contribution to the resonance hybrid for an amide ... 

In this case, the lengthening of the N-H and C=0 bonds, and the shortening of the C—N bonds as a consequence of hydrogen-bond formation can be measured by careful X-ray or neutron diffraction analyses, as described in Chapter 5. This type of -cooperativity is especially important in the main-chain hydrogen bonding of proteins, where it increases the double-bond character and hence the torsional rigidity of the peptide C-N bond. 

The C-N bond in the peptide groups has double bond character due to the -conjugation. 

The carbon-nitrogen bond is strengthened by its double-bond character, and the carbonyl carbon atom is less electrophilic and less susceptible to nucleophilic attack than are the carbonyl carbon atoms in compounds such as carboxylate esters. Consequently, to promote peptide-bond cleavage, an enzyme must facilitate nucleophilic attack at a normally unreactive carbonyl group. 

The partial double bond character of the peptide bond ... 

Figure 36.1. Geometry of the peptide link. Carbon-nitrogen bond has much double bond character. Carbonyl carbon, nitrogen, and atoms attached to them lie in a plane.

The double-bond character is also expressed in the length of the bond between the CiO and the NH groups. The C—N distance in a peptide bond is typically 1. .12 A. which is between the values expected for a C—N single... 

The concept of cis-trans (Z-E) isomerism, originally used for the description of the relative geometry of olefins, has been extended to many other functions which feature a double bond character (pseudo double bonds), such as amides, as well as single bonds with a partial or complete limited rotation due to steric or stereoelec-tronic effects. Cis-trans isomerization (CTI) therefore exists in non-re-bonded or overcrowded molecules that switch from a given stable conformational state to another. This is the case of biaryl compounds which have been utilized in organic chemistry as the basis of molecular switches and rotors [1,2]. Nature has also exploited CTI of single bonds to increasing molecular diversity, in particular with the bulky thyroxin, a thyroid hormone, and the well-known disulfide bond which plays a critical role in the structure of peptides and in the conformation of proteins. 

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