Amide V mode

The amide V mode is largely an NH out-of-plane bend with some CN torsion. 

The amide V mode, which seems to be very sensitive to chain conformation, is found as a strong IR band at 708 cm" and is fairly well predicted by the calculation. Its assignment to the Bu(l) species is likely on the basis of the structure, but it could also have an Au( ) component because of the orientation of the peptide group this can be decided only from polarized IR spectra on an oriented sample. 

The amide V mode, similar to (Gly) I, appears as a strong IR band at 706 cm" . The essential absence of any significant dichroism in this band in well-oriented specimens of )3-(Ala)n (Itoh et al., 1968) suggests the near superposition of components having parallel and perpendicular polarization. As can be seen, this is supported very well by the results of the calculation, which additionally indicate that a weak Raman band at 698 cm" should be assigned to amide V. 

The amide V mode is again found in the IR near 705 cm", and would seem to be a relatively constant band for )3 structures. 

The amide V modes also appear to be distinctive for )8 turns. Such modes are found, and calculated, in the a helix near 660 and 618 cm , and in the APPS near 705 cm. Except for the highest frequency, which seems to be characteristic of the turn type, these modes generally occur at lower frequencies 575-570 forjSi, 607-571 for)3n, and 589-573 for )8in- The presence of N-deuteration-sensitive bands in these lower frequency regions may therefore be diagnostic for a j8 turn. 

Observed and calculated frequencies of this molecule are compared in Table XXIX the agreement is reasonably good, except for some amide V modes. The strong amide I modes at 1670 (Raman) and 1650 (IR) cm" are well predicted, despite their frequency differences from modes of the standard structure (cf. Table XXIV). The strong amide II modes at 1543 and 1530 cm" are well accounted for, conformations 4 and 2... 

The amide V mode in NMA consists of CN t plus NH ob, although CO ob can make a small contribution (Rey-Lafon et al., 1973). In the polypeptide chain, CN t and NH ob are also the main components but other coordinates contribute significantly. Thus, the frequency of this mode depends not only on the strength of the hydrogen bond (Miyazawa, 1962), but also on the side-chain structure. We present in Table XXXIX the PEDs together with their N O and H — O bond lengths, for observed amide V modes of structures for which the normal-mode calculations have been done. 

Potential Energy Distributions" for Observed Amide V Modes... 

The amide V mode is at a similar frequency to that in )9-PLA, even though the PGI hydrogen bond is weaker. This may be because of the large CN t contribution and/or the somewhat different nature of the modes. 

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