Amide III mode

The purpose of the vibrational analysis of (Aib) was to determine the structure of this polymer in the thin films used for the electron-diffraction studies (Malcolm, 1977, 1983). It is therefore of interest to note from the results that a Sjo-helix structure is clearly favored. This is not so evident from the amide I modes, even though a larger splitting is predicted and observed between A and Ei modes for the 3io than for the a helix. Similarly, a smaller splitting (as observed) is predicted for the amide II modes of the 3io helix. Somewhat better agreement with the 3io helix is also evident for the amide III mode at 1280 cm but signifi-... 

From the comparisons in Table XV between calculated frequencies of a-(Ala) and a-(Aib) , we can also gain further insight into the effect of (in this case unusual) side-chain variation. The amide I and II modes are hardly affected, but signihcant changes are seen for amide III modes. For a-(Ala) , medium-intensity IR bands are observed corresponding to calculated 1278- (Ei) and 1262-cm" (A) modes for a-(Aib) , there is no... 

The predicted amide III modes of groups 2-4 fall roughly into two groups at 1289 1 cm" and fairly uniformly distributed in the range 1311-1296 cm". If external hydrogen bonding is not included, these frequencies are at 1280 2 and 1298-1287 cm". The observed amide... 

The calculations on insulin /3 turns, however, clearly indicate that the band at 1303 cm , and probably part of that at 1284 cm , can be assigned to )3 turns. In addition, normal-mode calculations on canonical /3 turns (Bandekar and Krimm, 1979a Krimm and Bandekar, 1980) have shown that they have characteristic amide III modes above 1300 cm" , in a region where such modes are not found for a-helix and -sheet structures. The 1303-cm" band assignment is thus strongly supported by these calculated results. Whereas the 1284-cm" band could be associated with the a helix, the fact that a band is predicted near this position for the j8 turns of insulin indicates that, at the very least, this band should be considered to be partly due to the presence of the latter structures. 

Although the so-called amide III mode has been described as the localized counterpart to amide II (Fraser and Price, 1952), and, as we have seen, contains NH ib and CN s in NMA, the situation is in fact much more complex for the polypeptide chain. The main point is that... 

Potential Energy Distributions for Observed Nonweak Amide III Modes... 

The amide III mode is also a mixture of NH ib and CN s, although other coordinates make significant contributions. Since CH3 symmetric bend (sb) is an important one, CH3 point-mass calculations [52, 5] distort the relative importance of CC s. As seen from Table 5-1, CO ib is a relatively large contributor in NMA and a... 

The amide III modes demonstrate an increasing complexity compared with the... 

The amide III mode region is quite complex, with mainly NH ib, CN s contributing near 1300 and 1200 cm where only weak bands are observed. In the expected region (1300-1200 cm ), the strong bands are due to CH twist (tw)-dominated vibrations. The NH ib contributions now extend to bands about 1400 and below 1200 cm . 

The ratio of the absorbance intensities of the infrared bands at 1265 and 1235 cm is commonly used in fibroin crystallinity estimations (27,28,29). The band at 1235 cm" is assigned to the Amide III mode of the random coil conformation, and the corresponding band of the P-sheet confonnation has been identified at 1265 cm" (30). Since these two peaks were not well resolved in the spectra under consideiation, intensity measurement of the two peaks was... 

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