Band assignments amides

Further evidence for these a-helix ROA band assignments in the extended amide III region comes from the ROA spectrum of poly-L-alanine dissolved in a mixture of chloroform (70%) and dichloracetic acid (30%), known to promote a-helix formation (Fasman, 1987), which shows strong positive ROA bands at 1305 and 1341 cm-1 (unpublished results), and of the cv-helix forming alanine-rich peptide AK21 (sequence Ac-AAKAAAAKAAAAKAAAAKAGY-NHg) in aqueous solution which shows strong positive ROA bands at 1309 and 1344 cm-1 (Blanch et al., 2000). 

Table 4-6 lists observed frequencies and band assignments of structure-sensitive amide vibrations. Here, we discuss only amide I and III bands for which abundant data are available. The general trends shown in the table below were found by correlating x-ray structural data with Raman frequencies. 

Table 4-6 Band Assignments of Amide Vibrations in /V-Methylacetamide (cm 1)...

Using this pulse sequence to estimate the nature of derivatization of Suwannee River fulvic acid with N-enriched hydroxylamine to leam more about the carbonyl functionality of fulvic acid, Thom et al.(76) obtained signals for the primary products as oximes. Additional signals of secondary products arising from Beckmann rearrangements of the initial oxime derivatives were identified as nitriles, secondary amides and lactams. The bands assigned to hydroxamic acid result from a reaction of esters with NH2OH and are evidence for the presence of esters in the fulvic acid. 

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. 

The best method to use for the estimation of protein secondary structure involves band-fitting the amide I band. The parameters required, and the number of component bands and their positions are obtained from the resolution-enhanced spectra. The fractional areas of the fitted component bands are directly proportional to the relative amounts of structure that they represent. The percentages of helices, -structures and turns are estimated by addition of the areas of all of the component bands assigned to each of these structures and then expressing the sum as a fraction of the total amide I area. The... 

In protein solutions the absorbance of a band near 1669 cm l is usually assigned to the antiparallel-B sheet conformation. However, both experimental observations and theoretical calculations indicate that B-sheet amide 1 vibrations have at least two bands, a strong absorption near 1635 cm, and a smaller one near 1680 cm l (25,31-33). Thus the assignment of this initial 1669 cm l band in the absence of a 1635 cm band to an B-sheet conformation may be incorrect. Other possibilities for this band assignment are an unordered conformation (1656-1658 cm l) (25) or a B-tum conformation (1680 cm l) (31), although the latter is less likely since this B-tum vibration has been observed to disappear... 

Table 7.4 Characteristic amide I band assignments of protein secondary structures. From Stuart, B., Biological Applications of Infrared Spectroscopy, ACOL Sales,...

Another tissue type—nails— was studied by Sowa et al., both in vivo and ex vivo [122]. Mid-IR (MIR) and NIR spectra were collected for viable and clipped human nails. Depfh profiling by MIR was performed non-intrusively by phofoacousfic specfroscopy (PAS). Near-infrared ATR, NIR diffuse reflecfance, and PAS were compared. Band assignments were made, such as the N-H stretch-amide II bend combination centered at 4868 cm in this basic study. They concluded that the lower-energy NIR-ATR, for purposes of fheir sfudy, gave the best results. 

Near-infrared spectra of lactams primarily show bands attributable to nonhydrogen-bonded amides. This is in contrast to linear secondary amides, which do show hydrogen-bonded peaks. The near-infrared region provides a means of distinguishing cis (cyclic) and trans (linear) amides, especially for hydrogen-bonding studies. Table 8.7 summarizes the band assignments for the unassociated lactam amide bands. 

N-H/C-N/C=0 [2 X amide I (2vC=0 stretching) and amide III deformation (C-N stretching/N-H in-plane bending) combination] for gamma-val olactam CHv-tCCV (15 + 9), benzene band assignment... 

Only those bands are given which are assigned to the reacting amide group. 

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