Amide secondary, combination bands

There is some correlation between molecular structure and band position for certain bands, but because these are often overtone and combination bands, their positions are not as structure-dependent as the fundamental bands in the mid-IR. For example, primary amines, both ahphatic and aromatic, have two absorption bands, one at about 1500 nm and the second at about 1990 nm. Secondary amines have only one band at about 1500 nm. As expected, a tertiary amine has no NH band. Amides with an — NH2 group can be distinguished from R— NH—R amides by the number and position of the N—H bands. The reference by Goddu has a detailed table of NIR structure-wavelength correlations. 

Sutherland, 1953). Secondary amides have a characteristic band near 3100cm". Miyazawa (1960) describes this band as the result of Fermi resonance of N—H stretching with the combination band of C=0 stretching and N—H in-plane bending in cis-amides, and the result of Fermi resonance of the N—H stretching with the overtone of the amide II band in tra/ts-amides. (When an overtone or combination band is located near a fundamental frequency, the band intensity of the former may... 

Primary amines show characteristic first overtone bands at 1450, 1550 and 1000 nm which represent the first and second overtones of N-H stretching bands. Tertiary amines produce no N-H overtones, but do produce C-H and 0-H stretching combination bands at 1260-1270 nm. The first overtones of the N-H stretching bands of aliphatic amines are shifted to lower wavelengths. Primary amides may be characterized by combination bands at 1930-2250 nm and an N-H stretching overtone band at 1450-1550 nm. Secondary amides produce overtone bands in the 1350-1550 nm region and combination bands in the 1990-2250 nm region. 

Because of the cyclic structure the NH and C=0 groups are forced into the cis configuration so that no band comparable to the amide 11 band in trans secondary amides occurs in lactams. A characteristically strong NH stretching absorption near 3200 cm occurs in the infrared, which is only weak to medium in the Raman. A weaker infrared band near 3100 cm" is due to a combination band of the C=0 stretching and NH bending vibrations. 

The main combination bands of secondary amides are summarized in Table 8.5. These bands are important in the analysis of proteins. As explained by Murray in his chapter on spectral comparisons,24 two of the combination bands of proteins lie on either side of the OH combination band of carbohydrates. Therefore, the shape of the spectral region near 4760 cm- (2100 nm) is... 

Baughman, E.H. and Mayes, D., NIR applications in process analysis. Am. Lafe, 54-58, October 1989. Krikorian, S.E. and Mahpour, M., The identification and origin of N-H overtone and combination bands in the near-infrared spectra of simple primary and secondary amides, Spectrochim. Acta, 29A, 1233-1246, 1973. 

N-H [vN-H and amide II deformation (N-H in-plane bending) combination] for secondary amides in proteins CONHj combination of amide A and amide II N-H stretching and C=0 stretching (amide I) combination N-H (vN-H and 5N-H combination) for gamma-valerolactam N-H combination band found in the spectrum of native RNase A (C=0 amide I band)... 

N-H combination band from secondary amides in proteins N-H [vN-H and amide 11 deformation (N-H in-plane bending) combination] for secondary amides in proteins N-H from protein... 

N-H combination band from secondary amides in native RNase A 2075 4820... 

In addition, for solid samples or peptides in nonaqueous solvents, the amide II (primarily in-plane NH deformation mixed with C—N stretch, -1500-1530 cm-1) and the amide A (NH stretch, -3300 cm-1 but quite broad) bands are also useful added diagnostics of secondary structure 5,15-17 Due to their relatively broader profiles and complicated by their somewhat weaker intensities, the frequency shifts of these two bands with change in secondary structure are less dramatic than for the amide I yet for oriented samples their polarization properties remain useful 18 Additionally, the amide A and amide II bands are highly sensitive to deuteration effects. Thus, they can be diagnostic of the degree of exchange for a peptide and consequently act as a measure of protected or buried residues as compared to those fully exposed to solvent 9,19,20 Amide A measurements are not useful in aqueous solution due to overlap with very intense water transitions, but amide II measurements can usefully be measured under such conditions 5,19,20 The amide III (opposite-phase NH deformation plus C—N stretch combination) is very weak in the IR and is mixed with other local modes, but has nonetheless been the focus of a few protein-based studies 5,21-26 Finally, other amide modes (IV-VII) have been identified at lower frequencies, but have been the subject of relatively few studies in peptides 5-8,18,27,28 ... 

These kinetics studies required development of reproducible criteria of subtraction of foe H-O-H bending band of water, which completely overlaps foe Amide I (1650 cm 1) and Amide II (1550 cm"1) bands (98). In addition, correction of foe kinetic spectra of adsorbed protein layers for foe presence of "bulk" unadsorbed protein was described (99). Examination of kinetic spectra from an experiment involving a mixture of fibrinogen and albumin showed that a stable protein layer was formed on foe IRE surface, based on foe intensity of the Amide II band. Subsequent replacement of adsorbed albumin by fibrinogen followed, as monitored by foe intensity ratio of bands near 1300 cm"1 (albumin) and 1250 cm"1 (fibrinogen) (93). In addition to foe total amount of protein present at an interface, foe possible perturbation of foe secondary structure of foe protein upon adsorption is of interest. Deconvolution of foe broad Amide I,II, and m bands can provide information about foe relative amounts of a helices and f) sheet contents of aqueous protein solutions. Perturbation of foe secondary structures of several well characterized proteins were correlated with foe changes in foe deconvoluted spectra. Combining information from foe Amide I and m (1250 cm"1) bands is necessary for evaluation of protein secondary structure in solution (100). 

There are a number of methods based on using the spectra of proteins with secondary structures known from X-ray data [707]. An example is the method of Williams [8,116] which analyzes the amide I band of the Raman spectrum for a protein of unknown structure in terms of linear combinations of amide I bands for proteins with known X-ray structure. Significant correlations were observed between the Raman and X-ray diffraction estimates of helix, P-strand, turn, and undefined. Correlations were also observed between a-helix and disordered helix, and between parallel and antiparallel p-sheets. 

The combination of infrared spectroscopy and hydrogen-deuterium exchange is a powerful technique for revealing small differences in protein secondary structure. Few proteins are composed solely of one type of structure, therefore several amide I and amide II frequencies may contribute to any amide I and II band. It is often difficult to resolve all of these frequencies in the difference spectrum, since some of the peaks have bandwidths which are smaller than the amide I or amide II bandwidth and are thus effectively hidden within the main peak. To resolve overlapping bands, second derivative spectra may be generated using a computer programme. The resultant spectrum is presented as absorbance/(wavenumber)2 versus wavenumber. 

In the IR spectra (table 2) of the encapsulated manganese complexes amide-bands are the dominating spectral features, just as for the free complexes. Evidence for one or another way of coordination comes from the analysis of the amide modes. The amide I bands, attributed to CO-absorption bands in the range 1650-1630 cm for secondary amides, are visible for most of the Mn(bpR)-Y samples. The amide II band is a combination of C-N stretch and C-N-H bending. 

The analysis of the amide I band to obtain the estimation of protein secondary structure content in terms of percentage helix, j3 strand, and reverse turn that was developed by Williams has proved very successful and has now been used by numerous workers.In this method the amide I region is analyzed as a linear combination of the spectra of the reference proteins whose structures are known. As noted above the Raman spectra of globular proteins in the crystal and in solution are almost identical, reflecting the compact nature of the macromolecules. Thus one may use the fraction of each type of secondary structure determined in the crystalline state by the X-ray diffraction studies for proteins in solution. If there are n reference proteins with the Raman spectrum of each of them represented as normalized intensity measurements at p different wave numbers, then this information is related by the following matrix equation ... 

In addition to the main 3280 cm" absorption, a number of secondary amides absorb more weakly at 3080 cm". This band is also associated with NH modes and, like the 3280 cm" band, it vanishes in dilute solution and is replaced by a single absorption at 3420 cm". The 3080 cm" band in trans amides has been identified as originating in an overtone of the amide II band (see below). However the band persists in cis amides and lactams when it must be ascribed to a combination tone. A similar explanation is given for the appearance of this band in soUd thioamides [85]. 

---