Amid I band

Hamm P, Urn M and Hochstrasser R M 1998 Structure of the amide I band of peptides measured by femtosecond nonlinear-infrared spectroscopy J. Phys. Chem. B 102 6123-38... 

Figure 11a shows a force-distance profile measnred for poly(L-glutamic acid) brushes (2C18PLGA(44)) in water (pH = 3.0, 10 M HNO3) deposited at 40 mN/m from the water subphase at pH = 3.0. The majority of peptides are in the forms of an a-helix (38% determined from the amide I band) and a random coil. Two major regions are clearly seen in... 

It is a supposition that the )9-sheet structure of neurotoxin is an essential structural element for binding to the receptor. The presence of -sheet structure was found by Raman spectroscopic analysis of a sea snake neurotoxin (2). The amide I band and III band for Enhydrina schistosa toxin were at 1672 cm and 1242 cm" respectively. These wave numbers are characteristic for anti-parallel -sheet structure. The presence of -sheet structure found by Raman spectroscopic study was later confirmed by X-ray diffraction study on Laticauda semifasciata toxin b. 

Silk fibers, a basic system with a uniaxial symmetry, have also been investigated by Raman spectromicroscopy [63] that is one of the rare techniques capable of providing molecular data on such small (3-10 pm diameter) single filaments. The amide I band of the silk proteins has been particularly studied to determine the molecular orientation using the cylindrical Raman tensor approximation. In this work, it was assumed that Co Ci, C2 and the a parameter was determined from an isotropic sample using the following expression of the depolarization ratio... 

Figure 10 shows polarized spectra of two types of silks recorded by Raman spectromicroscopy the dragline silk (the lifeline) of the spider Nephila edulis and the cocoon silk of a wild silkworm Sarnia cynthia ricini. The position of the amide I band at 1,668-1,669 cm-1 for both threads is characteristic of the /i-sheet... 

Both methods are also limited in accuracy of secondary structure determinations because spectral peaks must be deconvolved estimates are made of the overlapping contributions of different structural regions. These estimates may introduce error based on the reference spectra used and because deconvolution methods equate crystallographic secondary structure with the secondary structure of the protein in solution (Pelton and McLean, 2000). As amyloid fibrils are neither crystalline nor soluble, there may be even greater error in estimates of secondary structure. To compound the problem, estimates of /f-sheet content are less reliable than those of a-helix, because of the flexibility and variable twist of / -structure (Pelton and McLean, 2000). In addition, / -sheet and turn bands overlap in FTIR spectroscopy (Jackson and Mantsch, 1995 Pelton and McLean, 2000). Side chains also contribute to spectral peaks in both methods, and they can skew estimates of secondary structure if not properly accounted for. In FTIR spectra, up to 10-15% of the amide I band may arise from side chain contributions (Jackson and Mantsch, 1995). 

Fig. 9.28 Analysis of the CH-stretching region (3000-2800 cm ) and the amide I band around 1650 cm V (a) ER-FTIR spectrum of poly(2-ethyl-2-oxazoline) (PEOx) as grown on the triflate functionalized HUT SAM. (b) ER-FTIR spectrum of HUT SAM. (c) Subtraction result of (a)-(b). (d) Bulk spectrum of PEOx. In the spectrum to the left, a significant shift...

In the literature Raman spectroscopy has been used to characterize protein secondary structure using reference intensity profile method (Alix et al. 1985). A set of 17 proteins was studied with this method and results of characterization of secondary structures were compared to the results obtained by x-ray crystallography methods. Deconvolution of the Raman Amide I band, 1630-1700 cm-1, was made to quantitatively analyze structures of proteins. This method was used on a reference set of 17 proteins, and the results show fairly good correlations between the two methods (Alix et al. 1985). 

All amides show a carbonyl absorption band known as the amide I band. Its position depends on the degree of hydrogen bonding and, thus, on the physical state of the compound. 

FIGURE 3.28. 2-methylpropanamide. A. The N—H stretch, coupled, primary amide, hydrogen bonded asymmetric, 3352 cm-1 symmetric, 3170 cm1. B. Aliphatic C—H stretch, 2960 cm-1. C. Overlap C=0 stretch, amide I band, 1640 cm-1 see Table 3.3. 

C=0 Stretching Vibrations (Amide I Band) The C=0 absorption of amides occurs at lower frequencies than normal carbonyl absorption due to the resonance effect (see Section 3.6.10.1). The position of absorption depends on the same environmental factors as the carbonyl absorption of other compounds. 

Primary amides (except acetamide, whose C=0 bond absorbs at 1694 cm-1) have a strong amide I band in the region of 1650 cm-1 when examined in the solid phase. When the amide is examined in dilute solution, the absorption is observed at a higher frequency, near 1690 cm-1. In more concentrated solutions, the C=0 frequency is observed at some intermediate value, depending on the degree of hydrogen bonding. 

Simple, open-chain, secondary amides absorb near 1640 cm-1 when examined in the solid state. In dilute solution, the frequency of the amide I band may be raised to 1680 cm-1 and even to 1700 cm-1 in the case of the anilides. In th anilide structure there is competition between thering and the C=0 for the non-bonded electron pair of the nitrogen. 

All primary amides show a sharp absorption band in dilute solution (amide II band) resulting from NH2 bending at a somewhat lower frequency than the C=0 band. This band has an intensity of one-half to one-third of the C=0 absorption band. In mulls and pellets the band occurs near 1655-1620 cm-1 and is usually under the envelope of the amide I band. In dilute solutions, the band appears at lower frequency, 1620-1590 cm-1, and normally is separated from the amide I band. Multiple bands may appear in the spectra of concentrated solutions, arising from the free and associated states. The nature of the R group... 

Transient IR spectroscopy in the range of the amide I band is a direct tool to follow the structural dynamics of the peptide moiety. IR difference spectra on the bicyclic molecule bc-AMPB are plotted in Fig. 5. Shortly after excitation the absorption is dominated by a red shift. Such a red shift is expected for a strong vibrational excitation of the molecule. On the time-scale of a few picosecond this red shift decays to a large extent and is replaced by a dispersive feature of opposite sign at tD = 20 ps. At later delay times this feature changes details of its shape, it sharpens up and some substructure appears around 1680 cm 1. After 1.7 ns the shape is similar, but not completely identical to the difference spectrum recorded with stationary FTIR spectroscopy. This time dependence shows that the dominant structural change responsible for the IR difference spectrum occurs on the 20 ps time-scale and that minor structural changes continue until nanoseconds and even later times. 

Fig.1. (a) Absorption spectra and (b) 2D-IR pump probe spectra of the C=0 mode of crystalline ACN. 2D-IR spectra record the absorption change as a function of probe frequency and the center frequency of a narrow band pump pulse. The contour intervals represent a linear scale. Response of the amide I band upon selective excitation of the self-trapped states (c) and the free exciton peak (d) for two different delay times. The arrows indicate the position of the narrow band pump pulse. 

Besides self trapping two alternative explanations, Fermi resonance and conformational substates, have been previously discussed as well [2]. In a recent study [6] we compared the 2D-IR spectrum of ACN with those of two molecular systems, which show the same splitting in the amide I band, and which were chosen as simple representatives of the alternative mechanisms. The three 2D-IR spectra differ completely, albeit in a well understood way. Based on the 2D-IR spectroscopic signature Fermi resonance and conformational sub-states can be definitely excluded as alternative explanations for the anomalous spectra of ACN. The 2D-IR spectrum of the amide I mode in ACN, on the other hand, can be naturally explained by self-trapping, as dicussed above. 

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