Amide vibrational modes, spectroscopy

IR spectroscopy is not the most useful tool for probing the structures of metal amide complexes. The assignment of M—N vibrational modes is not a simple task as such bands can be readily coupled to other vibrational modes involving the NR2 moiety.1... 

The possibility of characterizing the /1-turn content of proteins by i.r. spectroscopy has been advanced following normal mode calculations upon five-residue models of /3-turn, which show that the amide III vibrational mode (but not the I mode) is predicted at distinctly higher frequencies than earlier calculations of the same mode for tr-helices and /6-sheets. Further calculations have been reported in which the bond dihedral angles are fixed at the four typical sets of values found in insulin. The vibrational spectrum of an o-helix has been obtained at the harmonic approximation. Low frequency modes, the elasticity of the helix and the time dependence of fluctuations in local structural features were discussed. 

Vibrational spectroscopy has been used in the past as an indicator of protein structural motifs. Most of the work utilized IR spectroscopy (see, for example, Refs. 118-128), but Raman spectroscopy has also been demonstrated to be extremely useful (129,130). Amide modes are vibrational eigenmodes localized on the peptide backbone, whose frequencies and intensities are related to the structure of the protein. The protein secondary structures must be the main factors determining the force fields and hence the spectra of the amide bands. In particular the amide I band (1600-1700 cm-1), which mainly involves the C=0-stretching motion of the peptide backbone, is ideal for infrared spectroscopy since it has an large transition dipole moment and is spectrally isolated... 

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