Publisher Summary The vibrational spectrum of a molecule is determined by its three-dimensional structure and its vibrational force field. An analysis of this (usually infrared (IR) and Raman) spectrum can therefore provide information on the structure and on intramolecular and intermolecular interactions. The more probing the analysis, the more detailed is the information that can be obtained. Detailed analyses of the vibrational spectra of macromolecules, however, have provided a deeper understanding of structure and interactions in these systems. An important advance in this direction for proteins came with the determination of the normal modes of vibration of the peptide group in N-methylacetamide, and the characterization of several specific amide vibrations in polypeptide systems. Extensive use has been made of spectra-structure correlations based on some of these amide modes, including attempts to determine secondary structure composition in proteins. Polypeptide molecules exhibit many more vibrational frequencies than the amide modes. Over the years, some normal-mode calculations have provided greater insight into the spectra of particular molecules. However, these have often been based on approximate structures or have employed limited force fields. These force fields can now serve as a basis for detailed analyses of spectral and structural questions in other polypeptide molecules. The aim of this chapter is to present these recent developments in the vibrational spectroscopy of peptides, polypeptides, and proteins.

Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins.

Amide modes and protein conformation.

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A valence force field for the amide group

The infrared spectra of N,N-dimethylformamide (DMF) and N,N-dimethylthioformamide (DMTF) have been investigated in the range 4000–250 cm−1 Assignment of the frequencies of DMF has been made on the basis of normal coordinate analysis for DMF, DMF-15N, and DMF-d7 using Urey-Bradly, modified Urey-Bradley, and symmetrized valence force fields Calculations have been extended to N,N-dimethylthioformamide and N,N-dimethylselenoformamide, using the Urey-Bradley and symmetrized valence force fields The assignments for DMF from the modified Urey-Bradley field are found to be more satisfactory The frequency shifts on isotopic substitution and on complexation have been explained The results of the calculations are discussed in comparison with other related molecules

Infrared spectra and normal vibrations of n,n-dimethylformamide and n,n- dimethylthioformamide.

We review various visible and UV-resonance Raman experiments on model peptides such as N-methylacetamide and di- and triglycine which are aimed at exploring the structure and dynamics of these molecules. Whereas visible Raman spectroscopy probes the electronic ground state, the UV Raman technique is utilized additionally to obtain structural information about excited electronic states. This research is aimed at obtaining a spectroscopically determined force field, which can be transferred to polypeptides and proteins. We further argue that the capability of vibrational spectroscopy to probe the structure of peptides and proteins can be significantly improved by combining computational and spectroscopic studies on appropriate model peptides to calibrate wavenumbers and intensities of Raman and IR bands for the quantitative determination of structural parameters such as the dihedral angles. Copyright © 2001 John Wiley & Sons, Ltd.

J. Jakeš

Papers

Normal coordinate calculation of N-methylacetamide