Infrared spectroscopy model-compound approach

Vibrational spectroscopy has played a very important role in the development of potential functions for molecular mechanics studies of proteins. Force constants which appear in the energy expressions are heavily parameterized from infrared and Raman studies of small model compounds. One approach to the interpretation of vibrational spectra for biopolymers has been a harmonic analysis whereby spectra are fit by geometry and/or force constant changes. There are a number of reasons for developing other approaches. The consistent force field (CFF) type potentials used in computer simulations are meant to model the motions of the atoms over a large ranee of conformations and, implicitly temperatures, without reparameterization. It is also desirable to develop a formalism for interpreting vibrational spectra which takes into account the variation in the conformations of the chromophore and surroundings which occur due to thermal motions. 

The ligand-model vibrational spectroscopy approach has contributed strongly to fairly reliable identifications on metal surfaces of C2 species of the types 1, 2 (ethene type II spectra) (17), 3 (ethene type I spectra), 4 (ethene type I spectra), 8, and 13 (ethyne type B spectra) as well as to possible identifications of types 5, 7, 15 (ethyne type A spectra), 16, and 20. Approximate band positions and associated intensity distributions in the spectra from normal and perdeutero species should be considered together (/ 7). The correspondence of the infrared spectrum from 4 with type I spectra is less satisfactory for the C2D4 ligand than in most other cases. However an extra structural variable in this case is the degree of nonplanarity of the cyclic C2M2 skeleton, which may differ between the model compound and the surface species. 

This approach— the use of model compounds— is one of the best ways to put the technique of ultraviolet spectroscopy to work. By comparing the UV spectrum of an unknown substance with that of a similar but less highly substituted compound, you can determine whether or not they contain the same chromophore. Many of the books listed in the references at the end of this chapter contain large collections of spectra of suitable model compounds, and with their help you can estabHsh the general structure of the part of the molecule that contains the K electrons. You can then utilize infrared or NMR spectroscopy to determine the detailed structure. 

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