Raman spectroscopy backbone vibrations

Raman spectroscopy can offer vibrational information that is complementary to that obtained by IR. Furthermore, since the Raman spectrum reveals the backbone structure of a molecular entity [55], it is particularly useful in the examination of polymer film-coated electrodes. There are also some distinct advantages over in situ IR. For example, both the mid and far infrared spectral regions can be accessed with the same instrumental setup (in IR spectroscopy, these two regions typically require separate optics) [55]. Second, solvents such as water and acetonitrile are weak Raman scatterers thus the solvent medium does not optically obscure the electrode surface as it does in an in situ IR experiment. 

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... 

Raman Spectroscopy. The conformation of the PDHS backbone can be monitored by observation of the Raman spectrum, as reported by Kuz-many et al. (9) (Figure 10). Very intense bands associated with the vibration of the silicon atoms are observed at +17 C. The bands below 700 cm" have been assigned to the silicon backbone, whereas the weaker bands... 

Very few of the infrared studies of proteins have been carried out on aqueous solutions of the proteins. Except for the work of Koenig and Tabb (1), the few aqueous IR studies have been on single proteins. Correspondingly, most of the assignments of the backbone vibrations (the so-called Amide I, II, III, etc. vibrations) have been based on either Raman spectra of aqueous solutions (2) or on infrared spectra of proteins in the solid state (3). Where infrared solution spectra have been obtained, it has mostly been on D2O solutions (4) - not H2O solutions. Since these Amide I, II, III, etc. vibrations involve motion of the protein backbone, they are sensitive to the secondary structure of the protein and thus valid assignments are necessary in order to use infrared spectroscopy for determining the conformations of proteins. 

Polymer Structure. In addition to visualization, profiling, thickness measurements and chemistry of polymer wear it is frequently desirable to know whether the polymer is in the amorphous or crystalline state because other properties relate to state. Raman spectroscopy is very useful in studying very low frequency modes associated with vibrations of polymer chain backbones and the lattice modes of polymer crystals. It complements infrared spectroscopy. 

In addition to the structural information on proteins that is obtained from the vibrations of the polypeptide backbone, the vibrations of the side chains can also give valuable information on the environment of the side chain and sometimes on the accessibility to protons and deuterons. The ability to probe the accessibility of the side chains of a protein is one of the important features of Raman spectroscopy for the study of protein dynamics. 

Qualitative analysis by Raman spectroscopy is very complementary to IR spectroscopy and in some cases has an advantage over IR spectroscopy. The Raman spectrum is more sensitive to the organic framework or backbone of a molecule than to the functional groups, in contrast to the IR spectrum. IR correlation tables are useful for Raman spectra, because the Raman shift in wavenumbers is equal to the IR absorption in wave-numbers for the same vibration. Raman spectral libraries are available from commercial and government sources, as noted in the bibliography. These are not as extensive as those available for IR, but are growing rapidly. 

Summary Ab initio calculations predict the existence of anti and gauche rotamers for the disilanes /BuXaSiSiXatBu (X = Br and I). For the chloro compound a third backbone conformer with a CSiSiC dihedral angle of 95° ortho) was located on the potential energy surface. Due to the fact that the vibrational spectra of these disilanes are hardly sensitive to the conformation around the Si-Si bond we have not been able to determine energy differences between conformers from variable-temperature Raman spectra. Infrared and Raman spectroscopy suggest that anti and twisted conformers are present in liquid and solid tBuCbSiSiCh/Bu. For X = Br and I the anti conformation is adopted in the solid state, as proven by X-ray diffraction and vibrational spectroscopy. 

Raman spectroscopy is a vibrational spectroscopic technique which can be a useful probe of protein structure, since both intensity and frequency of vibrational motions of the amino acid side chains or polypeptide backbone are sensitive to chemical changes and the microenvironment around the functional groups. Thus, it can monitor changes related to tertiary structure as well as secondary structure of proteins. An important advantage of this technique is its versatility in application to samples which may be in solution or solid, clear or turbid, in aqueous or organic solvent. Since the concentration of proteins typically found in food systems is high, the classical dispersive method based on visible laser Raman spectroscopy, as well as the newer technique known as Fourier-transform Raman spectroscopy which utilizes near-infrared excitation, are more suitable to study food proteins (Li-Chan et aL, 1994). In contrast the technique based on ultraviolet excitation, known as resonance Raman spectroscopy, is more commonly used to study dilute protein solutions. 

IR and Raman spectroscopies are very important tools for characterization of the chemical and physical nature of polymers. Due to the high sensitivity of IR spectroscopy to changes in the dipole moment of a given vibrating group, this technique is intensively used to identify polar groups. In contrast, Raman spectroscopy is especially helpful in the characterization of the homonuclear polymer backbone due... 

Note dimer refers to 2,4-diphenylpentane and trimer refers to 2,4,6-triphenylheptane Data from B. Jasse, R.S. Chao andd J.L. Koenig, Journal of Raman Spectroscopy, 1979, 8, 244. Data obtained by Kellar and co-workers [52] i8> > 4> 2 ll fundamental vibrational modes. Herzberg nomenclature 6b> 4 lob i6b> lu )> )> and Vjo = fundamental vibrational modes, Wilson Nomenclature. vibrational assignment not made. On Wilson Nomenclature Vp v - derived from in-plane vibrations of phenyl ring, Vjj, v, and P (CH2j derived from out of plane modes or backbone motions, t = trans form polymorph, g = gauche form polymorph Reprinted with permission from E.J.C. Kellar, C. Galiotis and E.H. Andrews, Macromolecules, 1996, 29, 10, 3515. 1996, ACS [52] ... 

Conventional MS in the energy domain has contributed a lot to the understanding of the electronic ground state of iron centers in proteins and biomimetic models ([55], and references therein). However, the vibrational properties of these centers, which are thought to be related to their biological function, are much less studied. This is partly due to the fact that the vibrational states of the iron centers are masked by the vibrational states of the protein backbone and thus techniques such as Resonance Raman- or IR-spectroscopy do not provide a clear picture of the vibrational properties of these centers. A special feature of NIS is that it directly reveals the fraction of kinetic energy due to the Fe motion in a particular vibrational mode. 

In summary, NIS provides an excellent tool for the study of the vibrational properties of iron centers in proteins. In spectroscopies like Resonance Raman and IR, the vibrational states of the iron centers are masked by those of the protein backbone. A specific feature of NIS is that it is an isotope-selective technique (e.g., for Fe). Its focus is on the metal-ligand bond stretching and bending vibrations which exhibit the most prominent contributions to the mean square displacement of the metal atom. 

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