Assignments normal mode analyses

Integration over the PDOS in Fig. 9.35a yields much smaller composition factors for the resonances at Vi, V2, and V3. This finding suggests that Vj, V2 and V3 are not pure stretching modes but contain considerable contributions from bending modes [89]. Normal mode analysis confirms this qualitative assignment [91]. 

From the resonance Raman spectra of phthalocyanine monolayers on different metals and a normal mode analysis, Palys et al7, conclude that the Raman band at 678 cm" is described by an in-plane macrocycle mode coupled to an out of plane CH deformation. Moreover they conclude that the phthalocyanine molecule is bonded via nitrogen atoms to a glassy carbon surface, and through the metal ion when the molecule interacts with a gold surface. On this basis it was proposed that this band is due to an in and out of plane concerted tt electronic system motion, corresponding to the breathing mode coupled to the out of plane CH vibration (pCH). This assignment explains the presence of this band in the... 

The study of the confoimational defects in polymethylene chains has been tackled some time ago in a systematic way by the school of Snyder by normal mode analysis of short-chain molecules (see, for example [104]) and by our group at Milano using NET [95, 101]. The results by both techniques are very similar. In the previous discussion in Figure 3-14 we have pointed out that a few peaks in the calculated g(v) for infinite trans polyethylene do not find corresponding infrared and/or Raman lines to be assigned to k = 0 motions. These additional experimental peaks are just an evidence of the existence of extra structures which we can identify as conformational defects using the theory we are presently discussing. 

Because most of the molecules of interest in biophysics have very low symmetry, their vibrational modes cannot be described accurately as being either symmetric or antisymmetric, and the peaks in a Raman or resonance Raman spectrum cannot be assigned on the basis of simple selection rules. However, normal-mode analysis often can be used to identify the vibrational modes that are coupled most strongly to excitation of a chromophore. Isotopic labeling, chemical modifications of the chromophore, or site-directed mutagenesis can be used to shift a particular vibration to higher or lower frequency. 

The far-infrared band due to the B, vibration at KXT K was observed at 78.6 cm by Bertie and Whalley (1964). This vibrational assignment was supported by the deuteration study of Krimm and Bank (1965) and by the polarization study of Bank and Krimm (1968). On the other hand, a far-infrared band due to the B2 vibration was hardly observed at 100° K Tasumi and Krimm (1967) made a normal-mode analysis of the Bi and B2 lattice vibrations, but the negligible intensity of the B2 bands as compared with the Bj band was not due to a difference of hybridizations of CH2 rocking modes. However, at 2 K, a weak far-infrared band possibly due to the B2 lattice vibration was reported at 109 cm by Dean and Martin (1967). 

Normal mode analysis is a versatile technique which is capable of providing a compact description of the vibrational dynamics of both small molecules and proteins and nucleic acids. For small molecules in particular, the technique is closely coupled to both the interpretation of vibrational spectroscopic data and the development of molecular mechanical force fields. When normal modes are determined using a force field model, vibrations of specific frequencies can be assigned to particular correlated atomic displacements. Force field parameters can be tested and refined by comparing... 

IR absorptions of these species were assigned to fundamental modes by comparison with the spectra of stable perfluoroorganic compounds. Normal coordinate analysis of the perfluoroethyl radical was performed and the valence force field of C2F5 was calculated (Snelson et al., 1981). 

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