Normal mode methyl groups

This table gives the displacements for the normal mode corresponding to the imaginary frequency in terms of redundant internal coordinates (several zero-valued coordinates have been eliminated). The most significant values in this list are for the dihedral angles D1 through D6. When we examine the standard orientation, we realize that such motion corresponds to a rotation of the methyl group. 

The IETS intensities for the methyl group vibrations of this species are shown in Fig. 9. The theoretical predictions of Kirtley and Hall (34) using KSH, and taking methyl group dipole derivatives from infrared measurements of ethane, assuming the C-S bond normal vs parallel to the interface, are also shown in Fig. 9. Note that for an orientation with the C-S bond normal, the symmetric C-H modes ( 2 and 9 ), which have net dipoles parallel to the C-S bond, are favored over the anti-symmetric modes ( 4,7, and 11), which have net dipole moments perpendicular to the C-S bond, but that for the C-S bond parallel to the surface the situation is reversed. The better, although by no means perfect, agreement between theory and experiment for the C-S bond normal tends to support the proposed orientation of Hall and Hansma. 

The early work of Miyazawa [109] described the normal modes of vibration for a polypeptide backbone in terms of the normal modes of 77-methyl acetamide (NMA). This established the basis for understanding these complex spectra in terms of normal coordinate analysis (NCA) f 7/0]. A detailed review of the development of this methodology is given by Krimm [7/7]. The foundation for the use of NCA resides in the useful approximation that the atomic displacements in many of the vibrational modes of a large molecule are concentrated in the motions of atoms in small chemical groups, and that these localized modes are transferrable to other molecules. This concept of transferability is the basic principle for the use of spectroscopic techniques for studying problems associated with peptide structure [777],... 

In this species the C-O bond is tilted awy from the surface normal and the CH2 group becomes a favorable position forythe excitation of both symmetric and asymmetric vibrations. Both vibrations would also be active for the methyl group. This species can therefore explain the spedtrum of ethanol adsorbate. The dipole moment of the C - O bond in the ethoxide may have a negligible component perpendicular to the surface, a situation which is unfavorable to observation of the corresponding mode (expected at c. 1000-1050cm ). 

Figure 2. Normal modes of cytochrome c in vacuum, (a) 4357th mode (CD mode) with co = 2129.1 cm-1, (b) 3330th mode (angle bending mode of Met80) with co = 1330.9 cm-1, (c) 1996th mode (a stretch-bend mode in Met80) with co = 829.9 cm-1. Only vectors on the terminal methyl group of Met80 in cyt c are depicted. These modes are strongly coupled with the Fermi resonance.

As shown in Figs. 2b and 2c, these modes are localized near the terminal methyl group of Met80 as well as near the CD mode. In such a case, resonant energy transfer (Fermi resonance) is expected as shown by Moritsugu, Miyashita, and Kidera [21]. We have observed similar behavior in cyt c when the CD mode was excited, and the energy immigration to other normal modes facilitated by resonance was followed. 

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