Issei Harada

Fundamental vibrational frequencies of 109 molecular forms of 38 polyatomic chain molecules consisting of the CH3, CD3, CH2 CD2, CHD, O, and S groups are given as an extension of tables of molecular vibrational frequencies published in the NSRDS-NBS publication series and in this journal. On preparing the tables in this part, an approach, different from that in the previous parts, based on the calculations of normal vibration frequencies was adopted. A set of force constants which explains all the frequencies of small molecules for which the assignments had been established was obtained and then the frequencies of larger molecules was calculated and compared with the frequencies observed in the infrared and Raman spectra. The tables provide a convenient source of information for those who require vibrational energy levels and related properties in molecular spectroscopy, thermodynamics, analytical chemistry, and other fields of physics and chemistry.

The doublet at 850 and 830 cm-1 in the Raman spectra of proteins containing tyrosyl residues has been examined as to its origin and the relation of its components to the environment of the phenyl ring, the state of the phenolic hydroxyl group, and the conformation of the amino acid backbone. Raman spectral studies on numerous model molecules related to tyrosine, including certain deuterium derivatives, show that the doublet is due to Fermi resonance between the ring-breathing vibration and the overtone of an out-of-plane ring-bending vibration of the para-substituted benzenes. Further examination of the effects of pH and solvents on the Fermi doublet and of the crystallographic data demonstrates that the intensity ratio of the two components depends on changes in the relative frequencies of the two vibrations. These in turn are found to be sensitive to the nature of the hydrogen bonding of the phenolic hydroxyl group of its ionization, but much less so to the environment of the phenyl ring and the conformation of the amino acid backbone. By use of the relative intensities of the doublet in model systems where the phenolic hydroxyl group is strongly hydrogen-bonded, weakly hydrogen-bonded, free or ionized, the reported Raman intensities of the doublets observed in the Raman spectra of several proteins have been interpreted. The results are compared with those obtained by other techniques.

In order to elucidate the structural details of doped polyacetylene (a highly conducting organic polymer), the optical absorption, Raman, and infrared spectra of not only trans-(CH)x doped with iodine, AsF5, and SO3 but also β-carotene doped with iodine and SO3 were studied. The infrared spectra of two kinds of isotopically substituted polyacetylenes (CD)x and (13CH)x doped with iodine were also observed. Analysis of the experimental results shows that upon doping each of the four vibrational branches (ν1–ν4) in the 1600–900 cm−1 region of a polyene chain splits into two groups, namely, the higher frequency group and the lower frequency one. The former group consists of the ’’gerade’’ vibrations of polyene parts which are not directly attacked by dopants but are perturbed along the chain, whereas the latter is made up of the ’’ungerade’’ vibrations of the positively charged polyene part with the doped site at its center. The Raman bands in the higher-frequency group of ν1 (mainly the C=C stretching mode) observed with various laser lines give definite information on the segments of conjugated trans double bonds existing in doped polyacetylene. The Raman spectra are also useful for clarifying the structures of dopants. In the infrared spectra of doped trans-(CD)x and (13CH)x the bands appearing on doping all showed respective isotope shifts which confirmed the view that these bands are of vibrational origin. In many respects doped β-carotene proved to be a useful model of doped trans-polyacetylene.

Abstract Raman Spectra of seven tryptophan derivatives in the crystalline state were examined to find Raman bands whose frequencies reflect the strength of hydrogen bonding at the N 1 H site of the indole ring or the conformation of the indole ring relative to the amino acid backbone. Two indole ring vibrations, W4 around 1490 cm −1 and W6 around 1430 cm −1 , showed a correlation between their Raman frequencies and the infrared frequency of the N‐1‐H stretching mode, an indicator of hydrogen bond strength. W4 and W6 increase in frequency with increase in hydrogen bond strength and the frequency variation is particularly large for W6. On the other hand, another indole ring vibration, W3, observed around 1550 cm −1 , changes in frequency as a function of the torsional angle, χ 2,1 , of the C‐2C‐3C‐βC‐α linkage. As the absolute value of χ 2,1 becomes larger and the C‐α atom moves away from the C‐2 atom, the W3 frequency increases. In the Raman spectra of proteins excited with visible radiation, the W3 band is usually strong and can be used as a conformational marker, whereas the W4 band is very weak and the W6 band is overlapped by strog scattering due to C–H bending vibrations of aliphatic side‐chains. In UV resonance Raman spectra, however, all these Raman bands are enhanced and may provide key information on the hydrogen bonding and conformation of tryptophan side‐chains.

Two Raman bands at 880 and 1360 cm-1 of tryptophan (Trp) side chains have been found useful in structural studies of the side chains in proteins. The frequency of the 880-cm-1 band reflects the strength of H bonding at the N1H site of the indole ring: the lower the frequency is, the stronger the H bonding is. The intensity of the 1360-cm-1 band, on the other hand, is a marker of the hydrophobicity of the environment of the indole ring: particularly strong in hydrophobic environments. It is also demonstrated that a combination of stepwise deuteration of the tryptophan side chains and difference spectrum techniques is useful to observe these marker bands due to each side chain separately. The states of six tryptophans in lysozyme revealed by this Raman spectroscopic method in solution are compared with those by X-ray diffraction in crystal. The Raman data on the outer four Trp's are consistent with the X-ray structure, whereas significant differences between solution and crystal are suggested for the strength of H bonding of the most and second most buried Trp's. Characterization of four Trp's in alpha-lactalbumin shows that the two outer Trp's are moderately H bonded to solvent water and closely surrounded by aliphatic side chains while the inner two are not H bonded nor closely surrounded by aliphatic side chains.