S. Higuchi

A preliminary investigation on the molecular structure of rice dwarf virus ribonucleic acid

X-Ray diffraction and infrared absorption measurements have been made of a ribonucleic acid obtained from rice dwarf virus which was isolated from the infected rice leaves. On a fibre diagram obtained at 75% relative humidity, 52 independent reflections were observed. All of them are indexed on a hexagonal lattice with a = 40·0 A and c = 30·5 A. It was found that the unit cell contains three molecules, each of which is displaced along the c-axis direction by c /3 from the neighbours. Intensities of the reflections were used to calculate the cylindrically symmetrical Patterson function. From this Patterson function it was concluded that the ribose-phosphate chains form two intertwined helices one of which is displaced along the helix axis by 13·0 A from the other. Each helix has its axis parallel to the c -axis, a pitch of 30·5 A, and ten nucleotide residues per turn. On the basis of the infrared dichroism observed for the 1225 cm −1 and 1084 cm −1 bands, the orientation of the PO 2 − group has been determined. The O…..O line makes an angle of about 70° and the bisector of 2 − group in the A and B forms of DNA.

Intra-red absorption spectra of the single crystals of 1-methyl-thymine, 9-methyladenine and their 1:1 complex

Abstract Infra-red absorption spectra have been observed of thin sections of the single crystals of 1-methylthymine, 9-methyladenine, and their hydrogen-bonded 1:1 complex (AT dimer) by using the polarized radiation in the spectral region of 4000-400 cm −1 . The absorption bands due to the in-plane and out-of-plane vibrations are distinguished in the spectra of the sections perpendicular to the molecular plane. The directions of the transition moments were determined of some of the absorption bands in the spectra of the sections parallel to the molecular plane. Assignments of the absorption bands due to the NH and NH 2 deformation were made on the basis of the observed N-deuteration effects. A marked difference was observed between the spectra of the AT dimer and an equimolar mechanical mixture of 1-methylthymine and 9-methyladenine. The frequencies assignable to the out-of-plane vibrations of the NH and NH 2 groups were found to be sensitive to the manner of their hydrogen bonding.

Some considerations on the out-of-plane vibration bands of PhnX type molecules in the 800-670 cm−1 region in relation to the estimation of the twist angle θ of benzente rings from their intensities

Abstract The i.r. intensities of the out-of-plane CH bending and the ring out-of-plane deformation vibrations of 11 Ph n X type molecules ( n = 2 or 3) were analyzed in terms of the simple model that, when the intensities of the two modes belonging to the same symmetry species are summed up, the relative magnitudes between those sums belonging to the different species are determined by the twist angle θ of benzene rings. It was shown that the analysis of the intensities always yields the proper values of θ under one of the assumed assignments of the bands; thus, the assignments were examined in relation to the obtained values of θ . Finally, the spectra of the samples in CS 2 rigid solutions at low temperature were presented and discussed from a similar viewpoint.

Infrared spectra of transfer RNA's: II. Formylmethionine transfer RNA from Escherichia coli in aqueous solution

Abstract Infrared absorption spectrum has been observed in the 1450–1750 cm −1 region of formylmethionine transfer RNA (tRNA) from Escherichia coli in deuterium oxide solution with 0.2 M Na + or 0.005 M Mg 2+ . At 33°, the spectrum shows seven absorption peaks in the spectral region in question. On the basis of the positions and relative intensities of these peaks, the amounts of the adenine-uracil (AU) base pair, guanine-cytosine (GC) base pair, free adenine, uracil, guanine and cytosine residues are estimated. A calculated spectrum of 2 AU+17 GC+13 A+6 U+7 G+8 C (which corresponds to the “clover leaf” arrangement of the nucleotide sequence of this tRNA determined by Dube et al. 11,12 , is in agreement with the observed spectrum. On heating the solutions, marked changes are observed in the positions and intensities of the absorption peaks. These changes are explained as what are caused by breaking down the AU and GC hydrogen-bonded base pairs. The amounts of the remaining base pairs are estimated at each temperature.

Some considerations about the substituent effect on the infrared absorption intensities of symmetric stretching and bending vibrations of methyl group

Abstract Infrared absorption intensities of symmetric stretching and bending modes of methyl group have been measured for 13 compounds. Quite different dependences of intensities on the substituents attached to methyl group have been observed for each of the two modes. The similarity of the intensity behaviours between the substituent and solvent effects has been referred to. The factors determining the intensity changes have been discussed in terms of the electric effects of substituents. Finally, it is demonstrated that the qualitative understanding of the different intensity behaviours observed for each of the modes is possible with the approximate application of the Valence—Optical theory.

Experimental investigations on the concentration-dependences of the half-band widths of NO2 symmetric stretching vibration bands

Abstract The concentration-dependences of the half-band widths have been examined for the very intense i.r. absorption bands of NO 2 symmetric stretching vibrations of nitrobenzene, o -, m - and p -nitrotoluenes. It is shown that the linear character is remarkably pronounced in the patterns of the changes in the band widths with the concentrations. It is demonstrated that the observed data of the half-band widths (including those for the pure liquids) are expressed well enough by the empirical formulas, which contain, not only the term proportional to the square roots of the concentrations, but also the one proportional to the concentrations. The former corresponds to the vibrational relaxation of the resonance type, and the latter is inferred to be related to the local field effect.

Some considerations about the temperature dependences of half-band widths of infrared absorption bands

Abstract The temperature dependence of half-band widths of six i.r. absorption bands has been investigated for samples in solution. For the parallel bands of a molecule in the same solvent, a linear correlation between band widths and the reciprocals of the viscosity of the solvent has been used to suggest that the band broadening in this case is caused by the Brownian rotational motions of solute molecules. From the fact that the potential barriers determined from the temperature dependencies of half-band widths are characteristic of the solvents used, the role of the media in the broadening of bands has been considered.

Some considerations about the solvent effect on the infared absorption intensities of methyl iodide and methyl iodide-d3

Abstract Infrared absorption intensities of the bands corresponding to the three totally symmetric modes of methyl iodide and methyl iodide- d 3 have been measured in ten solvents. Quite different solvent dependences have been observed for each of the three modes. With the object of correlating these experimental data, an attempt has been made to interpret the intensity behaviours in terms of Gribovs bond-moment theory in which the complete set of bond—bond interaction terms is taken into consideration. It is demonstrated that the qualitative understanding of the different intensity behaviours observed for each of the modes is possible when consideration is given to the detailed forms of each of the major contributing terms.

Some considerations about the solvent effect on the half-band widths of i.r. absorption bands

Abstract The half-band widths of the CN stretching vibration band of CH 3 SCN in various solvents have been discussed in terms of the reorientational and the vibrational relaxations. The widths due to the two effects have been separated from the overall widths through the examinations of the temperature- and the concentration-dependences of the band widths, and the effect of solvents on each of the contributions of the two effects has been investigated. It is demonstrated that, first, as for the rotational effect, not only the viscosities of solvents but also their molecular weights act an important role in the band broadening due to the effect; second, as for the vibrational effect, the widths due to this cause are extremely sensitive to the polarity of solvents.