Masamichi Tsuboi

OPTICALLY ACTIVE LATTICE VIBRATIONS AS TREATED BY THE GF-MATRIX METHOD.

A general description has been given of an application of the Wilsons GF‐matrix method to the treatment of optically active lattice vibrations. As examples, formulas are derived for the calculation of the frequencies of the lattice vibrations of a one‐dimensional, the diamond, and CaF2 lattices.

Application of Infrared Spectroscopy to Structure Studies of Nucleic Acids

Abstract The purpose of this review is to show the extent to which infrared spectroscopy has been and will be useful for elucidating the molecular structures of nucleic acids.

Interaction of poly-l-lysine and nucleic acids

Interactions of poly- L -lysine with poly (I + C) and with thymus DNA in dilute solutions and in low ionic strength have been studied. The helix-coil transition of the polynucleotides in the reaction was followed by optical density at 248 mμ, or 260 mμ Both of these poly- L -lysine plus polynucleotide solutions gave a two-step transition, one of which (at a lower temperature) corresponds to the melting of the free polynucleotide double helix and the other (at a higher temperature) corresponds to the melting of a poly- L -lysine-polynucleotide complex. These transition temperatures are independent of the poly- L -lysine concentration added. However, as the poly- L -lysine concentration increases in the mixture, the hyperchromicity at the first transition decreases proportionately, together with a corresponding increase of hyperchromicity at the second transition. The poly- L -lysine-polynucleotide complex and the free polynucleotide were resolved by means of sucrose density-gradient electrophoresis. The behavior of the DNA molecules in the binding reaction can be monitored by the help of 32P-labeled DNA in the electrophoresis experiments. These results show that at room temperature and in a dilute salt solution, the poly- L -lysine-polynucleotide binding reaction is quantitative, irreversible and with a definite stoichiometric ratio. The lysine/nucleotide ratio in the poly- L -lysine-DNA complex was determined to be 1 : 1 and in the poly- L -lysine-poly (I + C) complex to be 0-5 : 1.

Molecular Geometry in an Excited Electronic State and a Preresonance Raman Effect

Observations of Raman spectra of various molecules at different exciting laser wavelengths lead to an empirical rule. If a Raman line becomes stronger when the exciting frequency is brought closer to the frequency of an electronic band, this means that the equilibrium conformation of the molecule is distorted along the normal coordinate for the Raman line in the transition from the ground to the excited electronic state.

Assignments of the vibrational frequencies of glycine

Abstract Infra-red spectra of α-glycine, α-glycine-D3, glycine-hydrochloride, glycine-hydro-chloride-D3, Na-glycinate, and Na-monochloroacetate have been compared in the NaCl region. Infra-red spectra of α- and γ-glycine and α- and γ-glycine-D3 have been observed in the KBr region. A dichroic measurement has been made on the single crystal of γ-glycine, in which all the glycine molecules are arranged almost in the same direction. Based on the results a complete assignment has been made of the fundamental vibrational frequencies of glycine observed in the 1800–400 cm−1 region.

Infrared absorption spectra of protonated and deprotonated nucleosides

Abstract Infrared absorption spectra have been observed in the 1800-1450 cm−1 region of four nucleosides: cytidine, adenosine, uridine, and guanosine, in their deuterium oxide solutions at various pDs. The spectra have also been observed in their solid states obtained from acidic, neutral (H2O and D2O), and alkaline solutions. The authors discuss (a) the identity and non-identity of the general features of the spectra obtained at different pHs and pDs, (b) the double-bond stretching frequencies observed in the deuterated nucleosides, (c) the NH2 and NH bending frequencies observed in the undeuterated nucleosides, and (d) the probable configurations of the protonated or deprotonated nucleosides with their correlations to the observed spectra.

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.

Conformation-sensitive Raman lines of mononucleotides and their use in a structure analysis of polynucleotides: guanine and cytosine nucleotides

Abstract Raman spectra are presented for nine crystals containing the guanosine residue and ten crystals containing the cytidine residue whose conformations are known from their X-ray crystallographic analyses. A nearly complete set of assignments of all the observed Raman lines in the 1700—150 cm−1 range is proposed on the basis of a previous normal coordinate treatment of guanine and cytosine with a set of force constants determined by an ab initio MO method, and on the basis of a mutual comparison of the observed spectra. A number of conformation sensitive Raman lines are found here, and several rules on the structure—spectrum correlations are proposed. Raman spectral features in the 1400—1300 cm−1 and 700—600 cm−1 ranges seem to reflect sensitively and regularly the conformation of the guanosine residue, namely its ribose-ring puckering state at the torsion angle around its glycosidic bond. A spectral feature in the 1300—1200 cm−1 range is found to be sensitive to the cytidine conformation. The position of a strong Raman line in the 900—750 cm−1 region, on the other hand, seems to indicate a particular set of torsion angles along the PO5′C5′C4′C3′O3′ backbone. In the light of these proposed rules, the so-called B-form poly [d(GC)].· poly[d(GC)] in solution must have an O4′endo-anti guanosine, a C2′endo-anti cytidine, and an “alternating B” backbone as proposed by Klug [7] while its Z-form should have a C3′ endo-syn guanosine, a form of cytidine in between C2′endoC1′exo-anti cytidine, and a ZI form backbone, as defined by Wang [41].

Normal vibrations of glycine and deuterated glycine molecules

Abstract Infrared absorption spectra of the α-form crystals of glycine (NH3+CH2COO−), glycine-d3 (ND3+CH2COO−), glycine-d2 (NH3+CD2COO−) and glycine-d5 (ND3+CD2COO−) have been observed in the spectral region of 4000–280 cm−1. A normal co-ordinate treatment has been made of each of these four molecules as a seven-body system. Based upon the results of these observations and treatment, discussions are given on the normal vibrations of glycine molecules.

15N isotope effects on the vibrational frequencies of aniline and assignments of the frequencies of its nh2 group

Infrared absorptions of aniline in which 31.9% of nitrogen is N/sup 15/ and 68.1% is N/sup 14/ were examined in dilute CCl/sub 4/ and CS/sub 2/ solutions by means of a grating instrument. For five bands at 3481.4, 3395.2. 1618.9, 1276.1, and 1114.6 cm/sup -1/ appreciable isotope shifts were observed. It was shown that these bands are to be assigned, respectively, to NH/sub 2/ antisymmetric stretching, NH/sub 2/ symmetric stretching, NH/sub 2/ bending, C-N stretching and NH/sub 2/ rocking (or twisting) vibrations. (auth)