Koichi Ushizawa

Raman scattering tensors of tyrosine

Polarized Raman scattering measurements have been made of a single crystal of L-tyrosine by the use of a Raman microscope with the 488.0-nm exciting beam from an argon ion laser. The L-tyrosine crystal belongs to the space group P2(1)2(1)2(1) (orthorhombic), and Raman scattering intensities corresponding to the aa, bb, cc, ab and ac components of the crystal Raman tensor have been determined for each prominent Raman band. A similar set of measurements has been made of L-tyrosine-d4, in which four hydrogen atoms on the benzene ring are replaced by deuterium atoms. The effects of NH3-->ND3 and OH-->OD on the Raman spectrum have also been examined. In addition, depolarization ratios of some bands of L-tyrosine in aqueous solutions of pH 13 and pH 1 were examined. For comparison with these experimental results, on the other hand, ab initio molecular orbital calculations have been made of the normal modes of vibration and their associated polarizability oscillations of the L-tyrosine molecule. On the basis of these experimental data and by referring to the results of the calculations, discussions have been presented on the Raman tensors associated to some Raman bands, including those at 829 cm-1 (benzene ring breathing), 642 cm-1 (benzene ring deformation), and 432 cm-1 (C alpha-C beta-C gamma bending).

Vibrational modes in thymine molecule from an ab initio MO calculation

Abstract Ab initio self-consistent field molecular orbital (SCF MO) calculations have been made of the thymine molecule for the equilibrium geometry, harmonic force constants, vibrational frequencies, vibrational modes, infrared intensities, and Raman intensities. The results have been correlated with the observed Raman and infrared spectra of thymine crystalline powder.

Raman tensors for the tryptophan side chain in proteins determined by polarized Raman microspectroscopy of oriented N-acetyl-l-tryptophan crystals

Abstract Polarized Raman spectra have been obtained from oriented single crystals of N -acetyl-l-tryptophan by use of a Raman microscope and 488.0 nm argon excitation. The crystal, of orthorhombic space group P2 1 2 1 2 1 , provides the relative Raman intensities I aa , I bb and I cc corresponding to the aa, bb and cc components of the crystal Raman tensor. The polarized Raman spectra of the crystal have been combined with depolarization ratios from solution spectra of randomly oriented N -acetyl-l-tryptophan and l-tryptophan to yield Raman tensors for each of the following vibrational normal modes of the indole moiety: N 1 H stretch (≈3416 cm −1 ), WI (≈1617 cm −1 ), W 2 (≈1576 cm −1 ), W 3 (≈1557 cm −1 ), W 4 (≈1487 cm −1 ), W 5 (≈1458 cm −1 ), W 6 (≈1424 cm −1 ), W 7 (≈1357 cm −1 ), W 7′ (≈1332 cm −1 ), W 16 (≈1010 cm −1 ) and W 18 (≈757 cm −1 ). These Raman tensors determined for the tryptophan residue in N -acetyl-l-tryptophan are proposed as being transferable to tryptophan side chains in proteins. A knowledge of Raman tensors for the tryptophan side chain should facilitate the determination of indole ring orientation in biological complexes amenable to investigation by the method of polarized Raman microspectroscopy.

Raman spectroscopic study on {100} facet of boron-doped chemical-vapour-deposited diamond crystals with Fano line fitting

We have investigated polarized Raman spectra on the {100} facet of B-doped CVD diamond single crystals grown under different diborane additions in the gas phase. An asymmetrical feature was observed on the one-phonon Raman line shape of B-doped diamond crystal which depended on the boron concentration. We have performed Fano line fitting for each one-phonon line of the Raman components. Fano parameters which were calculated from Fano line fitting quantitatively represented the asymmetry of the one-phonon line. The relation between Fano parameters and boron concentrations obtained in this study can predict a certain amount of boron concentration of B-doped diamond. The difference of the Fano asymmetric parameters q between that obtained from 〈100〉 and 〈110〉 decreased with increasing boron concentration. This tendency was similar to that observed in the relation between the crystallinity and boron concentration. We suggest that the asymmetry of the one-phonon line is dominantly induced by crystalline disorder with boron incorporation. Copyright

Raman scattering tensors in thymine molecule from an ab initio MO calculation

Abstract Ab initio SCF MO calculations have been made of the thymine molecule for the permanent polarizability and the polarizability derivatives with respect to the normal coordinates. The latter correspond to the components of the Raman tensors, and each of these tensors was brought into a visualized form by a transformation of the tensor axes into the principal system. For a comparison with such computational findings, a polarized Raman spectroscopic measurement has been made of a single crystal of thymine with 488.0 nm excitation. For most of the in-plane vibrations, calculated tensors were found to be well correlated with the observed Raman scattering anisotropy. On the basis of such correlations, discussions are given as for the polarizability oscillations caused by the atomic displacements in the molecule.

Localized raman tensors in some biopolymers

Abstract A general survey is given of the relations between the anisotropy of the Raman scattering intensities of a crystal and the effective Raman tensor of the molecule corresponding to the molecular vibration in question. Some of the Raman tensors determined by the use of these relations are discussed. The Raman tensor assignable to the CH 2 scissoring vibration at 1400 cm −1 is found to be not transferable between different molecules in different crystals. However, the amide I Raman tensor of the peptide group is found to remain nearly unchanged on going from a dipeptide crystal to a synthetic polypeptide fiber. The usefulness of such knowledge in determining the orientation of a functional group in a biological system is suggested.

Local Raman tensors in adenosine triphosphoric acid

Abstract A polarized laser (488.0 nm) Raman spectroscopic measurement has been made on a single crystal of a disodium salt of adenosine triphosphoric acid (Na 2 ATP·3H 2 O) by the use of a Raman microscope. The crystal belongs to an orthorhombic system of the space group P 2 1 2 1 2 1 , and has dimensions of 10, 100 and 100 μm along the crystallographic axes a , b and c , respectively. For each Raman band in the 300–1800 cm −1 range, the scattering intensity ratio I bb / I cc of the bb and cc polarization components has been determined. For a few bands, the relative intensities of the bc components were also estimated. To augment the data, the depolarization ratio of each Raman band of ATP has also been determined for its acidic (pH = 2.42) H 2 O and D 2 O solutions. From these experimental results, the shapes and orientations of the Raman scattering tensors which are considered to be localized in the adenine-H + portion and in the phosphate portion of the molecule have been derived.

Raman scattering tensors of thymidine

Abstract Polarized Raman scattering measurements have been made of a single crystal of thymidine by use of a Raman microscope with 488.0 nm excitation. The crystal belongs to the space group P 2 1 2 1 2 1 (orthorhombic) and the Raman scattering intensities of I aa , I bb , I cc , I bc , I ca and I ab , which correspond to the aa, bb, cc, bc, ca and ab components, respectively, of the crystal Raman tensor, have been determined for each Raman band. The depolarization ratios of the Raman bands of this nucleoside have also been measured for fully random molecular orientation in an aqueous solution. A single crystal of thymidine- 13 C 5 in which five carbon atoms of the deoxyribose moiety are uniformly substituted with 13 C atoms was also prepared and subjected to examinations similar to those for the normal thymidine crystal. From these experimental data, and by taking the known crystal structure into account, molecular Raman tensors have been determined for the 1665, 1642, 1365, 1235, 771 and 494 cm −1 bands assignable to the thymine moiety, and for the 898, 852 and 736 cm −1 bands assignable to the deoxyribose moiety. This information about Raman tensors is considered to be useful for determining the orientations of thymidine residues in a biological complex from polarized Raman scattering measurements of such a complex.

Local Raman tensors of cytidine and their orientations in poly(rI)·poly(rC)

Abstract Polarized Raman spectra of a cytidine single crystal have been observed with 488.0 nm excitation by use of a Raman microscope. For each Raman band, the relative intensities of aa, bb, cc, ab and bc tensor components have been determined. The depolarization ratios were also determined in a cytidine solution. The shape and orientation of the local Raman tensor were deduced for each prominent Raman band, i.e. its principal axes and relative magnitudes of its components ( r 1 = α xx α zz , r 2 = α yy α zz ). The tensor for a strong Raman band at 1254 cm −1 was assumed to have the principal x axis along the N1-C4 line, the y axis along the N3-C5 line, and r 1 = 13.2, r 2 = −6.1. The tensor of the 793 cm −1 band was assumed to have a similar axis system, and r 1 = 3.8, r 2 = 3.2. The tensor of the anisotropic band at 603 cm −1 was assumed to have the principal x axis along the C2-N1 line, the y axis along the C2-C4 line, and r 1 = −0.2, r 2 = 20. Such information about the cytidine tensors is useful in determining the orientation of this residue in a biological fiber. As an example, a poly(rI)·poly(rC) duplex fiber has been subjected to an examination.

Polarized raman spectrum of a single crystal of AZT

Polarized Raman scattering measurements have been made of a single crystal of AZT (3′-azido-3′-deoxythymidine) by the use of a Raman microscope with the 488.0 nm exciting beam from an argon-ion laser. The AZT crystal belongs to the space group P21 (monoclinic), and Raman scattering intensities, corresponding to the aa, bb, c′c′, and bc′ components of the crystal Raman tensor, have been determined for each prominent Raman band. Here, c′-axis was defined as an axis perpendicular to the a-axis in the ac plane. From these experimental data, and on the basis of the known crystal structure, localized Raman tensors have been determined, which are assignable to azido vibrations at 2088 and 1259 cm−1, to thymine at 1666, 1392, 1238, 771, and 495 cm−1 and deoxyribose vibrations at 870, 849 and 739 cm−1. The knowledge of these localized Raman tensors are considered to be useful for probing the orientation of the AZT molecule in a biological system involving it.