Exoskeletons of diatoms are constituted of amorphous silica and organic matter, called frustules. They are composed of two valves fit each other like a petri-dish, and connected by girdle bands. In this study, structural analyses of the silica-based compound in frustules were carried out using Fourier transform polarized infrared microspectroscopy (pol-mFTIR). Unpolarized spectrum of diatoms show strong peaks at ν≈1100 cm
−1 and small peaks at 800 cm
−1 in the region of ν=700-1500 cm
−1. The feature is similar to those of low-quartz and fuzed silica glass indicating the existence of the SiO
4 network structure. The slight difference of three band shapes may indicate different linkage ordering of SiO
4 tetrahedra in these materials. Polarized IR spectra of a pennate diatom show an anisotropy of absorption band, showing the existence of two Si-O bonds with different distances. Polarized IR spectra of Si-O band with long distances shows a sharp peak in the region ν=1051-1081 cm
−1. When the long-axis of pennate diatoms was set parallel to IR light oscillation, the absorbance took a maximum. Whereas the polarized IR spectra of short Si-O bonds shows a broad peak at ν≈1227 cm
−1. When the long-axis of pennate diatoms was set parallel to IR light oscillation, the absorbance took a minimum value. These results indicate that Si-O bonds with long distances exists along the long-axis of the diatom and short Si-O bonds exist along the short-axis. We applied models suggested by Seifert et al. (1982) to interpret Si-O-Si angle in the frustules. Si-O-Si angle from long Si-O bonds was smaller than ones from short Si-O bonds. The structural distortion generated with the anisotropic SiO
4 network may be stabilized by the presence of organic matters in diatoms. The pol-mFTIR technique used in this study has a possibility for the application to investigate structural anisotropy in other amorphous materials that show a broad amorphous profile in X-ray diffraction method.
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