Infrared (IR) vibrational spectroscopy is a well-established tool in materials and life-science research. This technique can obtain information regarding fundamentally important microchemical properties. Although it is widely used to analyze microchemical properties, the identification of chemical structure using vibrational spectroscopy at infrared wavelengths has been problematic because of the diffraction limits of conventional infrared microscopy, which result in low spatial resolution. For example, the spatial resolution of infrared (IR) spectroscopy is approximately 10 mm, but that of newly developed near-field IR spectra (NFIR) is 1 mm, or less. Therefore, sub-micrometer to sub-nanometer scale chemical structure analysis is difficult to achieve by conventional IR. Specifically, scientists have been hampered by difficulty to separate protein-associated small chemical compounds from biomineralized organisms. We have overcome this limitation by applying a newly developed nearfield optical technique and near-field optical microscope through NFIR with high spatial resolution. The combination of nearfield microscopy and spectroscopy enables spectra to be obtained with subwavelength spatial resolution for visible light. However, the application of the near-field optical technique to the mid-IR region has only been reported for microscopy thus far.1 The primary reason for this limitation is lack of availability of high-intensity sources and detectors for the IR region.In the present study, this technique was used with a soft coral, Lobophytum crassum, as a model calcifying organism. Soft coral is an important and integral part of marine ecosystems. It has an important role in benthic-pelagic coupling processes as a source of food for demersal grazers and predators, as a host of highly diverse microbial biomass, and as a bioeroder. Soft coral contains small spicules of calcium carbonate, called "sclerites." Sclerites can strengthen the base of the soft coral, and are used by scientists to assist in the identification of soft coral species. Sclerites are the major mineralized structures present in these organisms. To address this importance, in vitro crystallization experiments were carried out in the presence of matrix proteins extracted from sclerites.A supersaturated solution of Ca(HCO3)2 was prepared by purging a stirred aqueous suspension of CaCO3 with carbon dioxide. 2 An aragonitic solution was obtained by adding 50 mM MgCl2 to supersaturated solution. Crystallization experiments were carried out with and without the addition of 700 mg of soluble proteins (extracted from sclerites) to the solution (500 ml). The solutions were then allowed to sit for one month without further manipulation. The protein concentration in the organic matrix was measured by method of Lowry et al. 3 using chicken ovalbumin (Kanto Chemical, Tokyo, Japan) as standard. The precipitate crystals were harvested from the solution after completion of each experiment, and each sample was stored for near-field probing analysis. An aperturele...