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ICR’s Shared Facilities, Equipment, and Resources

Equipment (facility)
Research field
(Principal investigator)
Features, performance, specifications, etc.

Organoelement Chemistry
(TOKITOH, Norihiro)

This X-ray single crystal structure analysis equipment irradiates an X-ray on a single crystal, collects, and analyzes its diffraction data to determine the atomic arrangement and molecular structure. This equipment employs a specialized X-ray reflection device, which enables data collection from microscopic single crystal samples that usually provide only weak reflection data with conventional equipment, allowing sufficient data to be obtained from compounds that only give microscopic single crystals.

Organoelement Chemistry
(TOKITOH, Norihiro)

Magnetic circular dichroism (MCD) measures circular dichroism (CD) spectra in a magnetic field. This is used to investigate the electron transition spectrum, transition assignment, and ring π conjugated systems, which cannot or are difficult to observe using conventional methods. The MCD spectrum is a plot of the differences in the molar attenuation coefficients against wavelength and wave number, or molar ellipticity in a magnetic field.

Structural Organic Chemistry
(MURATA, Yasujiro)

This device with a CCD detector is used to determine the structure of organic compounds and organic metal compounds. The measurement time ranges from approximately 6 to 24 hours at −173 °C or at room temperature (SMART APEX manufactured by Bruker Corporation).

Fine Organic Synthesis
(KAWABATA, Takeo)

This is an inverse placed double-focusing mass spectrometer with an ion optical system comprising magnetic and electric fields. It supports fast atom bombardment (FAB) and electron ionization (EI) as ionization methods. The maximum resolution is 60,000 (10% valley), allowing composition formulae to be determined. A mass range up to 2,400 Dalton can be measured at the maximum acceleration. It is equipped with an automatic tuning function for the ion source and various parameters.

Fine Inorganic Synthetic Chemistry
(TERANISHI, Toshiharu)

High-sensitivity X-ray diffraction (XRD) analysis on diverse samples, including crystalline states, powders, trace amounts, large bulk samples, and thin films. This diffractometer supports various measurements such as identification, quantitation, and orientation, stress application, microscopic parts, temperature variations, and high-resolution measurements.

Fine Inorganic Synthetic Chemistry
(TERANISHI, Toshiharu)

The BELSORP-miniX measures the specific surface area (m2/g) and pore size distribution (0.7~500 nm) by volumetric nitrogen gas adsorption technique. Up to four samples can be simultaneously analyzed with high level of precision.

Fine Inorganic Synthetic Chemistry
(TERANISHI, Toshiharu)

This heating system with a clean and energy-saving design enables rapid heating to ultrahigh temperatures (>2000°C within 1 minute) by utilizing electromagnetic induction. It is useful not only for ultra-high temperature rapid heating in the development of metallic and ceramic materials, but also for heat treatment of various samples under oxidizing, reducing, and inert atmosphere.

Polymer Controlled Synthesis
(YAMAGO, Shigeru)

A high brightness X-ray is concentrated using a multilayer film mirror and irradiated over a sample. The resulting diffraction/scattering intensity is quickly digitized using a two-dimensional semiconductor detector (PILATUS). The accompanying software performs structural analysis. The system supports both transmission and reflection measurement methods. The various attachments include heating and cooling, and tensile and shear stresses.

Polymer Controlled Synthesis
(YAMAGO, Shigeru)

Electronic spin resonator (ESR) (E500 manufactured by Bruker Corporation); X-band (9.4 GHz,) (CW), Magnet -5mT~1.45T. Temperature during a measurement (100-500 K) can be adjusted.

Polymer Controlled Synthesis
(YAMAGO, Shigeru)

Bruker Daltonics IMS-QTOF. An ion mobility Spectrometry (IMS) device coupled with quadrupole time-of-flight mass spectrometer (QTOF). IMS-QTOF offers a unique dimension of characterization and separation in complex mixtures by the difference in the collision cross-sections of molecules. Several ion sources such as ESI, APCI, APPI, and CSI, and MS/MS analysis are available.
Electron beam lithography equipment

Nano-Spintronics
(ONO, Teruo)

Electron beam lithographer can draw nanometer-scale patterns on a sample coated with a resist layer.

Biofunctional Design Chemistry
(FUTAKI, Shiroh)

This MicroFlex Reflectron, manufactured by the Bruker Daltonics, can measure the mass of biological polymers such as proteins, synthetic polymers, and organic compounds easily at high resolution. Mass measurements are possible for compounds of several tens of thousands Dalton. This is a powerful tool for determining the structures of polymers that have been difficult by nuclear magnetic resonance (NMR) spectroscopy. (Note: Usage terms and conditions and fees of the University Consortium for Joint Use of Research Facilities are applicable to use this equipment.)

Biofunctional Design Chemistry
(IMANISHI, Miki)

• Fluorescence (red, green, blue; LD488, SHG532, LD635), densitometry, phosphor imaging
• Scanning area (40×46 cm)

Molecular Biology
(AOYAMA, Takashi)

Microscopic particles of gold or tungsten coated with DNAs, which are accelerated using the pressure of helium gas, are introduced into cells. Targets include plant tissue, cultured animal cells, and cultured plant cells.

Chemical Biology
(UESUGI, Motonari)

Nipkow spinning disk confocal microscopy equipped with microlens array. Excitation laser wavelength: 405, 488, 561 nm; Objective lens: 10x to 100x; Features: autofocus, multi-point and timelapse measurement with a stage incubator.

Chemical Biology
(UESUGI, Motonari)

The only commercially available instrument that measures DLS and SLS, for size and molar mass, directly in situ in standard 96, 384 or 1536 microwell plates. Measures second virial coefficient A2 and diffusion interaction parameter kD.
Molecular Materials Chemistry
(KAJI, Hironori)
800 MHz NMR: Both liquid and solid can be imaged. Multinuclear probe, 5 mmφ 1H/109Ag to 31P; triple inverse probe, 5 mmφ 1H/13C and 15N; multinuclear probe, 10 mmφ 1H/109Ag to 31P; triple resonance Cross Polarization/Magic Angle Spinning (CP/MAS) probe; and high-speed rotation CP/MAS probe can be performed. Temperature can be adjusted.
Molecular Materials Chemistry
(KAJI, Hironori)
This device measures the carrier mobility in an organic semiconductor material by generating optically excited carriers within an organic layer using a nitrogen laser (excitation wavelength: 337 nm), and then conducting such excited carriers to the direction of the electric field. Temperature during a measurement can be adjusted.
Molecular Materials Chemistry
(KAJI, Hironori)
Thermal physical properties, such as the glass transition temperature, crystallization temperature, and melting point can be measured (manufactured by METTLER TOLEDO).

Molecular Materials Chemistry
(KAJI, Hironori)

600 MHz NMR. Multinuclear probe (5 mmφ, 1H/109Ag – 31P-19F) and triple-inverse probe (1.7 mmφ, 1H/13C, 15N) can be used. Temperature can be adjusted.

Molecular Materials Chemistry
(KAJI, Hironori)

400 MHz NMR. CP/MAS probe (4 mmφ), CP/MAS probe (7.5 mmφ), and orientation probe can be used. Temperature can be adjusted. Pulse width is 4 μs or shorter.

Molecular Materials Chemistry
(KAJI, Hironori)

600 MHz nuclear magnetic resonance (NMR) for liquids, which can perform multinuclear and multi-dimensional measurements of 1H to 14N. This NMR can also perform diffusion measurements by applying a magnetic gradient field (up to 1000 G/cm).
Hydrospheric Environment Analytical Chemistry
(SOHRIN, Yoshiki)
Finnigan ELEMENT2, Thermo Fisher This is a trace-element analysis system with the highest sensitivity and precision in the world. The target element is measured by ionizing with argon plasma and separating from interfering ions using a double-focusing mass spectrometer (resolution: 300 to 10,000). Simultaneous multi-element quantitative analysis is possible on more than 70 elements, down to the ppq (10-15) level.
Hydrospheric Environment Analytical Chemistry
(SOHRIN, Yoshiki)
ELAN DRC II, Perkin Elmer
This is a quadrupole Inductively Coupled Plasma Mass Spectrometry (ICP-MS) with a dynamic reaction cell (DRC). The DRC is placed between the ion lens and the quadrupole mass separating part. Molecular ions that pass through the ion lens are removed using a reactant gas (NH3) and the low-amplitude high-frequency quadrupole. The remaining target atom ions enter the quadrupole mass separating part without being affected by the reactant gas, and are separated by the mass-to-charge ratio (m/Z) before reaching the detector, dramatically reducing the detection limit for elements such as Fe and Ca that receive interference from molecular ions. A simultaneous multi-element quantitative analysis can be performed on approximately 70 elements down to the ppt (10-12) level.
Triple quadrupole LC/MS/MS system
(API 3000 LC/MS/MS system, manufactured by Applied Biosystems)
Molecular Microbial Science
(KURIHARA, Tasuo)
Mass range: 30 to 3,000 m/z. This equipment is suitable for mass spectrometry of polymeric compounds (e.g., proteins), quantitative analysis of various compounds, and fragment ion analysis using tandem quadrupole. MS/MS analyses, including product ion scan, precursor ion scan, and neutral loss scan, can be performed. It is connected to high performance liquid chromatography (HPLC), and is capable of Liquid Chromatography/Mass Spectrometry (LC/MS) and LC/MS/MS. In addition to a normal ion spray, a turbo ion spray is also available.

Molecular Aggregation Analysis
(MURDEY, Richard)

This photoelectron spectrometer, equipped with an electric-field deflection type electronic energy analyzer, observes the valence electronic structure and core electron level primarily for solid organic matter under an ultra-high vacuum. In observations of these structure and levels, vacuum ultraviolet ray (helium resonant line) and X-ray (magnesium alpha K-ray) are used as light sources, respectively. In situ measurements of a thin film that is formed by vacuum vapor deposition in a sample preparation room can be performed. Angle-resolved ultraviolet electron spectroscopy is also available by moving the energy analyzer.
Linear electron accelerator
(Currently out of service)

Particle Beam Science
(WAKASUGI, Masanori)

An electron beam from 60 to 100 MeV is available (maximum current, 100 mA; pulse width, 40 to 100 ns; a maximum repetition rate; 20 Hz). This is used for, for example, to calibrate detectors for the Tokai to Kamioka (T2K) neutrino experiments.
Electron accumulation ring
KSR

(Currently out of service)

Particle Beam Science
(WAKASUGI, Masanori)

This equipment can provide beams with duty factors (a ratio of beam supply time to a unit time) as high as several tens of percent by irradiating and accumulating electron beams from a linear electron accelerator (from 60 to 100 MeV) using the effects of resonance. This beam can be accelerated to 300 MeV to produce synchrotron radiation. It is also possible to place an internal target within the ring and analyze it through electron beam scattering on the target. Past work includes analysis of the nucleus structure of an atom captured in an ion trap placed in the ring through the scattering with a circling electron beam.

Laser-Matter Interaction Science
(INOUE, Shunsuke)

The system delivers 1 J (at the maximum), 10-fs pulses at a center wavelength of 800 nm and a variable repetition rate from a single shot to 10 Hz. This system also has a convergent irradiation system (in vacuum), which enables irradiation experiments on various types of materials. In addition, a short-pulse mode synchronous oscillator and a Q-switched Nd:YAG laser for excitation, which both are components of this system, can be used separately.

Laser-Matter Interaction Science
(INOUE, Shunsuke)

The ultrafast electron microscope for pump-probe measurements, which is composed of ultrafast electron pulses (pulse width: 90 fs, energy 350 keV, charge: 10 fC, repetition rate: 5 Hz, timing jitter < 15 fs RMS in several hours) and laser pulses from the ultra-high intensity ultrashort laser system.

Electron Microscopy and Crystal Chemistry
(KURATA, Hiroki)

Transmission electron microscopes and scanning electron microscopes with acceleration voltages ranging from 120 to 200 kV can be used. State analysis using atomic resolution observations, electron energy loss spectrometry energy filter imaging. or observations at the temperatures of liquid nitrogen and liquid helium can be also performed. A series of equipment to support sample preparation, including focused ion beam machining equipment, cryo-microtome, and ion-milling equipment, can also be used.
X-ray diffraction equipment for biological organisms

Structural Molecular Biology
(FUJII, Tomomi)

Single protein crystal X-ray diffraction equipment, which is comprised of two parts: (1) a monochromator and a total reflection mirror concentrating system, and (2) an imaging-plate (IP) type two-dimensional detector. This equipment can be configured according to the nature of the crystal, lattice constants, etc. A cryogenic device blowing nitrogen gas enables diffraction measurement at 100 K.

Organic Main Group Chemistry
(NAKAMURA, Masaharu)

Ultraprecision mass spectrometry [resolution: 1 million FWHM (full width at half maximum)] can be performed for a mass range from 100 to 10,000 m/Z with a sensitivity of 100 amol using a 7.2-T superconducting ion cyclotron detector. Atmospheric pressure matrix-assisted laser desorption/ionization (MALDI) and Electrospray ionization (ESI) are supported. MS/MS/MS analysis can be performed by the collision-induced dissociation (CID), electron-capture dissociation (ECD), or electron-transfer dissociation (ETD) method.
High-pressure synthesis equipment

Advanced Solid State Chemistry
(SHIMAKAWA, Yuichi)

This large high-pressure generator can reach beyond 50,000 atm and 2,000 °C (sample capacity 1 ml). Another piece of equipment can reach 150,000 atm (sample capacity 0.04 ml), allowing novel substances to be developed in extreme conditions.
Laser vapor deposition equipment

Advanced Solid State Chemistry
(SHIMAKAWA, Yuichi)

Pulsed irradiation from a KrF excimer laser (wavelength: 248 nm) on a material can generate a thin film by evaporating undesired materials. This equipment can observe the reflection high-energy electron diffraction during thin-film growth, allowing film growth to be controlled at the unit lattice level.

Chemical Life Science
(OGATA, Hiroyuki)

Supercomputer system, which is partly used for the GenomeNet service (http://www.genome.jp/), whose main service is the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, is available for internal use. This system centers on SGI UV1000 (total number of CPU cores is 3,072) equipped with databases related to molecular biology, chemistry, and drug discovery and wide-ranging software applications.