BL02B1
Single crystal structure analysis using the large cylindrical Image-Plate camera
Lecturer: Kunihisa Sugimoto (JASRI/SPring-8)
Nobuhiro Yasuda (JASRI/SPring-8)
1. Outline of lecture
In this lecture we study to observe the X-ray diffraction of single crystal using thelarge cylindrical Image-Plate (IP) camera at BL02B1. Thus, we perform the data
reduction from image data and the determination of crystal structure.
2. The advantage of 2-D detector for data collection of single crystal X-ray diffraction
In general, there are two kind of two dimensional (2-D) detector for data collection ofsingle crystal X-ray diffraction, which one is IP, the other is a charge coupled device(CCD) detector. The advantages of 2-D detector are as follows;
1) A number of diffraction spots can be observed at one X-ray shot. It means total
measurement time is reduced.
2) Because the measured image is the projection image of reciprocal space, we caneasily understand a diffuse scattering or spots based on super-structure.
3) It is easy to re-perform data reduction from measured image after data collectionbecause all diffraction spots are recorded on images.
These advantages are very important factor even for synchrotron X-ray diffraction
experiment, which is limited experiment time.
3. Image Plate (IP)
IP of two dimension detector is the plastic film coated by the phosphor; BaFBr:Eu2+(Eu2+ doped BaFBr). It is possible for IP to record X-ray diffraction as a distribution of‘color centers’ in phosphor, which can proportionally estimate the intensity of X-ray.
‘Color centers’ generated by X-ray diffraction are read out by counting the intensity
fluorescence (λ≈ 390 nm), which stimulated by scanning the surface of IP by He-Nelaser (λ≈ 633 nm) beam. After reading out data, color centers are erased by the visible
light exposure, therefore, we can reuse the same IP for next measurement.
The advantages of IP are high dynamic range, large active area, good linearity ofdetected X-ray intensity and good efficiency for the wide X-ray wavelength. On the other
hand, the mechanical scanning of large area causes longer read-out time than CCD
detector which directly read out by electronic signals. For the details of IP and CCDdetector, refer the papers [1, 2].
4. Large cylindrical IP camera
In order to the development of the investigation of relationship between structure andfunction, the large cylindrical image-plate camera was installed in BL02B1 beamline
since 2007 (Figure 1) [3]. The features of this camera are as follows,
1) Large size image plate detector (350 x 683 mm)2) Two types of goniometers (single axis goniometer and three axes 1/4χ goniometer)
3) Helium flow type low temperature measurement system (20~400 K)
The details of this camera are tabled in Table 1.
Table 1Specifications of large cylindrical IP camera
Size of IP

350 mm x 683 mm

Pixel size

100 μm x 100 μm

Camera radius

191.3 mm

Resolution on 2θ

0.030°/pixel2θ coverage-60° ～ +145°

Figure 1 Large cylindrical IP camera
For the structure and electron density analysis, we must collect the X-ray intensity
data set with high accuracy. The advantages described in section 3 satisfy therequirements for the structure and electron density analysis. The large camera radius(191.3 mm) realized to collect the high resolution data using high energy X-ray beamand to install the equipments for the external field response experiment.
There are two goniometers on the large cylindrical IP camera (Figure 1). The 1/4 χ-axis goniometer can rotate the crystal to collect the complete data set with high angle
2θ. On the other hand, the single-axis goniometer can be installed the large and/or
heavy equipment to adapt for the various experiment conditions such as the low- andhigh- temperature cryostat, the humidity controller chamber, the gas absorption control
system and so on.
The data collection and reduction software are prepared for the external user, whichhave almost same interface as that of conventional instrument. Basically, it is easy tounderstand to perform the data collection and reduction with the large cylindrical IP
camera.
5. Observation of a reciprocal lattice map and three-dimensional structure
determination of organic compoundIn this lecture, we will carry out the sequential procedure of single crystal structure
analysis with a single crystal of organic compound. The contents are observation ofreciprocal lattice map, extraction of the diffraction intensity data from IP images anddetermination of three-dimensional structure. In this lecture, the experiment procedure
is as follows,1)

Brief introduction of the large cylindrical IP camera.

2)

Hold the single crystal on the top of the glass capillary by a glue.

3)

Mount the goniometer head to the large cylindrical IP camera.

4)

For centering of the crystal, adjust the crystal position to the center ofgoniometer with screw driver so that the crystal stays on the rotation center ofgoniometer, which the crystal remains in X-ray beam during measurement.

5)

Set the collimator and beam stop to the IP camera. The light and TV monitor
should be turned off. The light guide should move not to make a shade of X-raydiffractions.

6)

Close the experimental hutch (Exit sequence) and open down-stream shutter(DSS) to induce the synchrotron radiation into experimental hutch.

7)

Input the measurement conditions (ω, Δω, φ, χ and exposure time) to themeasurement software. For evaluation of the crystal, a few diffraction images(ω=0, 45, 90°) are measured to index to the diffraction spots.

8)

Check the shape of diffraction spots.

9)

For indexing, in order to know the orientation of measurement crystal, indexesof diffraction spot (hkl) are assigned with the data reduction software. If you
success the indexing, the three types of boxes (green, yellow and red boxes) arecovered on the diffraction spots. ‘Right-click’ on the box indicates the hkl index ofthat diffraction spot. If you find a series of hkl index (h00, 0k0 or 00l), you canunderstand a rule between the index and diffraction spot.

10) If you success the indexing correctly, you get a primary lattice parameter andlattice volume. You can approximately estimate the number of molecule in unit
cell (Z) with the equation, Z=V/(20×N), where V is lattice volume N is thenumber of the non-hydrogen atom in molecule.
11) Input the measurement conditions (ω, Δω, φ, χ and exposure time) to collect thewhole diffraction spots in the measurement software.
12) During the measurement, the detail of the compound and measurement areexplained.
13) For integration, diffraction intensities are extracted with the data reduction
software after measurement. The resolution is set to 0.7Å.
14) For merge data, intensities of diffraction spot extracted from each diffraction
image are merged. The data reduction software provides the crystal information
file and the intensity file (texray.inf and f2plus.dat).
15) With two files and structure determination software (shelxs-97 [4]), the crystal
structure is solved. The atom position and thermal parameters are refined withthe structure refinement software (shelxl-97 [4]).
16) Discussions on the determined structure.
6. Summary
In this lecture, we have determined the three dimensional (3-D) crystal structure oforganic compound using the large cylindrical IP camera at BL02B1. The single crystal
structure analysis can also determine the absolute structure as well as the 3-Dstructure with a precision of 0.001Å. In pharmaceutical field, the determination ofabsolute structure is essential to take a patent of a new medicine.
The visualization of 3-D structure gives one of the most important information toinvestigate the relations between the crystal structure and the functions, even if they
are induced by small change of electronic state. In BL02B1 beamline, the large
cylindrical IP camera will lead the precise structure analysis of single crystal such as
investigation of relationship between structure and function.
7. References
1. Y. Amemiya, J. Synchrotron Rad. (1995). 2, 13–21
2. Crystallographic Instrumentation (1998), edited by L. A Aslanov, G. V. Fetisov and J.
A. K. Howard, 95–112. Oxford University Press.
3. K. Sugimoto et al., AIP Conf. Proc. (2010) Volume 1234, 887–890
4. G. M. Sheldrick, (2008). Acta Cryst. A64, 112–122.