Volume 28(2) - Summer 2012

During data collection in single crystal structure analysis, a crystal is kept within the X-ray beam and rotated and oriented in various directions for hours to days. Therefore, the crystal mount should satisfy two contradictory conditions: it should hold the crystal steady for a relatively long period of time without blocking the incident X-ray beam. Some additional points should be considered when choosing the crystal mount. An ideal crystal mount, if such a thing exists, should meet all of the following conditions:

1. it should be completely transparent to the incident beam,
2. it shouldn’t block any diffraction from the crystal,
3. it should produce no extra diffraction,
4. it should be stable throughout data collection,
5. it should allow the crystal to be completely bathed in the X-ray beam, and
6. it should not damage the crystal.

It is almost impossible to satisfy all of these conditions simultaneously, but efforts should be made to satisfy as many as possible.

Conventionally, the crystal is glued to the tip of a glass fiber. This is a versatile method applicable to a wide range of crystals. However, there are some other useful options. By employing an appropriate mounting method, one can collect a good data set from a difficult crystal. In this article, the latest crystal mounting methods and tools will be introduced.
 

The method of single crystal structure determination has generally been applied to characterize crystalline material. However, due to the poor quality of crystal, micro crystals or twin crystals, data collection and/or the single crystal structure analysis cannot be employed on some samples. Furthermore, even if single crystals with the good properties are obtained, there may be some restrictions to the measurement environment.  For example, the crystals might have to be kept at low temperature or in the mother liquor. There is another method for determining single crystal structures, which uses powder diffraction data. Generally, it is easier to obtain a well-behaved powder sample than a single one.  Structure determination from powder diffraction data has been applied to powder samples of single crystals.  This has been accelerated by the rapid progress in instruments and software. At the same time, however, the powder crystal structure determination has an intrinsic disadvantage. The problem is that diffraction peaks in a whole pattern profile observed from a powder crystal are sometimes difficult to be resolved because of overlapping of more than two reflections. One source of overlapping reflections is the use of Kα₁–Kα₂ radiation.  Overlapping reflections can be caused by the X-ray wave length used or the optics. In other words, it is a key point to observe the whole pattern profile with less overlapping so that the structure determination from powder diffraction data can be successful.

A molecular complex containing more than two chemical compounds in a unit cell is called “cocrystal”. Presently, a cocrystal which includes an Active Pharmaceutical Ingredient (API) is often an ingredient for new pharmaceuticals. The physicochemical properties, such as the solubility, the rate of solution and the hygroscopicity of API itself, of the cocrystal are suggested are designed to be superior to the native API. Thus, pharmaceutical companies have been trying to make a variety of cocrystals. It is necessary to determine the pharmaceutical properties for each of the chemical compounds contained in the cocrystals.  Moreover, since a cocrystal may be difficult to produce in single crystal form, ab initio powder crystal structure determination is a necessary tool.

The separation of the characteristic Kα radiation into the Kα₁ and Kα₂ components is often difficult because of the low angular resolution of the optics utilized in general laboratory instruments used in the powder diffraction measurement. As a result, the presence of profiles observed by Kα₁ and Kα₂ lines makes the structure determination from powder diffraction data more difficult. In the present technical note, a multi-purpose X-ray diffractometer equipped with a high-resolution multilayer mirror, eliminating the Kα₂ component, is introduced. Moreover, an application of ab inito power crystal structure analysis is also introduced, utilizing the above mentioned instrument.  The high-resolution multilayer mirror system is “Kα₁ optical system”.

The fusion method in X-ray fluorescence (XRF) analysis is an effective sample preparation technique for getting accurate analysis results of powder samples, since the technique eliminates heterogeneity due to grain size and mineralogical effect. In addition, the homogenization of material property by vitrification makes it possible to expand the calibration range, such as making synthetic calibration curves by the use of reagents or applying the calibration to diverse materials.

A benchtop wavelength-dispersive X-ray fluorescence (WDXRF) spectrometer Supermini is compact and yet has excellent resolution and sensitivity for light elements. This report demonstrates that single calibration for diverse minerals and ores was established by the fusion method on the Supermini.

Crystallite size and strain affect the physical (mechanical, electric, magnetic and optical) properties of materials. It is quite important to quantify size and strain, and to clarify the relationship between them in the field of material science.

The effects of finite crystallite size and lattice strain can be observed as deformations in the shape of diffraction curves. Thus, information can be obtained by investigating their shapes. However, the deformation occurs due to not only size-strain effects but also instrumental effects.

In conventional estimation, only the width of the peaks is used, not the whole peak shape. To eliminate the instrumental effect, width correction is carried out by measuring standard samples and subtracting the breadths of peaks of the width standard sample from those of a sample being investigated. With the 2-theta dependence of the corrected peak width, we can extract the crystallite size and lattice strain quantities.

However, the method of subtraction depends on whether the peak shape is assumed to be Gaussian or Lorentzian. In addition to this, the peak shape will not necessarily express a Gaussian or Lorentzian function.  Moreover, so-called “super Lorentzian” peak shapes are reported for samples with broader distribution of crystallite size. Based on this, applied width corrections may have limited validity.

In contrast to the above, the fundamental parameter method (FP method) has recently been used to analyze the effect of profile shape originated from instrumental conditions. In the FP method, the peak shape is calculated by convoluting the instrumental profile shapes assuming a theoretical model of instrument and profiles originated from crystallite size and lattice strain.  In this way, we can obtain size-strain information and eliminate the instrumental effects without measuring standard samples.

Size distribution can also be quantified by analyzing the precise peak shape. Size distribution affects the sharpness close to the peak top and slow fading off of its tails.

In PDXL 2, crystallite size, size distribution and strain can be analyzed with the FP method more easily than the ordinary Rietveld method. In this report, theoretical background to analyze them and some applications of actual samples using PDXL are described.
 

In January 2012, Rigaku released the MiniFlex300 and the MiniFlex600, the latest models in the MiniFlex benchtop XRD series. The numerical designations indicate the generator performance of these systems, 300 W and 600 W respectively.

MiniFlex diffractometers are widely used in a variety of fields, such as ceramics, minerals, inorganic materials and pharmaceutical ingredients. They are small compared with conventional X-ray diffractometers— about one-twentieth the volume and one-tenth the weight.

Small-angle X-ray scattering (SAXS) is an important technique for generating low resolution structures of proteins in native solution. Moreover, SAXS provides information on aggregation, folding, unfolding, assembly and conformational changes of proteins in solution despite of the low resolution. BioSAXS-1000 is a two dimensional compact Kratky camera for SAXS measurements of biological macromolecules.  BioSAXS-1000 can be installed on a new Rigaku microfocus X-ray generator, such as the MicroMax-007 HF, FR-E+SuperBright or MicroMax-003, or on an existing Rigaku microfocus X-ray generator with an open port.

For the purpose of protein structure determination, one often uses X-ray crystallography, electron crystallography and NMR spectroscopy. X-ray and electron crystallography are methods for determining three dimensional structures of high molecular weight protein complexes at atomic resolution. However, X-ray and electron crystallography require single crystals or two-dimensional crystals, respectively. Furthermore, the crystal structures from X-ray and electron crystallography are static, restrained by the packing energy of the crystal. NMR spectroscopy requires stable isotope labeling and multi-dimensional experiments.  Moreover, NMR spectroscopy has molecular weight limitations.

Proteins are highly dynamic, and conformational and ordered-disordered structural changes play a crucial role in their functions. Static structural information is not suf?cient for investigating protein function. SAXS determines the dynamic three-dimensional solution structures of proteins in various solution conditions.  The acquired diverse information is useful both pre- and post-structure determination by X-ray crystallography.  SAXS provides complementary structure information for structural biology.

BioSAXS-1000 is a powerful tool to investigate dynamic structural biology.