Goniometer Head Research Articles

Tracing structural changes in energy materials: A novel multi sample capillary setup for in house powder X‐ray diffraction

AbstractLithium ion batteries (LIBs) are currently a major subject of applied electrochemical research as there is a fast growing demand of electrochemical energy storage, driven by the transformation of the automotive sector and the expansion of renewable energies. One of the key strategies to improve LIBs is the optimization of the cathode active materials (CAMs). Therefore, in order to find structure property relations, both crystallographic and electrochemical properties need to be investigated and well understood. However, standard laboratory powder X‐ray diffraction (PXRD) possibly comes to its limit when minor structural variations such as atomic defects, cation order, or minor impurity phases are addressed. In order to focus on such minor structural changes and to find decisive differences in crystalline properties of battery materials, a multi‐sample capillary setup for a multipurpose in‐house PXRD setup was developed. The latter is made up from a six‐circle diffractometer, a microfocus molybdenum rotating anode, and a 2D area detector. The capillary spinner itself is made from commercial components and simple custom‐made adapters. A goniometer head is installed on a rotary module and sample spinning is enabled by a 12 V gear motor. Mounted on a xyz‐stage of the diffractometer, the position of the rotating capillary exposed to the primary beam can be varied while remaining perfectly aligned in the center of the diffractometer. Hence, by packing up to 10 different powder samples separated from each other into a single glass capillary, subsequent measurements of all samples can be carried out without remounting or readjustment. Within a series of samples, the setup is extremely reliable, precise, and accurate, while errors originating from sample displacement, misalignment, or calibration are minimized.

Determination of the Friction Angle between the Wheat Ear and Stripper Fingers

Introduction. Determining the angle of friction between stripper fingers and a wheat ear is an important task aimed at finding the optimal design parameters and operating modes of stripping devices. When stripper fingers and wheat ears interact, the relative position of the ear glumes, flower glumes, and grains is densified. In this case, the spikelet surface roughness changes. Materials and Methods. A series of experiments was carried out to determine the angles of friction between a steel stripper fingers and wheat ears. Wheat varieties “Moskovskaya 40” and “Moskovskaya 56” were selected for the study. The experimental measuring installation is a frame with a rotatable platform mounted on it with the adjustable angle of rotation. The goniometer head provides the ability to fix the platform rotation angle value. The weight suspended from the stem of the plant imitated the forces arising in the process of stripping. The width and thickness of the wheat ear were also measured and recorded. Results. The influence of the size of the wheat ear on the angle of friction is determined. The results of the study are divided into two groups. The following values of the friction angles were obtained: 26.4–31.5° for the wheat with ear width of less than 10.4 mm; 22.0–27.1° for the wheat with ear width of more than 10.4 mm. Discussion and Conclusion. The angles of friction of wheat ears on the stripper fingers for wheat varieties specific to the Central region are obtained. The dependence of the angle of friction on the ratio of the geometric dimensions of the wheat ear and the slit width of the stripper fingers is established. When a wheat ear width is less than 10.4 mm, an effect of pinching the spikelets between the stripper fingers was observed. In this case, the coefficient of friction noticeably increased.

Fixed-Target Serial Synchrotron Crystallography Using Nylon Mesh and Enclosed Film-Based Sample Holder

Serial crystallography (SX) technique using synchrotron X-ray allows the visualization of room-temperature crystal structures with low-dose data collection as well as time-resolved molecular dynamics. In an SX experiment, delivery of numerous crystals for X-ray interaction, in a serial manner, is very important. Fixed-target scanning approach has the advantage of dramatically minimizing sample consumption as well as any physical damage to crystal sample, compared to other sample delivery methods. Here, we introduce the simple approach of fixed-target serial synchrotron crystallography (FT-SSX) using nylon mesh and enclosed film (NAM)-based sample holder. The NAM-based sample holder consisted of X-ray-transparent nylon-mesh and polyimide film, attached to a magnetic base. This sample holder was mounted to a goniometer head on macromolecular crystallography beamline, and translated along vertical and horizontal directions for raster scanning by the goniometer. Diffraction data were collected in two raster scanning approaches: (i) 100 ms X-ray exposure and 0.011° oscillation at each scan point and (ii) 500 ms X-ray exposure and 0.222° oscillation at each scan point. Using this approach, we determined the room-temperature crystal structures of lysozyme and glucose isomerase at 1.5–2.0 Å resolution. The sample holder produced negligible X-ray background scattering for data processing. Therefore, the new approach provided an opportunity to perform FT-SSX with high accessibility using macromolecular crystallography beamlines at synchrotron without any special equipment.

Microplates for Crystal Growth and in situ Data Collection at a Synchrotron Beamline

An efficient data collection method is important for microcrystals, because microcrystals are sensitive to radiation damage. Moreover, microcrystals are difficult to harvest and locate owing to refraction effects from the surface of the liquid drop or optically invisible, owing to their small size. Collecting X-ray diffraction data directly from the crystallization devices to completely eliminate the crystal harvesting step is of particular interest. To address these needs, novel microplates combining crystal growth and data collection have been designed for efficient in situ data collection and fully tested at Shanghai Synchrotron Radiation Facility (SSRF) crystallography beamlines. The design of the novel microplates fully adapts the advantage of in situ technology. Thin Kapton membranes were selected to seal the microplate for crystal growth, the crystallization plates can support hanging drop and setting drop vapor diffusion crystallization experiments. Then, the microplate was fixed on a magnetic base and mounted on the goniometer head for in situ data collection. Automatic grid scanning was applied for crystal location with a Blu-Ice data collection system and then in situ data collection was performed. The microcrystals of lysozyme were selected as the testing samples for diffraction data collection using the novel microplates. The results show that this method can achieve comparable data quality to that of the traditional method using the nylon loop. In addition, our method can efficiently and diversely perform data acquisition experiments, and be especially suitable for solving structures of multiple crystals at room temperature or cryogenic temperature.

Testing of a `hard' X-ray interferometer for experimental investigations.

A `hard' X-ray LLL interferometer is tested for experimental investigations. The interferometer has both a base and a `ceiling', which are rigidly connected through columns. As a result, the interferometer does not have uncontrollable preliminary moiré. The intensity distribution is uniform in the interfering beams. It is shown that the interferometer is very sensitive to minor mechanical stresses. As a result, the interferometer must be freely placed on the goniometer head. Constant-thickness fringes are obtained using a wedge with a vertically placed apex. The volumes available for specimen placement are limited due to the existence of the ceiling. These difficulties can be overcome. The hard interferometer can be used for object and deformation investigations.

A flow cell for the study of gas-solid reactions via in situ powder X-ray diffraction

This paper describes the development and testing of a novel capillary flow cell for use in in situ powder X-ray diffraction experiments. It is designed such that it achieves 200° of rotation of the capillary whilst still allowing the flow of gas through the sample and the monitoring of off gas via mass spectrometry, gas chromatography, or other such analytical techniques. This high degree of rotation provides more uniform heating of the sample than can be achieved in static cells or those with lower rotational ranges and consequently also improves particle statistics. The increased uniformity of heating provides more accurate temperature calibration of the experimental setup as well. The cell is designed to be held in a standard goniometer head and is therefore suitable for use in many laboratory and synchrotron instruments.

Magnetic electron density in Fe3O4 examined by RXMS at Fe K edge

"It is known that a difference-Fourier synthesis of the Fourier series provides a mean for the location of bonding electrons, by subtracting out the electron density of all atoms in the crystal structure. Here the Fourier technique in X-ray diffraction was applied to observe the magnetic electron density of magnetite Fe3O4. An asymmetrical ratio in the resonant X-ray magnetic scattering (RXMS) provides information on the magnetic moments, which can be estimated from an intensity difference between the right-handed and left-handed polarized X rays. The ratio is proportional to the real part of the product of the spin-contributed structure factor F(hkl) and the complex conjugation of charge-scattered F(hkl). Expanding the equations in difference–Fourier formalization, the spin density can be represented with the observed f""m of RXMS. Synchrotron RXMS experiments were performed at the PF-BL-6C beamline using an AFC-5u four-circle diffractometer. Through a diamond phase retarder the incident X rays were circularly polarized at the Fe K absorption edge, where a wavelength of λ = 1.7439 Å (E = 7.1094 keV) was selected within the pre-edge. A spherical crystal of 0.13 mm in diameter was mounted along the a3 axis with the glass fiber on rare-earth magnet and goniometer head. The intensity data of RXMS were collected for Bragg reflections up to 2θ = 1310. After crystal-structure refinements with scaling of the RXMS data, difference-Fourier syntheses were made in triclinic symmetry with a total of 165 reflections by using the software FRAXY. The syntheses are superior in examining the magnetic effect in the polarization difference and eliminating other effects such as charge scattering, experimental errors and the termination effect. The difference of magnetic electron density between left-handed and right-handed circular polarizations at E was estimated in the Fourier series of partially observed F(hkl). The magnetic electron density on Fourier maps will be discussed in the presentation."

Resonant X-ray magnetic scattering study of Ti-Mn-doped Ba ferrites

BaFe12O19 has M-type hexaferrite structure, giving strong uniaxial anisotropy of the magnetization along c axis. In doped BaTixMnxFe12-2xO19, the substitution of Fe3+ by a pair of Ti4+ and Mn2+ results in a weakening of the magnetic interactions due to the canting of magnetic moments. The crystal structure has a sequence of (Fe6O8) spinel and (BaFe6O11) hcp blocks, associated with five independent Fe sites: tetrahedral 4f1, bipyramidal 2b, and octahedral 2a, 4f2 and 12k sites. Single crystals synthesized by a flux method have cell dimensions of a = 5.8953(2) and c = 23.1887(8) Å and a = 5.9039(2) and c = 23.2047(8) Å for samples of x = 0.5 and 1.0, respectively. Each crystal was mounted with short glass fiber on rare-earth magnet and goniometer head. Conventional intensity measurements were made using a Rigaku AFC7 four-circle diffractometer with a graphite (002) monochromator for Mo Kα radiation. Site-occupancy experiments were performed by using a vertical-type four-circle diffractometer at PF-BL-10A. In this study the magnetic structure has been examined to use resonant X-ray magnetic scattering (RXMS) at the Fe K absorption edge in PF-BL-6C. Circularly polarized X rays produced by a diamond phase retarder were switched between right-handed (helicity=+1) and left-handed polarizations. An AFC-5u four-circle diffractometer was used in the geometry of horizontal scattering plane. Intensity measurements were made to collect as many as possible of Bragg reflections. Based on an asymmetrical ratio of the intensities between right- and left- handed circular polarizations, the intensity difference in the RXMS was estimated for each of reflections. A set of observed asymmetrical ratios was fitted to a model of spin orientation in crystal-structure calculations with the resonant magnetic scattering factors. A residual function in the least-squares fitting is useful to evaluate magnetic moments for individual sites, which is a multiplicity parameter refined in terms of atomic scattering factor. It gives a minimum in plot between site-multiplicity and residual function, assigning the multiplicity related to the canting of magnetic moment in the Fe sites. The magnetic structure obtained in this study is compared with those of M-type BaFe12O19 and BaTiCoFe10O19.

Structure determination from in situ diffraction with the Rigaku PlateMate

As crystallographers face increasing problems with crystallizing new proteins, in-situ screening in crystallization trays at room temperature is experiencing a renaissance. It saves a lot of time when screening large numbers of crystallization hits and it helps avoid crystal damage caused by human manipulation error (harsh manual handling, bad freezing) or changes in crystal properties (dehydration, wrong cryo-conditions). In certain cases, it is also possible to go beyond screening and collect enough data for structure solution, especially on an X-ray home source where a less intense beam helps minimize the devastations of radiation damage occurring at room temperature. The Rigaku PlateMate has proved itself as an efficient and easy-to-use in-situ screening tool on the field for the past two years. It is as easily mounted on a goniometer as a regular goniometer head and thanks to a plate adapter with SBS footprints, it accommodates most 96-wells plate types, from sitting and hanging drop to LCP plates. In addition, thanks to its narrow dimensions and aided by software to prevent collisions with the detector and the crystal viewing camera, the PlateMate can be used to easily collect data from crystals in situ. In this work, we present structure solution results obtained from data collected with the PlateMate on crystals from various proteins (native crystals or containing gold or iodine) and using one or multiple crystals to make up a complete data set.

Joint neutron/Xray cryocrystallography: developments for cryocooling experiments

Cryo-cooling of protein crystals is not often used in neutron crystallography. However cryo-temperatures are used to block the reaction processes at specific intermediate stages, and this has been widely used in X-ray studies (1); (2). In order to develop this area for joint neutron/X-ray applications, trypsin was chosen as a suitable system for which its interaction with the substrate succinyl-Ala-Ala-Pro-Arg-p-nitro-aniline could be studied (3). Here the neutron developments were carried out in parallel with complementary X-ray techniques, and also using in crystallo UV-visible and Raman spectroscopy. Various strategies for doing this have been tested. The installation of an N2-gas-cryostream system on the D19 single crystal diffractometer at the Institut Laue Langevin (ILL) and the development of a new carboloop mounting system, has opened new avenues to perform cryo-cooling experiments using a neutron source. Preliminary data collection carried out at the ILL and at the European Synchrotron Radiation Facility (ESRF), have confirmed the feasibility of the approach. A full description of the experimental procedures and results will be presented. As part of this a new carboloop mounting system has been developed that is suitable for both X-ray and neutron data collection. These mounts resolve the problems of activation and hydrogen incoherent scattering in neutron experiments We describe the use of these and their advantages over conventional X-ray mounting systems - including compatibility with standard magnetic goniometer heads and resistance to cryogenic temperatures.

ESRF/DBT/EMBL:BM14-2: MX station for in situ, dehydration and MAD experiments

BM14 was the first dedicated macromolecular crystallography (MX) beamline to come into operation at the ESRF during 1995. This experimental station has been designed specifically to produce MX diffraction data using Single/Multiple-wavelength Anomalous Diffraction (SAD/MAD) methods (www.bm14.eu). Currently, beamline is operated by a consortium between the ESRF, the EMBL-Grenoble and the Department of Biotechnology (DBT), India. Recently, the beamline optics was fully upgraded (hence the new denomination BM14-2). A four-time increase in beam brilliance is achieved with the concomitant reduction in average exposure time (~5s today versus 20s before), leading to a substantial gain in the screening capacity. Upgrade includes a new channel-cut crystal equipped with a second crystal pusher to reject high-energy harmonics. The latter device turned to be crucial for Sulphur-SAD experiment success rate. The special goniometer head is installed on microdiffractometer (MD2) goniometer which is capable of handling the CrystalDirect (CD) nanocrystallisation plates [1] so that any crystallisation hit can be exposed to the beam. The plate characteristics are optimal for in situ data collection and they produce diffraction patterns with significantly reduced background. A newly designed dehydration-to-cryogenic nozzle-changer device is also installed in order to avoid the down time between the experiments (such as, In situ screening, humidity control device (HC1), standard cryogenic data collection). European users may apply for access via the Biostruct-X program (www.biostruct-x.eu) both for CD plate nanocrystallisation trials and for beamtime. Users from India are encouraged to apply from DBT-Portal (http://process.mbu.iisc.ernet.in/BM14/index.jsp) for beamtime. The optics hutch refurbishment and implementation of the novel devices in the experimental hutch opens promising perspectives for collecting data at room temperature and that are of importance to the MX users.

Data collection and processing

Data collection and processing

The use of a mini-κ goniometer head in macromolecular crystallography diffraction experiments.

Most macromolecular crystallography (MX) diffraction experiments at synchrotrons use a single-axis goniometer. This markedly contrasts with small-molecule crystallography, in which the majority of the diffraction data are collected using multi-axis goniometers. A novel miniaturized κ-goniometer head, the MK3, has been developed to allow macromolecular crystals to be aligned. It is available on the majority of the structural biology beamlines at the ESRF, as well as elsewhere. In addition, the Strategy for the Alignment of Crystals (STAC) software package has been developed to facilitate the use of the MK3 and other similar devices. Use of the MK3 and STAC is streamlined by their incorporation into online analysis tools such as EDNA. The current use of STAC and MK3 on the MX beamlines at the ESRF is discussed. It is shown that the alignment of macromolecular crystals can result in improved diffraction data quality compared with data obtained from randomly aligned crystals.

Micro-PIXE on thin plant tissue samples in frozen hydrated state: A novel addition to JSI nuclear microprobe

Recently we completed a construction of a cryostat at Jožef Stefan Institute (JSI) nuclear microprobe enabling us to analyze various types of biological samples in frozen hydrated state using micro-PIXE/STIM/RBS. Sample load-lock system was added to our existing setup to enable us to quickly insert a sample holder with frozen hydrated tissue samples onto a cold goniometer head cooled with liquid nitrogen inside the measuring chamber.Cryotome-cut slices of frozen hydrated plant samples were mounted between two thin silicon nitride foils and then attached to the sample holder. Sufficient thermal contact between silicon nitride foils and sample holder must be achieved, as well as between the sample holder and the cold goniometer head inside the measuring chamber to prevent melting of the samples. Matrix composition of frozen hydrated tissue is consisted mostly of ice. Thinning of the sample as well as water evaporation during high vacuum and proton beam exposure was inspected by the measurements with RBS and STIM method simultaneously with micro-PIXE.For first measuring attempts a standard micro-PIXE configuration for tissue mapping was used with proton beam cross section of 1.2×1.2μm2 and a beam current of 100pA. The temperature of the cold goniometer head was kept below 130K throughout the entire proton beam exposure. First measurements of thin plant tissue samples in frozen hydrated state show minute sample degradation during the 10h period of micro-PIXE measurements.

Beamline AR-NW12A: high-throughput beamline for macromolecular crystallography at the Photon Factory

AR-NW12A is an in-vacuum undulator beamline optimized for high-throughput macromolecular crystallography experiments as one of the five macromolecular crystallography (MX) beamlines at the Photon Factory. This report provides details of the beamline design, covering its optical specifications, hardware set-up, control software, and the latest developments for MX experiments. The experimental environment presents state-of-the-art instrumentation for high-throughput projects with a high-precision goniometer with an adaptable goniometer head, and a UV-light sample visualization system. Combined with an efficient automounting robot modified from the SSRL SAM system, a remote control system enables fully automated and remote-access X-ray diffraction experiments.

Upgrade of automated sample exchanger SPACE

SPACE (SPring-8 precise automatic cryo-sample exchanger) is an automated sample exchanger for cryo-cooled protein crystals, developed at SPring-8. Since the start of its operation, SPACE has been continuously improved and upgraded to cope with the requirements of new beamlines and users. One important upgrade of SPACE provides support for conventional metal-base pins, which are attached to the goniometer head magnetically. Other hardware improvements include increasing the sample storage capacity. The upgraded version of SPACE, as reported here, is continuously operated and is an essential component of beamline operation at SPring-8.

Automatic loop centring with a high-precision goniometer head at the SLS macromolecular crystallographybeamlines.

Automatic loop centring has been developed as part of the automation process in crystallographic data collection at the Swiss Light Source. The procedure described here consists of an optional set-up part, in which the background images are taken, and the actual centring part. The algorithm uses boundary and centre-of-mass detection at two different microscope image magnifications. Micromounts can be handled as well. Centring of the loops can be achieved in 15-26s, depending on their initial position, and as fast as manual centring. The alignment of the sample is carried out by means of a new flexural-hinge-based compact goniometer head. The device features an electromagnet for robotic wet mounting of samples. The circle of confusion was measured to be smaller than 1 µm (r.m.s.); its bidirectional backlash is below 2 µm.

X-rays generated by relativistic electrons in a waveguide radiator mounted inside a betatron

We have observed X-ray emission from an X-ray waveguide radiator excited by relativistic electrons in the experiments carried out at Tomsk betatron B-35. A stratified radiator of a new type was mounted on a goniometer head inside the betatron toroid. The radiator consisted of the W–C–W layers placed on Si substrate. The photographs of the angular distributions of the radiation generated in the radiator by 20 and 33 MeV electrons showed the waveguide effect of the three-layer structure on X-rays generated in the radiator. The effect appeared in the angular distribution of the radiation as an additional peak attributed to guided X-rays inside a wide cone of usual Bremsstrahlung.

The Crystal Structure of Human Transketolase and New Insights into Its Mode of Action

The crystal structure of human transketolase (TKT), a thiamine diphosphate (ThDP) and Ca(2+)-dependent enzyme that catalyzes the interketol transfer between ketoses and aldoses as part of the pentose phosphate pathway, has been determined to 1.75 Å resolution. The recombinantly produced protein crystallized in space group C2 containing one monomer in the asymmetric unit. Two monomers form the homodimeric biological assembly with two identical active sites at the dimer interface. Although the protomer exhibits the typical three (α/β)-domain structure and topology reported for TKTs from other species, structural differences are observed for several loop regions and the linker that connects the PP and Pyr domain. The cofactor and substrate binding sites of human TKT bear high resemblance to those of other TKTs but also feature unique properties, including two lysines and a serine that interact with the β-phosphate of ThDP. Furthermore, Gln(189) spans over the thiazolium moiety of ThDP and replaces an isoleucine found in most non-mammalian TKTs. The side chain of Gln(428) forms a hydrogen bond with the 4'-amino group of ThDP and replaces a histidine that is invariant in all non-mammalian TKTs. All other amino acids involved in substrate binding and catalysis are strictly conserved. Besides a steady-state kinetic analysis, microscopic equilibria of the donor half-reaction were characterized by an NMR-based intermediate analysis. These studies reveal that formation of the central 1,2-dihydroxyethyl-ThDP carbanion-enamine intermediate is thermodynamically favored with increasing carbon chain length of the donor ketose substrate. Based on the structure of human transketolase and sequence alignments, putative functional properties of the related transketolase-like proteins TKTL1 and -2 are discussed in light of recent findings suggesting that TKTL1 plays a role in cancerogenesis.

Femtosecond laser processing of protein crystals grown in agarose gel

Manual manipulation of protein crystals is often required in order to obtain X-ray diffraction (XRD) data, but the success of the manual operation depends on the experience and fortuity of the operators. Here, we demonstrated the processing of protein crystals grown in semi-solid agarose gel using a femtosecond laser. This high-precision, reproducible processing could be achieved without unsealing the crystallization trays by using a focused femtosecond laser. We confirmed that the gel-immobilized crystals of hen egg white lysozyme, glucose isomerase and thaumatin could be processed by this technique. In contrast, the processing of protein crystals grown in non-gelled solution triggered polycrystallization or was unsuccessful. The processed gel-grown lysozyme crystal was subsequently captured by a nylon loop without difficulty and mounted onto the goniometer head of the XRD equipment for XRD data collection. The statistics of the obtained XRD data indicated that laser irradiation has little influence on crystallinity, suggesting that the processed protein crystals are virtually suitable for X-ray analysis. This approach provides a reliable method of processing protein crystals and may lead to an automated system for protein crystal processing.