Dose,exposure time and resolution in serial X‐ray crystallography

The resolution of X‐ray diffraction microscopy is limited by the maximum dose that can be delivered prior to sample damage. In the proposed serial crystallography method, the damage problem is addressed by distributing the total dose over many identical hydrated macromolecules running continuously in a single‐file train across a continuous X‐ray beam, and resolution is then limited only by the available molecular and X‐ray fluxes and molecular alignment. Orientation of the diffracting molecules is achieved by laser alignment. The incident X‐ray fluence (energy/area) is evaluated that is required to obtain a given resolution from (i) an analytical model, giving the count rate at the maximum scattering angle for a model protein, (ii) explicit simulation of diffraction patterns for a GroEL–GroES protein complex, and (iii) the spatial frequency cut‐off of the transfer function following iterative solution of the phase problem, and reconstruction of an electron density map in the projection approximation. These calculations include counting shot noise and multiple starts of the phasing algorithm. The results indicate counting time and the number of proteins needed within the beam at any instant for a given resolution and X‐ray flux. An inverse fourth‐power dependence of exposure time on resolution is confirmed, with important implications for all coherent X‐ray imaging. It is found that multiple single‐file protein beams will be needed for sub‐nanometer resolution on current third‐generation synchrotrons, but not on fourth‐generation designs, where reconstruction of secondary protein structure at a resolution of 7 Å should be possible with relatively short exposures.     

Coherent X‐ray diffractive imaging of protein crystals

The technique of coherent X‐ray diffraction imaging (CXDI) has recently shown great promise for the study of inorganic nanocrystals. In this work the CXDI method has been applied to the study of micrometer‐size protein crystals. Finely sampled diffraction patterns of single crystals were measured and iterative phase‐retrieval algorithms were used to reconstruct the two‐dimensional shape of the crystal. The density maps have limited reproducibility because of radiation damage, but show clear evidence for crystal facets. Qualitative analysis of a number of single‐crystal diffraction peaks indicates the presence of inward surface contraction on 2 µm size crystals. A survey of several hundred diffraction patterns yielded a number of examples with dramatic single‐sided streaks, for which a plausible model is constructed.     

The first microbeam synchrotron X‐ray fluorescence beamline at the Siam Photon Laboratory

The first microbeam synchrotron X‐ray fluorescence (µ‐SXRF) beamline using continuous synchrotron radiation from Siam Photon Source has been constructed and commissioned as of August 2011. Utilizing an X‐ray capillary half‐lens allows synchrotron radiation from a 1.4 T bending magnet of the 1.2 GeV electron storage ring to be focused from a few millimeters‐sized beam to a micrometer‐sized beam. This beamline was originally designed for deep X‐ray lithography (DXL) and was one of the first two operational beamlines at this facility. A modification has been carried out to the beamline in order to additionally enable µ‐SXRF and synchrotron X‐ray powder diffraction (SXPD). Modifications included the installation of a new chamber housing a Si(111) crystal to extract 8 keV synchrotron radiation from the white X‐ray beam (for SXPD), a fixed aperture and three gate valves. Two end‐stations incorporating optics and detectors for µ‐SXRF and SXPD have then been installed immediately upstream of the DXL station, with the three techniques sharing available beam time. The µ‐SXRF station utilizes a polycapillary half‐lens for X‐ray focusing. This optic focuses X‐ray white beam from 5 mm × 2 mm (H × V) at the entrance of the lens down to a diameter of 100 µm FWHM measured at a sample position 22 mm (lens focal point) downstream of the lens exit. The end‐station also incorporates an XYZ motorized sample holder with 25 mm travel per axis, a 5× ZEISS microscope objective with 5 mm × 5 mm field of view coupled to a CCD camera looking to the sample, and an AMPTEK single‐element Si (PIN) solid‐state detector for fluorescence detection. A graphic user interface data acquisition program using the LabVIEW platform has also been developed in‐house to generate a series of single‐column data which are compatible with available XRF data‐processing software. Finally, to test the performance of the µ‐SXRF beamline, an elemental surface profile has been obtained for a piece of ancient pottery from the Ban Chiang archaeological site, a UNESCO heritage site. It was found that the newly constructed µ‐SXRF technique was able to clearly distinguish the distribution of different elements on the specimen.     

IDATEN and G‐SITENNO: GUI‐assisted software for coherent X‐ray diffraction imaging experiments and data analyses at SACLA

Using our custom‐made diffraction apparatus KOTOBUKI‐1 and two multiport CCD detectors, cryogenic coherent X‐ray diffraction imaging experiments have been undertaken at the SPring‐8 Angstrom Compact free electron LAser (SACLA) facility. To efficiently perform experiments and data processing, two software suites with user‐friendly graphical user interfaces have been developed. The first is a program suite named IDATEN, which was developed to easily conduct four procedures during experiments: aligning KOTOBUKI‐1, loading a flash‐cooled sample into the cryogenic goniometer stage inside the vacuum chamber of KOTOBUKI‐1, adjusting the sample position with respect to the X‐ray beam using a pair of telescopes, and collecting diffraction data by raster scanning the sample with X‐ray pulses. Named G‐SITENNO, the other suite is an automated version of the original SITENNO suite, which was designed for processing diffraction data. These user‐friendly software suites are now indispensable for collecting a large number of diffraction patterns and for processing the diffraction patterns immediately after collecting data within a limited beam time.     

Radiation damage to protein specimens from electron beam imaging and diffraction: a mini‐review of anti‐damage approaches,with special reference to synchrotron X‐ray crystallography

Recent research progress using X‐ray cryo‐crystallography with the photon beams from third‐generation synchrotron sources has resulted in recognition that this intense radiation commonly damages protein samples even when they are held at 100 K. Other structural biologists examining thin protein crystals or single particle specimens encounter similar radiation damage problems during electron diffraction and imaging, but have developed some effective countermeasures. The aim of this concise review is to examine whether analogous approaches can be utilized to alleviate the X‐ray radiation damage problem in synchrotron macromolecular crystallography. The critical discussion of this question is preceded by presentation of background material on modern technical procedures with electron beam instruments using 300–400 kV accelerating voltage, low‐dose exposures for data recording, and protection of protein specimens by cryogenic cooling; these practical approaches to dealing with electron radiation damage currently permit best resolution levels of 6 Å (0.6 nm) for single particle specimens, and of 1.9 Å for two‐dimensional membrane protein crystals. Final determination of the potential effectiveness and practical value of using such new or unconventional ideas will necessitate showing, by experimental testing, that these produce significantly improved protection of three‐dimensional protein crystals during synchrotron X‐ray diffraction.     

Low‐temperature synthesis and Raman scattering of Mn‐doped ZnO nanopowders

Nanocrystalline Mn‐doped zinc oxides Zn_1−xMn_xO (x = 0–0.10) were synthesized by the sol–gel technique at low temperature. The calcination temperature of the as‐prepared powder was found at 350 °C using differential thermal analysis. A thermogravimetric analysis showed that there is a mass loss in the as‐prepared powder till 350 °C and an almost constant mass till 800 °C. The X‐ray diffraction patterns of investigated nanopowders calcined at 350 °C correspond to the hexagonal ZnO structure without any foreign impurities. The average grain size of the nanocrystal that was observed around ∼25–40 nm from transmission electron microscopy matched well with the crystallite size calculated from the line shape of X‐ray diffraction. The chemical bonding structure in Zn_1−xMn_xO nanopowders was examined using X‐ray photoelectron spectroscopy techniques, which indicate substitution of Mn²⁺ ions into Zn²⁺ sites in ZnO lattice. Micro Raman spectroscopy confirmed the insertion of Mn ions in the ZnO host matrix, and similar wurtzite structure of Zn_1−xMn_xO (x < 10%) nanocrystals. Temperature‐dependent Raman spectra of the nanocrystals displayed suppression of luminescence and enhancement in full width at half maximum in pure ZnO nanocrystals with increase in temperature, which suggests an enhancement in particle size at elevated temperature. Copyright © 2009 John Wiley & Sons, Ltd.     

Understanding the instrumental profile of synchrotron radiation X‐ray powder diffraction beamlines

A Monte Carlo algorithm has been developed to calculate the instrumental profile function of a powder diffraction synchrotron beamline. Realistic models of all optical elements are implemented in a ray‐tracing software. The proposed approach and the emerging paradigm have been investigated and verified for several existing X‐ray powder diffraction beamlines. The results, which can be extended to further facilities, show a new and general way of assessing the contribution of instrumental broadening to synchrotron radiation data, based on ab initio simulations.     

An in situ atomic force microscope for normal‐incidence nanofocus X‐ray experiments

A compact high‐speed X‐ray atomic force microscope has been developed for in situ use in normal‐incidence X‐ray experiments on synchrotron beamlines, allowing for simultaneous characterization of samples in direct space with nanometric lateral resolution while employing nanofocused X‐ray beams. In the present work the instrument is used to observe radiation damage effects produced by an intense X‐ray nanobeam on a semiconducting organic thin film. The formation of micrometric holes induced by the beam occurring on a timescale of seconds is characterized.     

Diffraction‐based automated crystal centering

A fully automated procedure for detecting and centering protein crystals in the X‐ray beam of a macromolecular crystallography beamline has been developed. A cryo‐loop centering routine that analyzes video images with an edge detection algorithm is first used to determine the dimensions of the loop holding the sample; then low‐dose X‐rays are used to record diffraction images in a grid over the edge and face plane of the loop. A three‐dimensional profile of the crystal based on the number of diffraction spots in each image is constructed. The derived center of mass is then used to align the crystal to the X‐ray beam. Typical samples can be accurately aligned in ～2–3 min. Because the procedure is based on the number of `good' spots as determined by the program Spotfinder, the best diffracting part of the crystal is aligned to the X‐ray beam.     

A flow‐through reaction cell for in situ X‐ray diffraction and absorption studies of heterogeneous powder–liquid reactions and phase transformations

A portable powder–liquid high‐corrosion‐resistant reaction cell has been designed to follow in situ reactions by X‐ray powder diffraction (XRD) and X‐ray absorption spectroscopy (XAS) techniques. The cell has been conceived to be mounted on the experimental stations for diffraction and absorption of the Spanish CRG SpLine‐BM25 beamline at the European Synchrotron Radiation Facility. Powder reactants and/or products are kept at a fixed position in a vertical geometry in the X‐ray pathway by a porous membrane, under forced liquid reflux circulation. Owing to the short pathway of the X‐ray beam through the cell, XRD and XAS measurements can be carried out in transmission configuration/mode. In the case of the diffraction technique, data can be collected with either a point detector or a two‐dimensional CCD detector, depending on specific experimental requirements in terms of space or time resolution. Crystallization processes, heterogeneous catalytic processes and several varieties of experiments can be followed by these techniques with this cell. Two experiments were carried out to demonstrate the cell feasibility: the phase transformations of layered titanium phosphates in boiling aqueous solutions of phosphoric acid, and the reaction of copper carbonate and l ‐isoleucine amino acid powders in boiling aqueous solution. In this last case the shrinking of the solid reactants and the formation of Cu(isoleucine)₂ is observed. The crystallization processes and several phase transitions have been observed during the experiments, as well as an unexpected reaction pathway.     

Performance of a fuel cell optimized for in situ X‐ray absorption experiments

A commercial fuel cell has been successfully modified to carry out X‐ray absorption spectroscopy (XAS) measurements under optimized in operando conditions. The design is conceived for the performance of XAS experiments in transmission mode over a wide range of X‐ray energies above 6 keV, owing to the reduced absorption of the cell. The wide angular aperture allows the collection of XAS in fluorescence mode and of X‐ray diffraction patterns when needed. Details of the design of the cell and its performances are given. The quality of the extended X‐ray absorption fine‐structure spectra under working conditions has been verified at the ESRF and ELETTRA synchrotron radiation facilities, showing that relatively fast and low‐noise transmission measurements on electrodes over a wide range of catalyst concentrations and energies are feasible.     

Non‐invasive measurement of X‐ray beam heating on a surrogate crystal sample

Cryocooling is a technique routinely used to mitigate the effects of secondary radiation damage on macromolecules during X‐ray data collection. Energy from the X‐ray beam absorbed by the sample raises the temperature of the sample. How large is the temperature increase and does this reduce the effectiveness of cryocooling? Sample heating by the X‐ray beam has been measured non‐invasively for the first time by means of thermal imaging. Specifically, the temperature rise of 1 mm and 2 mm glass spheres (sample surrogates) exposed to an intense synchrotron X‐ray beam and cooled in a laminar flow of nitrogen gas is experimentally measured. For the typical sample sizes, photon energies, fluxes, flux densities and exposure times used for macromolecular crystallographic data collection at third‐generation synchrotron radiation sources and with the sample accurately centered in the cryostream, the heating by the X‐ray beam is only a few degrees. This is not sufficient to raise the sample above the amorphous‐ice/crystalline‐ice transition temperature and, if the cryostream cools the sample to 100 K, not even enough to significantly enhance radiation damage from secondary effects.     

A new approach to synchrotron energy‐dispersive X‐ray diffraction computed tomography

A new data collection strategy for performing synchrotron energy‐dispersive X‐ray diffraction computed tomography has been devised. This method is analogous to angle‐dispersive X‐ray diffraction whose diffraction signal originates from a line formed by intersection of the incident X‐ray beam and the sample. Energy resolution is preserved by using a collimator which defines a small sampling voxel. This voxel is translated in a series of parallel straight lines covering the whole sample and the operation is repeated at different rotation angles, thus generating one diffraction pattern per translation and rotation step. The method has been tested by imaging a specially designed phantom object, devised to be a demanding validator for X‐ray diffraction imaging. The relative strengths and weaknesses of the method have been analysed with respect to the classic angle‐dispersive technique. The reconstruction accuracy of the method is good, although an absorption correction is required for lower energy diffraction because of the large path lengths involved. The spatial resolution is only limited to the width of the scanning beam owing to the novel collection strategy. The current temporal resolution is poor, with a scan taking several hours. The method is best suited to studying large objects (e.g. for engineering and materials science applications) because it does not suffer from diffraction peak broadening effects irrespective of the sample size, in contrast to the angle‐dispersive case.     

Sound velocities of compressed Fe3C from simultaneous synchrotron X‐ray diffraction and nuclear resonant scattering measurements

The applications of nuclear resonant scattering in laser‐heated diamond anvil cells have provided an important probe for the magnetic and vibrational properties of ⁵⁷Fe‐bearing materials under high pressure and high temperature. Synchrotron X‐ray diffraction is one of the most powerful tools for studying phase stability and equation of state over a wide range of pressure and temperature conditions. Recently an experimental capability has been developed for simultaneous nuclear resonant scattering and X‐ray diffraction measurements using synchrotron radiation. Here the application of this method to determine the sound velocities of compressed Fe₃C is shown. The X‐ray diffraction measurements allow detection of microscale impurities, phase transitions and chemical reactions upon compression or heating. They also provide information on sample pressure, grain size distribution and unit cell volume. By combining the Debye velocity extracted from the nuclear resonant inelastic X‐ray scattering measurements and the structure, density and elasticity data from the X‐ray diffraction measurements simultaneously obtained, more accurate sound velocity data can be derived. Our results on few‐crystal and powder samples indicate strong anisotropy in the sound velocities of Fe₃C under ambient conditions.     

High‐efficiency coherence‐preserving harmonic rejection with crystal optics

This work reports a harmonic‐rejection scheme based on the combination of Si(111) monochromator and Si(220) harmonic‐rejection crystal optics. This approach is of importance to a wide range of X‐ray applications in all three major branches of modern X‐ray science (scattering, spectroscopy, imaging) based at major facilities, and especially relevant to the capabilities offered by the new diffraction‐limited storage rings. It was demonstrated both theoretically and experimentally that, when used with a synchrotron undulator source over a broad range of X‐ray energies of interest, the harmonic‐rejection crystals transmit the incident harmonic X‐rays on the order of 10^?6. Considering the flux ratio of fundamental and harmonic X‐rays in the incident beam, this scheme achieves a total flux ratio of harmonic radiation to fundamental radiation on the order of 10^?10. The spatial coherence of the undulator beam is preserved in the transmitted fundamental radiation while the harmonic radiation is suppressed, making this scheme suitable not only for current third‐generation synchrotron sources but also for the new diffraction‐limited storage rings where coherence preservation is an even higher priority. Compared with conventional harmonic‐rejection mirrors, where coherence is poorly preserved and harmonic rejection is less effective, this scheme has the added advantage of lower cost and footprint. This approach has been successfully utilized at the ultra‐small‐angle X‐ray scattering instrument at the Advanced Photon Source for scattering, imaging and coherent X‐ray photon correlation spectroscopy experiments. With minor modification, the harmonic rejection can be improved by a further five orders of magnitude, enabling even more performance capabilities.     

Fabrication and testing of a newly designed slit system for depth‐resolved X‐ray diffraction measurements

A new system of slits called `spiderweb slits' have been developed for depth‐resolved powder or polycrystalline X‐ray diffraction measurements. The slits act on diffracted X‐rays to select a particular gauge volume of sample, while absorbing diffracted X‐rays from outside of this volume. Although the slit geometry is to some extent similar to that of previously developed conical slits or spiral slits, this new design has advantages over the previous ones in use for complex heterogeneous materials and in situ and operando diffraction measurements. For example, the slits can measure a majority of any diffraction cone for any polycrystalline material, over a continuous range of diffraction angles, and work for X‐ray energies of tens to hundreds of kiloelectronvolts. The design is generated and optimized using ray‐tracing simulations, and fabricated through laser micromachining. The first prototype was successfully tested at the X17A beamline at the National Synchrotron Light Source, and shows similar performance to simulations, demonstrating gauge volume selection for standard powders, for all diffraction peaks over angles of 2–10°. A similar, but improved, design will be implemented at the X‐ray Powder Diffraction beamline at the National Synchrotron Light Source II.     

The energy dispersive scheme of X‐ray fluorescence analysis with a crystal polarizer and polycapillary optics

The efficiency of the polarization scheme based on polycapillary optics and a diamond crystal polarizer was demonstrated. The scheme provides suppression of the background of scattered radiation in measuring X‐ray fluorescence spectra. A quasi‐parallel X‐ray beam with an angular divergence of 4.2 mrad was formed by a microfocus source with a copper anode and polycapillary half‐lens. Simultaneous polarization and monochromatization of radiation was obtained with a crystal of natural diamond, which was set at the diffraction reflection (113). The degree of polarization of CuK_α1 spectral line and the maximum radiation flux were respectively equal to 99.86% and 5 · 10⁶ photon/s. In the direction orthogonal to the plane of diffraction, the maximum attenuation of the background was up to 19 dB.     

Hard X‐ray‐induced damage on carbon–binder matrix for in situ synchrotron transmission X‐ray microscopy tomography of Li‐ion batteries

The electrode of Li‐ion batteries is required to be chemically and mechanically stable in the electrolyte environment for in situ monitoring by transmission X‐ray microscopy (TXM). Evidence has shown that continuous irradiation has an impact on the microstructure and the electrochemical performance of the electrode. To identify the root cause of the radiation damage, a wire‐shaped electrode is soaked in an electrolyte in a quartz capillary and monitored using TXM under hard X‐ray illumination. The results show that expansion of the carbon–binder matrix by the accumulated X‐ray dose is the key factor of radiation damage. For in situ TXM tomography, intermittent X‐ray exposure during image capturing can be used to avoid the morphology change caused by radiation damage on the carbon–binder matrix.     

In situ X‐ray diffraction study on the growth kinetics of NiO nanoparticles

The growth kinetics of NiO nanoparticles have been studied by in situ X‐ray diffraction using two detection systems (conventional and imaging plate). NiO nanoparticles were formed by thermal decomposition after heating of an amorphous compound formed by the coprecipitation method. It was found that the detection method using an imaging plate is more efficient than the conventional detection mode for observing changes in the crystallite growth of nanocrystalline materials. Studies have been carried out to investigate the effects of the heating rates on the particles growth. The results suggest that the growth process of the particles is accelerated when the samples are treated at low heating rates. The evolution of particles size and the diffusion coefficient obtained from X‐ray powder diffraction patterns are discussed in terms of the thermal conditions for the two types of detection.     

Zr and Ba edge phenomena in the scintillation intensity of fluorozirconate‐based glass‐ceramic X‐ray detectors

The energy‐dependent scintillation intensity of Eu‐doped fluorozirconate glass‐ceramic X‐ray detectors has been investigated in the energy range from 10 to 40 keV. The experiments were performed at the Advanced Photon Source, Argonne National Laboratory, USA. The glass ceramics are based on Eu‐doped fluorozirconate glasses, which were additionally doped with chlorine to initiate the nucleation of BaCl₂ nanocrystals therein. The X‐ray excited scintillation is mainly due to the 5d–4f transition of Eu²⁺ embedded in the BaCl₂ nanocrystals; Eu²⁺ in the glass does not luminesce. Upon appropriate annealing the nanocrystals grow and undergo a phase transition from a hexagonal to an orthorhombic phase of BaCl₂. The scintillation intensity is investigated as a function of the X‐ray energy, particle size and structure of the embedded nanocrystals. The scintillation intensity versus X‐ray energy dependence shows that the intensity is inversely proportional to the photoelectric absorption of the material, i.e. the more photoelectric absorption the less scintillation. At 18 and 37.4 keV a significant decrease in the scintillation intensity can be observed; this energy corresponds to the K‐edge of Zr and Ba, respectively. The glass matrix as well as the structure and size of the embedded nanocrystals have an influence on the scintillation properties of the glass ceramics.