In this report, we describe detailed procedures for carrying out single crystal X-ray diffraction experiments with a diamond anvil cell at the GSECARS 13-BM-C beamline at the Advanced Photon Source. ATREX and RSV programs are used to analyze the data.
In this report we describe detailed procedures for carrying out single crystal X-ray diffraction experiments with a diamond anvil cell (DAC) at the GSECARS 13-BM-C beamline at the Advanced Photon Source. The DAC program at 13-BM-C is part of the Partnership for Extreme Xtallography (PX^2) project. BX-90 type DACs with conical-type diamond anvils and backing plates are recommended for these experiments. The sample chamber should be loaded with noble gas to maintain a hydrostatic pressure environment. The sample is aligned to the rotation center of the diffraction goniometer. The MARCCD area detector is calibrated with a powder diffraction pattern from LaB6. The sample diffraction peaks are analyzed with the ATREX software program, and are then indexed with the RSV software program. RSV is used to refine the UB matrix of the single crystal, and with this information and the peak prediction function, more diffraction peaks can be located. Representative single crystal diffraction data from an omphacite (Ca0.51Na0.48)(Mg0.44Al0.44Fe2+0.14Fe3+0.02)Si2O6 sample were collected. Analysis of the data gave a monoclinic lattice with P2/n space group at 0.35 GPa, and the lattice parameters were found to be: a = 9.496 ±0.006 Å, b = 8.761 ±0.004 Å, c = 5.248 ±0.001 Å, β = 105.06 ±0.03º, α = γ = 90º.
Single crystal X-ray diffraction is one of the most efficient and well-established ways to determine the chemical composition and structure of a crystalline material at different experimental conditions. Recently there have been a number 1-5 of developments in high-pressure single crystal diffraction. Pressure is one of the major factors that influence the behavior and properties of Earth and planetary materials. High-pressure experiments routinely reveal new polymorphs of common materials and can uncover ways to synthesize chemicals which are impossible to make at ambient conditions. Recently, several new silicate polymorphs have been identified with high-pressure single crystal diffraction, which provide new insight into the properties of Earth's mantle 6-8.
Different from single crystal diffraction at atmospheric pressure, high-pressure single crystal diffraction requires a pressure vessel to generate and maintain pressure during data collection. The most common pressure vessel used in high-pressure single crystal diffraction is the diamond anvil cell (DAC), which is composed of a pair of diamond anvils held together by a metal frame/metal gasket, and a pressure transmitting medium to provide a hydrostatic environment in the sample chamber 4,9-11. Single crystal diffraction using a diamond anvil cell differs from diffraction at ambient conditions in several important ways. First, the coverage of reciprocal space is significantly reduced due to limited X-ray angular access through the body of the DAC and the backing plates. Second, the angle-dependent absorption of X-rays by the diamonds and backing plates must be determined and used to correct the diffraction signal so that accurate structure factors can computed. Third, any overlap of the sample's diffraction signal with scatter or diffraction from the DAC components, such as the diamonds, gasket and pressure transmitting medium, must be eliminated. Fourth, aligning the sample in the DAC to the center of the goniometer is difficult. The direction perpendicular to the load axis of the DAC is always blocked by the gasket, and is not accessible to either the optical microscope or the X-ray beam. In the axial direction, the optical microscope can only visualize a displaced image of the sample because of the high refractive index of the diamond. These differences require the invention of new high-pressure single crystal diffraction measurement methods.
The Partnership for Extreme Xtallography (PX^2) project is a new research initiative dedicated to high-pressure single crystal diffraction with DACs. The project is hosted at the GeoSoilEnviroCARS experimental station 13-BM-C at the APS, which provides most of the infrastructure including detectors, focused X-rays and a 6-circle heavy duty diffractometer 12,13 optimized for a variety of advanced crystallography experiments. The diffractometer has six angular degrees of freedom, four sample-orienting (µ, η, χ and φ) and two detector-orienting (δ and υ). The angular conventions from You 13 are used to describe the motion of the sample and the detector, although the η, χ and φ motions are pseudo-angles derived from the instrument's kappa geometry real motors. The experimental procedures have been optimized for high-pressure single crystal diffraction with DACs, and a suite of data processing and analysis software packages has been developed. In this manuscript, we present a detailed protocol for a typical high-pressure single crystal diffraction experiment using the BX-90 type DAC 9, as a guide to collect and analyze data at PX^2.
1. Sample Preparation
NOTE: The sample preparation process includes three major steps: preparing the empty DAC, loading the sample and loading the inert gas pressure transmitting medium. DAC preparation and sample loading have been described in detail in Lavina et al. 10, and pressure transmitting medium loading has been described in Rivers et al. 14 Here we briefly describe the typical sample preparation process.
2. Data Collection
3. Data Analysis
NOTE: The data analysis is carried out using the ATREX/RSV software suite 2,18. For a detailed explanation of the principles utilized in the software please see the work of Dera, et al. 2
We show one representative example of high-pressure single crystal diffraction on the silicate mineral omphacite (Ca0.51Na0.48)(Mg0.44Al0.44Fe2+0.14Fe3+0.02)Si2O6. The omphacite sample was loaded in a BX-90 type DAC with Boehler-Almax (BA) type diamond anvils and backing plates (Figure 1). The sample chamber was filled with a noble-gas pressure transmitting medium (helium in this case) to ensure a hydrostatic pressure environment. The pressure of the sample chamber was 0.35 GPa, determined by ruby fluorescence. The sample was aligned with the rotation center of the diffraction goniometer (Figures 3, 4). We calibrated the position and tilt of the MARCCD detector at ν = 0, δ = 0 with a LaB6 powder standard (Figure 5). During the experiment, η, χ and µ angles were fixed at 0. The diffraction peaks of the sample were first analyzed using the "Search" function of the ATREX software (Figure 6). Then, the lattice parameters and the UB matrix of the omphacite single crystal were refined using the RSV software (Figure 7). With the refined UB matrix of the crystal, more diffraction peaks were found using the "Predict" function of the software (Figure 8). The refined lattice parameters of this omphacite single crystal at this pressure are: a = 9.496 ±0.006 Å, b = 8.761±0.004 Å, c = 5.248 ±0.001 Å, β = 105.06 ±0.03º, α = γ = 90º (Tab. 1). The omphacite crystal was found to have a monoclinic lattice in the P2/n space group. Our refined lattice parameters are consistent with the published lattice parameters of omphacite with a similar chemical composition and at a similar pressure: P = 0.449 GPa, a = 9.5541 ±0.0005 Å, b = 8.7481 ±0.0007 Å, c = 5.2482 ±0.0003 Å, β = 106.895 ±0.004º 21.
Figure 1: Components of BX-90 DAC which is used for high pressure single crystal diffraction. (a) Boehler-Almax (BA) type diamond; (b) Re gasket; (c) BA type backing plate; (d) BA type diamond glued on BA type backing plate; (e) cylinder part of the BX-90 DAC; (f) piston part of the BX-90 DAC; (g) left-handed (black oxide finish) and right-handed (stainless-steel finish) compressing screws: (h) right-handed compressing screw with disk spring washers; (i) BX-90 DAC assembly ready for high pressure single crystal diffraction experiment. Please click here to view a larger version of this figure.
Figure 2: Microscope image of the DAC sample chamber before and after noble gas pressure transmitting medium loading. After the gas pressure transmitting medium loading, the sample chamber hole shrank by ~30% in diameter. Please click here to view a larger version of this figure.
Figure 3: Experimental setup for high-pressure single crystal diffraction at PX^2. The six angular degrees of freedom (µ, η, χ, φ, δ and υ) and the three translational directions (x, y and z) are labeled. The notation for angles follows the angular convention of You 13. Please click here to view a larger version of this figure.
Figure 4: Align the sample chamber to the rotation center. Left: sample chamber scans at the X-ray normal direction (blue) and φ-rotation by +Δφ (green) and -Δφ (red). Right: X-ray transmission profiles of the sample chamber scans at different φ angles. The offsets of the X-ray transmission profiles are used to calculate the positional correction along the incident X-ray direction. Please click here to view a larger version of this figure.
Figure 5: Calibrating the MARCCD detector using the data analysis software. LaB6 powder diffraction pattern is used to carry out the calibration. Please click here to view a larger version of this figure.
Figure 6: Diffraction peak search using the data analysis software. In total 63 diffraction peaks were found in this wide exposure image. Please click here to view a larger version of this figure.
Figure 7: Indexing the diffraction peaks and calculating the UB matrix of the sample using the RSV software. The indexing is carried out automatically by the software. Please click here to view a larger version of this figure.
Figure 8: Predicting the diffraction peaks with the data analysis software. 112 diffraction peaks were found with the same diffraction image as in Figure 6 using the peak-prediction function. Please click here to view a larger version of this figure.
Lattice parameter | Value |
a | 9.496 ±0.006 Å |
b | 8.761 ±0.004 Å |
c | 5.248 ±0.001 Å |
a | 90º |
b | 105.06 ±0.03º |
g | 90º |
Table 1: Lattice parameters of omphacite (Ca0.51Na0.48)(Mg0.44Al0.44Fe2+0.14Fe3+0.02)Si2O6 at 0.35 GPa. The omphacite crystal was found to have a monoclinic lattice in the P2/n space group.
In this report we show the detailed procedure for carrying out single crystal diffraction experiments with DACs at the GSECARS 13-BM-C beamline. BX-90 type DACs with BA-type diamond anvils and backing plates are recommended for single crystal diffraction experiments 2,9,15. The advantage of the BX-90 type DAC is its wider angular access compared to the traditional symmetric DACs, which provides for effective sampling of many diffraction peaks 9,15. The wide angular access becomes critical for samples with lower symmetry and with smaller unit cells: the former require more diffraction peaks to constrain the lattice parameters accurately, and the latter give fewer diffraction peaks within the given angular access 2. The more angular access one reaches in the experiment, the more accurate atomic positional parameters one measures 2,4. Restricted angular access may result in a two dimensional reciprocal vector dataset, making reliable data interpretation mathematically impossible 2.
One important, yet often overlooked step is to select suitable pressure transmission medium. Though pressure media such as argon, silicone oil or methanol-ethanol-water solution were used in previous single crystal diffraction experiments that did not exceed 10 GPa 21-23, these pressure media become significantly nonhydrostatic between 5-10 GPa 22, and greatly reduce the quality of the crystal during compression 2,22. Our general experience has been that only He and Ne result in high quality experiments up to 50 GPa (e.g., references6,7). At the APS, these gases can be conveniently loaded into DACs with the use of GSECARS/COMPRES gas-loading apparatus 14. When He or Ne is chosen as the pressure medium, the sample chamber shrinks during the gas loading (Figure 2). Once the sample directly touches the gasket, it breaks easily during the compression. So it is important to drill a big enough sample chamber, whose diameter is at least 2/3 of the culet diameter, to avoid the contact between the sample and the gasket after gas loading.
The synchrotron-based monochromatic single crystal diffraction setup at PX^2 is unique. Compared to the laboratory diffractometers, the synchrotron X-ray source provides a much higher flux (>104) 4,27,28, which significantly improves the signal-to-noise ratio and reduces the data collection time 4,27,28. Synchrotron based powder diffraction is also commonly used to determine the structure of materials at high pressures through the Rietveld approach 4. Single crystal diffraction has advantages over the Rietveld approach, because it decouples the fitting of lattice parameters and structural parameters 2,4. Powder diffraction with Rietveld fitting usually requires fitting both lattice parameters and structural parameters at the same time, while the number of independent observations is typically much lower than in single crystal diffraction 4. Another common structure determination method is Laue diffraction, which uses polychromatic radiation with an area detector 4. Compared to monochromatic data collection at PX^2, the reduction of Laue method data requires additional terms including harmonic deconvolution and intensity normalization, which adds additional difficulties in the data analysis 4,24. Monochromatic single crystal diffraction is a straightforward way of solving structures, yet it has its own limitations. An ideal dataset of monochromatic single crystal diffraction requires a defect-less crystal with a size of tens of µm, and the crystal quality needs to preserve at high pressures. These requirements can be difficult to meet for some non-quenchable minerals, such as bridgmanite 25.
Time resolved single crystal diffraction is capable of capturing the transient metastable states and transformation kinetics during pressure induced structural transitions, and is one of the future research directions for PX^2 26. Quantitative characterization of defects and lattice dynamics, based on analysis of X-ray diffuse scattering at high pressures is also under development at the PX^2 26. A compact optical platform for laser-heated high-pressure single crystal diffraction is being built, and will enable the earth-science community to study the behavior of materials under deep-earth conditions 26.
The authors have nothing to disclose.
This work was performed at GeoSoilEnviroCARS (Sector 13), Partnership for Extreme Crystallography program (PX^2), Advanced Photon Source (APS), and Argonne National Laboratory. GeoSoilEnviroCARS is supported by the National Science Foundation-Earth Sciences (EAR-1128799) and Department of Energy-Geosciences (DE-FG02-94ER14466). The PX^2 program is supported by COMPRES under NSF Cooperative Agreement EAR 11-57758. Use of the Advanced Photon Source was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-C02-6CH11357. Use of the COMPRES-GSECARS gas loading system was supported by COMPRES under NSF Cooperative Agreement EAR 11-57758 and by GSECARS through NSF grant EAR-1128799 and DOE grant DE-FG02-94ER14466. We would also like to thank Prof. R. T. Downs at the University of Arizona for kindly providing the samples from RRUFF collections.
Diamond | Almax | P01037 | Boehler-Almax type diamond |
Backing plate | Almax | P01289 | Backing plate's design should match the diamond's design |
Re gasket | Alfa Aesar | 10309 | |
Epoxy | Henkel Loctite | Stycast 2651 | |
Polymer micromesh | MiTeGen | M3-L18SP-25 | |
Goniometer head | Hampton Research | HR4-647 | |
Software: ATREX | Open source software | Website: https://github.com/pdera/GSE_ADA | |
Software: RSV | Open source software | Website: https://github.com/pdera/RSV | |
Software: cell_now | Bruker Corporation | ||
Software: CCD_DC | Free software |