Name: high pressure single crystal diffraction at px^2
Uploaded: 2017-01-16T13:00:00.000+00:00
Duration: 11 min 32 s
Description: Watch this Scientific Journal Video about High Pressure Single Crystal Diffraction at PX^2 at JoVE.com

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.

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.
<ol>
	<li>Select a pair of conical diamonds with matching backing plates.
	<ol>
		<li>Ensure that the flat tips of the diamond anvils (culets) are identical to each other. 
		NOTE: The diameter of the culet depends on the target maximum pressure of the experiment.</li>
		<li>Ensure that the conical housing of the backing plate matches the shape of the conical diamond. Ensure that the height of the diamond, the diameter of the back side of the diamond, the opening angle of the backing plate and the opening angle of the DAC are compatible with each other, so as to maximize the angular access for diffraction 9,15.</li>
	</ol>
	</li>
	<li>Clean the diamonds and backing plates in an acetone ultrasonic bath for 3-5 min. Set the ultrasonic cleaner to &#34;Sonic&#34; mode. Examine the diamonds and backing plates under an optical microscope, and remove all visible dust or debris.</li>
	<li>Place the diamond in the conical housing of the backing plate, and the assembly in a mounting jig.</li>
	<li>Apply a few kg of load to the diamond with compressing screws, so that it is in intimate contact with the backing plate. Then, apply about 0.1 g of epoxy around the outer circumference of the diamond. Heat the assembly to 70 &#176;C for 8 h to cure the epoxy.</li>
	<li>Clean the interior of the DAC, the back side of the backing plates and the culets of the diamonds with acetone, and place the backing plates with diamonds in the DAC.</li>
	<li>Adjust the positions of the diamonds with set screws that hold the backing plate in place, so that the anvil culets are concentric when the two opposing diamonds come into contact.</li>
	<li>Check the tilt angle between the two culets looking for interference fringes under an optical microscope. Adjust the tilt angle of the diamonds by fine-tuning the load of the set screws, so that the number of fringes is minimized 10.</li>
	<li>Place a piece of 250 &#181;m thick rhenium (Re) metal foil between the two diamonds, and fix it in place with wax. 
	NOTE: This Re foil acts as the gasket of the DAC.</li>
	<li>Apply load uniformly and slowly by tightening the four compressing screws of the DAC, and monitor the thickness change of the Re gasket with a micrometer by measuring the total thickness of the DAC assembly.</li>
	<li>When the thickness of the Re gasket is ~40 &#181;m, remove the load of the compressing screws slowly, and take out the pre-indented gasket.</li>
	<li>Use a laser milling machine to drill a hole at the center of the pre-indentation, whose diameter is at least 2/3 of the culet diameter. Align the gasket with an optical microscope, and set the intended diameter of the gasket hole in the laser milling machine user interface. Press the &#34;scan&#34; button to drill the hole.</li>
	<li>Soak the drilled gasket into acetone and clean it with an ultrasonic cleaner in normal mode. Clean the culets of the diamonds with acetone. Place the drilled gasket back in the DAC. 
	NOTE: The hole in the gasket serves as the sample chamber.</li>
	<li>Place a single crystal sample at the center of the gasket hole, which should also be the center of the diamond culet. 
	NOTE: The optimal sample size is 20 &#181;m x 20 &#181;m x 5 &#181;m (length x width x thickness).</li>
	<li>Place a small ruby sphere (~10 &#181;m in diameter) close to the sample. 
	NOTE: The ruby sphere serves as the pressure marker.</li>
	<li>Place the DAC with the sample inside the COMPRES/GSECARS gas loading vessel and load compressed helium (He) or neon (Ne) gas to a maximum pressure of about 25,000 psi to fill the vessel 14.</li>
	<li>Increase the pressure inside the DAC sample chamber by tightening the compressing screws of the DAC, and monitor the pressure with ruby fluorescence 16.</li>
</ol>
2. Data Collection
<ol>
	<li>Place ~1 mg LaB6 powder at the rotation center of the diffractometer, and collect powder diffraction patterns at several MARCCD detector positions varying by the&#160;&#948; angle. Collect the powder diffraction patterns by clicking the &#34;Start&#34; button of the MARCCD EPICS interface. Use this diffraction pattern to calibrate the detector-sample distance and the tilt of the MARCCD detector 2.</li>
	<li>After completing the detector calibration, remove the LaB6 standard from the diffractometer. Place the DAC in the sample holder, and put it on the diffractometer&#39;s sample stage.
	<ol>
		<li>Use a clamp-type holder to hold ambient temperature DACs, a water-cooled clamp-type holder for high temperature DACs, and polymer micromesh mounted on an ACA/IUCr standard goniometer head to hold a sample at ambient pressure and temperature. 
		NOTE: In the following steps (2.3-2.8), all the motion controls are achieved with the EPICS user interface (EUI).</li>
	</ol>
	</li>
	<li>Rotate the &#966; axis so that the sample chamber is perpendicular to the viewing zoom camera by setting the &#966; angle to 120 in the EUI.</li>
	<li>Find the sample chamber with the viewing camera at the minimum magnification first. Center the sample&#39;s image by changing the sample X, Y and Z in the EUI. Focus the image of the sample by changing the microscope Z in the EUI, and then zoom-in to the maximum magnification.</li>
	<li>Align the sample chamber&#39;s image to the center of the viewing camera by changing the sample X, Y and Z in the EUI. Adjust the sample position along the camera&#39;s axis until it is in focus (using a pre-determined camera focus to estimate the position of the rotation center in this direction). Then rotate the &#966; angle to 90 in the EUI so that the sample chamber is perpendicular to the incident X-ray beam.</li>
	<li>To correct for sample displacement from the center of the instrument along the DAC axis, scan the DAC position in both horizontal and vertical directions perpendicular to the incident X-ray using the SCANW software, using motorized translations built into the goniometer, while collecting transmitted beam intensity data with a photodiode detector placed behind the sample. 
	NOTE: The photodiode detector is mounted on a pneumatic actuator and can be moved in and out of the beam remotely from the control station.</li>
	<li>Find the center position in the collected intensity scan using the &#34;center&#34; function of SCANW, corresponding to maximum transmission. This is the center of the sample chamber.</li>
	<li>Rotate the sample using the goniometer &#966; axis by a few degrees using the EUI, and repeat the vertical transmission scan. Repeat the scan twice, at both positive and negative &#966; offsets.</li>
	<li>Calculate the sample position along the incident X-ray&#39;s direction with the following equation 17 
	<img alt="Equation 1" src="/files/ftp_upload/54660/54660eq1.jpg" /> 
	Where &#916;Y is the distance along the incident X-ray&#39;s direction that the sample is displaced from the center of the instrument, &#916;&#966; is the change in the &#966; angle between scans, &#916;Sx+ and &#916;Sx- are the positional offsets of X-ray&#39;s transmission profile when the &#966; angle is tilted by +&#916;&#966; and -&#916;&#966;. 
	NOTE: Several iterations of scans can be made to improve the accuracy of sample positioning.</li>
	<li>After aligning the sample, collect the single crystal diffraction data with the CCD_DC software 1.
	<ol>
		<li>At first, collect a &#966;-scan with a photodiode by clicking the &#34;scan&#34; button on the SCANW software to determine the maximum opening angle and to determine the functional-shape of the absorption effect of the diamond anvils and backing plates.</li>
		<li>After the &#966;-scan, carry out a wide &#966; exposure (during which the detector is left open while &#966; is rotated) to cover the maximum opening angle that the DAC allows, followed by a series of step &#966; exposures, each covering 1&#176;. Carry out this step by setting the &#34;total range&#34; to the maximum opening angle, and setting the &#34;Number of steps&#34; to the same number in the CCD_DC software. Collect wide &#966; scans at different detector positions by specifying the detector arm position in the&#160;&#948; and&#160;&#957; directions in the CCD_DC software, so as to allow access to more diffraction peaks. 
		NOTE: For crystals with a unit cell larger than 10 &#197;, collection of 10&#176; wide step scans covering the same angular range is also recommended. Exposure times are determined by the absorption from the diamond, and intensity of diffraction features from the sample. Usually select the exposure time that maximizes the intensities of the diffraction peaks without saturation. A typical exposure time is 1-5 s/&#176;. Typical data collection from one crystal at one detector position and one pressure takes about 30 min.</li>
	</ol>
	</li>
</ol>
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
<ol>
	<li>Process the LaB6 calibration file.
	<ol>
		<li>Open the LaB6 powder diffraction image collected at each detector position in the software. Input the wavelength of the incident X-rays (0.434 &#197;), and press the &#34;refine Cal&#34; button. 
		NOTE: The software will automatically calculate the sample-detector distance and the tilt of the detector with respect to the incident X-ray beam. Detector calibration is only conducted at detector positions &#957;=0, &#948;=0. The calibration images collected at non-zero &#957; and &#948; are used for verification of calibration quality.</li>
		<li>Save the calibration files for each detector position by manually editing the &#957; and &#948; settings, as necessary. 
		NOTE: ATREX stores detector calibration .cal files associated with each image series. When opening an image, the program checks if the associated .cal file is present. If it is not, there is the option to select such a file.</li>
	</ol>
	</li>
	<li>After saving the calibrations for all detector positions, create these associations by checking the &#34;Assign cal&#34; checkbox in the ATREX software, so that the program will remember which calibrations to use.</li>
	<li>Search for the sample&#39;s diffraction peaks, and fit the peak intensities.
	<ol>
		<li>Open the wide angle &#966; exposure in the software. Go to the &#34;Search&#34; panel, and search for the diffraction peaks in the wide angle exposure. Manually delete the over-saturated diffraction peaks from the diamond and the diffraction peaks close to the Re gasket rings.</li>
		<li>Fit the diffraction peaks to get their accurate positions and intensities. Search for the sample&#39;s diffraction peaks for all the detector positions by clicking the &#34;peak search&#34; button in software, and save the corresponding peak tables by clicking the &#34;save peaks&#34; button.</li>
	</ol>
	</li>
	<li>Reconstruct the diffraction peaks&#39; distribution in reciprocal space.
	<ol>
		<li>In the program, open the peak table for one detector position, and one image in the step &#966; scan, which is associated with the same detector position. If the detector calibration file has not yet been assigned to this file series, select the appropriate .cal file. Go to the &#34;Scan&#34; panel, and press the &#34;compute Prof. from scan&#34; button. 
		NOTE: This step will find the &#966; angle for each diffraction peak at which the peak intensity is the strongest.</li>
		<li>Save the resulting peak table .pks file. Repeat this step for all the wide rotation images at different detector positions.</li>
	</ol>
	</li>
	<li>Index the diffraction peaks.
	<ol>
		<li>Using the RSV software, open the first peak table file. Use the &#34;Append&#34; function to merge all additional peak tables. Use the RSV plugin to find the preliminary UB matrix of this crystal and to index the diffraction peaks. The software will automatically search for the most probable UB matrix.</li>
		<li>Open the preliminary UB matrix in RSV by importing the .p4p file, and refine the UB matrix with the d-spacing of each diffraction peak using the &#34;Refine w/ d-spac&#34; button. If the symmetry of the crystal is known, select appropriate crystal system constraints. 
		NOTE: When the refinement converges, the optimized UB matrix and the lattice parameters of the crystal (a, b, c, &#945;, &#946; and &#947;) are determined.</li>
		<li>Save the optimized UB matrix as a .ub file. 
		NOTE: In the initial peak search process the program might have missed some low intensity peaks that will be very valuable in the structure determination.</li>
	</ol>
	</li>
	<li>To search for these missing peaks go back to the software, and open the wide angle &#966; exposure image (the associated calibration file should be loaded automatically).</li>
	<li>In the &#34;Predict&#34; panel, open the UB matrix of the crystal and simulate the diffraction pattern. In the &#34;Peaks&#34; panel, search for the observed diffraction peaks, and remove the unobserved peaks (the text box next to the &#34;Observed&#34; button allows to specify the minimum pixel intensity threshold within the peak fitting box that is required for the peak to be considered &#34;observed&#34;). Fit the positions and intensities of the peaks by clicking the &#34;peak fit&#34; button, then save the peak table.</li>
	<li>Merge all the predicted peak tables at different detector positions with the RSV software using the &#34;append&#34; function. If different exposure settings (rotation speed in &#176;/sec) were used, use appropriate scaling factors when opening new .pks files.</li>
	<li>Export the merged peak table as a .hkl text file, which can be used to refine the crystal structure with the SHELX software package. Detailed procedures for conducting structure refinement with SHELX have been well described elsewhere 19,20.</li>
</ol>

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The authors declare no conflict of interest.

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 (&#62;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 &#181;m, 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.

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&#39;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&#39;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 (&#181;, &#951;, &#967; and &#966;) and two detector-orienting (&#948; and &#965;). The angular conventions from You 13 are used to describe the motion of the sample and the detector, although the &#951;, &#967; and &#966; motions are pseudo-angles derived from the instrument&#39;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.

<table><tbody><tr><td>Diamond</td><td>Almax</td><td>P01037</td><td>Boehler-Almax type diamond</td></tr><tr><td>Backing plate</td><td>Almax</td><td>P01289</td><td>Backing plate&#039;s design should match the diamond&#039;s design</td></tr><tr><td>Re gasket</td><td>Alfa Aesar</td><td>10309</td><td></td></tr><tr><td>Epoxy</td><td>Henkel Loctite</td><td>Stycast 2651</td><td></td></tr><tr><td>Polymer micromesh</td><td>MiTeGen</td><td>M3-L18SP-25</td><td></td></tr><tr><td>Goniometer head</td><td>Hampton Research</td><td>HR4-647</td><td></td></tr><tr><td>Software: ATREX</td><td>Open source software</td><td></td><td>Website: https://github.com/pdera/GSE_ADA</td></tr><tr><td>Software: RSV</td><td>Open source software</td><td></td><td>Website: https://github.com/pdera/RSV</td></tr><tr><td>Software: cell_now</td><td>Bruker Corporation</td><td></td><td></td></tr><tr><td>Software: CCD_DC</td><td>Free software</td><td></td><td></td></tr></tbody></table>

high pressure single crystal diffraction at px^2

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 &#177;0.006 &#197;, b = 8.761 &#177;0.004 &#197;, c = 5.248 &#177;0.001 &#197;, &#946; = 105.06 &#177;0.03&#186;, &#945; = &#947; = 90&#186;.

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 &#957; = 0, &#948; = 0 with a LaB6 powder standard (Figure 5). During the experiment, &#951;, &#967; and &#181; angles were fixed at 0. The diffraction peaks of the sample were first analyzed using the &#34;Search&#34; 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 &#34;Predict&#34; function of the software (Figure 8). The refined lattice parameters of this omphacite single crystal at this pressure are: a = 9.496 &#177;0.006 &#197;, b = 8.761&#177;0.004 &#197;, c = 5.248 &#177;0.001 &#197;, &#946; = 105.06 &#177;0.03&#186;, &#945; = &#947; = 90&#186; (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 &#177;0.0005 &#197;, b = 8.7481 &#177;0.0007 &#197;, c = 5.2482 &#177;0.0003 &#197;, &#946; = 106.895 &#177;0.004&#186; 21.
<img alt="Figure 1" src="/files/ftp_upload/54660/54660fig1.jpg" /> 
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. <a href="https://cloudflare-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/54660/54660fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" src="/files/ftp_upload/54660/54660fig2.jpg" /> 
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. <a href="https://cloudflare-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/54660/54660fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" src="/files/ftp_upload/54660/54660fig3.jpg" /> 
Figure 3: Experimental setup for high-pressure single crystal diffraction at PX^2. The six angular degrees of freedom (&#181;, &#951;, &#967;, &#966;, &#948; and &#965;) and the three translational directions (x, y and z) are labeled. The notation for angles follows the angular convention of You 13. <a href="https://cloudflare-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/54660/54660fig3large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" src="/files/ftp_upload/54660/54660fig4.jpg" /> 
Figure 4: Align the sample chamber to the rotation center. Left: sample chamber scans at the X-ray normal direction (blue) and &#966;-rotation by +&#916;&#966; (green) and -&#916;&#966; (red). Right: X-ray transmission profiles of the sample chamber scans at different &#966; angles. The offsets of the X-ray transmission profiles are used to calculate the positional correction along the incident X-ray direction. <a href="https://cloudflare-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/54660/54660fig4large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" src="/files/ftp_upload/54660/54660fig5.jpg" /> 
Figure 5: Calibrating the MARCCD detector using the data analysis software. LaB6 powder diffraction pattern is used to carry out the calibration. <a href="https://cloudflare-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/54660/54660fig5large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 6" src="/files/ftp_upload/54660/54660fig6.jpg" /> 
Figure 6: Diffraction peak search using the data analysis software. In total 63 diffraction peaks were found in this wide exposure image. <a href="https://cloudflare-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/54660/54660fig6large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 7" src="/files/ftp_upload/54660/54660fig7.jpg" /> 
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. <a href="https://cloudflare-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/54660/54660fig7large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 8" src="/files/ftp_upload/54660/54660fig8.jpg" /> 
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. <a href="https://cloudflare-jove-com.bdigitaluss.remotexs.co/files/ftp_upload/54660/54660fig8large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Lattice parameter</td>
			<td>Value</td>
		</tr>
		<tr>
			<td>a</td>
			<td>9.496 &#177;0.006 &#197;</td>
		</tr>
		<tr>
			<td>b</td>
			<td>8.761 &#177;0.004 &#197;</td>
		</tr>
		<tr>
			<td>c</td>
			<td>5.248 &#177;0.001 &#197;</td>
		</tr>
		<tr>
			<td>a</td>
			<td>90&#186;</td>
		</tr>
		<tr>
			<td>b</td>
			<td>105.06 &#177;0.03&#186;</td>
		</tr>
		<tr>
			<td>g</td>
			<td>90&#186;</td>
		</tr>
	</tbody>
</table>
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.

Watch this Scientific Journal Video about High Pressure Single Crystal Diffraction at PX^2 at JoVE.com

High Pressure Single Crystal Diffraction at PX^2

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 ...

high-pressure-single-crystal-diffraction-at-px2

Universidad San Sebastian

Research

JoVE Journal

Chemistry

21.4K Views.  University of Hawai’i at Manoa. 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.

Video: High Pressure Single Crystal Diffraction at PX^2

Synthesis and Microdiffraction at Extreme Pressures and Temperatures

High pressure compounds and polymorphs are investigated for a broad range of purposes such as determine structures and processes of deep planetary interiors, design materials with novel properties, understand the mechanical behavior of materials exposed to very high stresses as in explosions or impacts. Synthesis and structural analysis of materials at extreme conditions of pressure and temperature entails remarkable technical challenges. In the laser heated diamond anvil cell (LH-DAC), very high pressure is generated between the tips of two opposing diamond anvils forced against each other; focused infrared laser beams, shined through the diamonds, allow to reach very high temperatures on samples absorbing the laser radiation. When the LH-DAC is installed in a synchrotron beamline that provides extremely brilliant x-ray radiation, the structure of materials under extreme conditions can be probed in situ. LH-DAC samples, although very small, can show highly variable grain size, phase and chemical composition. In order to obtain the high resolution structural analysis and the most comprehensive characterization of a sample, we collect diffraction data in 2D grids and combine powder, single crystal and multigrain diffraction techniques. Representative results obtained in the synthesis of a new iron oxide, Fe4O5 1 will be shown.

The laser heated diamond anvil cell combined with synchrotron micro-diffraction techniques allows researchers to explore the nature and properties of new phases of matter at extreme pressure and temperature (PT) conditions. Heterogeneous samples can be characterized in situ under high pressure by 2D mapping and combined powder, single-crystal and multigrain diffraction approaches.

High pressure compounds and polymorphs are investigated for a broad range of purposes such as determine structures and processes of deep planetary ...

Engineering

Stress Distribution During Cold Compression of Rocks and Mineral Aggregates Using Synchrotron-based X-Ray Diffraction

We report detailed procedures for performing compression experiments on rocks and mineral aggregates within a multi-anvil deformation apparatus (D-DIA) coupled with synchrotron X-radiation. A cube-shaped sample assembly is prepared and compressed, at room temperature, by a set of four X-ray transparent sintered diamond anvils and two tungsten carbide anvils, in the lateral and the vertical planes, respectively. All six anvils are housed within a 250-ton hydraulic press and driven inward simultaneously by two wedged guide blocks. A horizontal energy dispersive X-ray beam is projected through and diffracted by the sample assembly. The beam is commonly in the mode of either white or monochromatic X-ray. In the case of white X-ray, the diffracted X-rays are detected by a solid-state detector array that collects the resulting energy dispersive diffraction pattern. In the case of monochromatic X-ray, the diffracted pattern is recorded using a two-dimensional (2-D) detector, such as an imaging plate or a charge-coupled device (CCD) detector. The 2-D diffraction patterns are analyzed to derive lattice spacings. The elastic strains of the sample are derived from the atomic lattice spacing within grains. The stress is then calculated using the predetermined elastic modulus and the elastic strain. Furthermore, the stress distribution in two-dimensions allow for understanding how stress is distributed in different orientations. In addition, a scintillator in the X-ray path yields a visible light image of the sample environment, which allows for the precise measurement of sample length changes during the experiment, yielding a direct measurement of volume strain on the sample. This type of experiment can quantify the stress distribution within geomaterials, which can ultimately shed light on the mechanism responsible for compaction. Such knowledge has the potential to significantly improve our understanding of key processes in rock mechanics, geotechnical engineering, mineral physics, and material science applications where compactive processes are important.

We report detailed procedures for compression experiments on rocks and mineral aggregates within a multi-anvil deformation apparatus coupled with synchrotron X-radiation. Such experiments allow quantification of the stress distribution within samples, that ultimately sheds light on compaction processes in geomaterials.

We report detailed procedures for performing compression experiments on rocks and mineral aggregates within a multi-anvil deformation apparatus (D-DIA) ...

Environment

Fully Autonomous Characterization and Data Collection from Crystals of Biological Macromolecules

High-brilliance X-ray beams coupled with automation have&#160;led to the use of synchrotron-based macromolecular X-ray crystallography (MX) beamlines for even the most challenging projects in structural biology. However, most facilities still require the presence of a scientist on site to perform the experiments. A new generation of automated beamlines dedicated to the fully automatic characterization of, and data collection from, crystals of biological macromolecules has recently been developed. These beamlines represent a new tool for structural biologists to screen the results of initial crystallization trials and/or the collection of large numbers of diffraction data sets, without users having to control the beamline themselves. Here we show how to set up an experiment for automatic screening and data collection, how an experiment is performed at the beamline, how the resulting data sets are processed, and how, when possible, the crystal structure of the biological macromolecule is solved.

Here, we describe how to use the automated screening and data collection options available at some synchrotron beamlines. Scientists send cryocooled samples to the synchrotron, and the diffraction properties are screened, the data sets are collected and processed and, where possible, a structure solution is carried out&#8212;all without human intervention.

High-brilliance X-ray beams coupled with automation have&#160;led to the use of synchrotron-based macromolecular X-ray crystallography (MX) beamlines for ...

Biochemistry

Measurements of Long-range Electronic Correlations During Femtosecond Diffraction Experiments Performed on Nanocrystals of Buckminsterfullerene

The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the results of femtosecond X-ray free electron laser (XFEL) experiments. An increasing number of experimental observations have shown that although nuclear motion can be negligible, given a short enough incident pulse duration, electronic motion cannot be ignored. The current and widely accepted models assume that although electrons undergo dynamics driven by interaction with the pulse, their motion could largely be considered &#39;random&#39;. This would then allow the supposedly incoherent contribution from the electronic motion to be treated as a continuous background signal and thus ignored. The original aim of our experiment was to precisely measure the change in intensity of individual Bragg peaks, due to X-ray induced electronic damage in a model system, crystalline C60. Contrary to this expectation, we observed that at the highest X-ray intensities, the electron dynamics in C60 were in fact highly correlated, and over sufficiently long distances that the positions of the Bragg reflections are significantly altered. This paper describes in detail the methods and protocols used for these experiments, which were conducted both at the Linac Coherent Light Source (LCLS) and the Australian Synchrotron (AS) as well as the crystallographic approaches used to analyse the data.

We describe an experiment designed to probe the electronic damage induced in nanocrystals of Buckminsterfullerene (C60) by intense, femtosecond pulses of X-rays. The experiment found that, surprisingly, rather than being stochastic, the X-ray induced electron dynamics in C60 are highly correlated, extending over hundreds of unit cells within the crystals1.

The precise details of the interaction of intense X-ray pulses with matter are a topic of intense interest to researchers attempting to interpret the ...

An All-in-one Sample Holder for Macromolecular X-ray Crystallography with Minimal Background Scattering

Macromolecular X-ray crystallography (MX) is the most prominent method to obtain high-resolution three-dimensional knowledge of biological macromolecules. A prerequisite for the method is that highly ordered crystalline specimen need to be grown from the macromolecule to be studied, which then need to be prepared for the diffraction experiment. This preparation procedure typically involves removal of the crystal from the solution, in which it was grown, soaking of the crystal in ligand solution or cryo-protectant solution and then immobilizing the crystal on a mount suitable for the experiment. A serious problem for this procedure is that macromolecular crystals are often mechanically unstable and rather fragile. Consequently, the handling of such fragile crystals can easily become a bottleneck in a structure determination attempt. Any mechanical force applied to such delicate crystals may disturb the regular packing of the molecules and may lead to a loss of diffraction power of the crystals. Here, we present a novel all-in-one sample holder, which has been developed in order to minimize the handling steps of crystals and hence to maximize the success rate of the structure determination experiment. The sample holder supports the setup of crystal drops by replacing the commonly used microscope cover slips. Further, it allows in-place crystal manipulation such as ligand soaking, cryo-protection and complex formation without any opening of the crystallization cavity and without crystal handling. Finally, the sample holder has been designed in order to enable the collection of in situ X-ray diffraction data at both, ambient and cryogenic temperature. By using this sample holder, the chances to damage the crystal on its way from crystallization to diffraction data collection are considerably reduced since direct crystal handling is no longer required.

A novel sample holder for macromolecular X-ray crystallography along with a suitable handling protocol is presented. The system allows crystal growth, crystal soaking and in situ diffraction data collection at both, ambient and cryogenic temperature without the need of any crystal manipulation or mounting.

Macromolecular X-ray crystallography (MX) is the most prominent method to obtain high-resolution three-dimensional knowledge of biological macromolecules. ...

Sample Preparation and Transfer Protocol for In-Vacuum Long-Wavelength Crystallography on Beamline I23 at Diamond Light Source

Long-wavelength macromolecular crystallography (MX) exploits the anomalous scattering properties of elements, such as sulfur, phosphorus, potassium, chlorine, or calcium, that are often natively present in macromolecules. This enables the direct structure solution of proteins and nucleic acids via experimental phasing without the need of additional labelling. To eliminate the significant air absorption of X-rays in this wavelength regime, these experiments are performed in a vacuum environment. Beamline I23 at Diamond Light Source, UK, is the first synchrotron instrument of its kind, designed and optimized for MX experiments in the long wavelength range towards 5 &#197;. 
To make this possible, a large vacuum vessel encloses all endstation components of the sample environment. The necessity to maintain samples at cryogenic temperatures during storage and data collection in vacuum requires the use of thermally conductive sample holders. This facilitates efficient heat removal to ensure sample cooling to approximately 50 K. The current protocol describes the procedures used for sample preparation and transfer of samples into vacuum on beamline I23. Ensuring uniformity in practices and methods already established within the macromolecular crystallography community, sample cooling to liquid nitrogen temperature can be performed in any laboratory setting equipped with standard MX tools. 
Cryogenic storage and transport of samples only require standard commercially available equipment. Specialized equipment is required for the transfer of cryogenically cooled crystals from liquid nitrogen into the vacuum endstation. Bespoke sample handling tools and a dedicated Cryogenic Transfer System (CTS) have been developed in house. Diffraction data collected on samples prepared using this protocol show excellent merging statistics, indicating that the quality of samples is unaltered during the procedure. This opens unique opportunities for in-vacuum MX in a wavelength range beyond standard synchrotron beamlines.

Here, we present a protocol for cryogenic sample preparation and transfer of crystals into the vacuum endstation on beamline I23 at Diamond Light Source, for long-wavelength macromolecular X-ray crystallography experiments.

Long-wavelength macromolecular crystallography (MX) exploits the anomalous scattering properties of elements, such as sulfur, phosphorus, potassium, ...

On-Chip Crystallization and Large-Scale Serial Diffraction at Room Temperature

Biochemical reactions and biological processes can be best understood by demonstrating how proteins transition among their functional states. Since cryogenic temperatures are non-physiological and may prevent, deter, or even alter protein structural dynamics, a robust method for routine X-ray diffraction experiments at room temperature is highly desirable. The crystal-on-crystal device and its accompanying hardware and software used in this protocol are designed to enable in situ X-ray diffraction at room temperature for protein crystals of different sizes without any sample manipulation. Here we present the protocols for the key steps from device assembly, on-chip crystallization, optical scanning, crystal recognition to X-ray shot planning and automated data collection. Since this platform requires no crystal harvesting nor any other sample manipulation, hundreds to thousands of protein crystals grown on chip can be introduced into an X-ray beam in a programmable and high-throughput manner.

This contribution describes how to set up protein crystallization on crystal-on-crystal devices and how to perform automated serial data collection at room temperature using the on-chip crystallization platform.

Biochemical reactions and biological processes can be best understood by demonstrating how proteins transition among their functional states. Since ...

Automated Protein Crystallization and Real-Time Data Collection

Crystallization and In Situ Room Temperature Data Collection Using the Crystallization Facility at Harwell and Beamline VMXi, Diamond Light Source

Protocols for robotic protein crystallization using the Crystallization Facility at Harwell and in situ room temperature data collection from crystallization plates at Diamond Light Source beamline VMXi are described. This approach enables high-quality room-temperature crystal structures to be determined from multiple crystals in a straightforward manner and provides very rapid feedback on the results of crystallization trials as well as enabling serial crystallography. The value of room temperature structures in understanding protein structure, ligand binding, and dynamics is becoming increasingly recognized in the structural biology community. This pipeline is accessible to users from all over the world with several available modes of access. Crystallization experiments that are set up can be imaged and viewed remotely with crystals identified automatically using a machine learning tool. Data are measured in a queue-based system with up to 60&#176; rotation datasets from user-selected crystals in a plate. Data from all the crystals within a particular well or sample group are automatically merged using xia2.multiplex with the outputs straightforwardly accessed via a web browser interface.

Author Spotlight: Advancing Protein Structure Analysis for Drug Development 

We present a protocol for the crystallization of proteins using the crystallization facility in the Research Complex at Harwell and subsequent in situ X-ray crystallographic data collection from crystals within the plates at Diamond&#39;s Versatile Macromolecular Crystallography in situ (VMXi) beamline. We describe sample requirements, crystallization protocols, and data collection guidelines.

Protocols for robotic protein crystallization using the Crystallization Facility at Harwell and in situ room temperature data collection from ...

X-ray Diffraction

Source: Faisal Alamgir, School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA
X-ray diffraction (XRD) is a technique used in materials science for determining the atomic and molecular structure of a material. This is done by irradiating a sample of the material with incident X-rays and then measuring the intensities and scattering angles of the X-rays that are scattered by the material. The intensity of the scattered X-rays are plotted as a function of the scattering angle, and the structure of the material is determined from the analysis of the location, in angle, and the intensities of scattered intensity peaks. Beyond being able to measure the average positions of the atoms in the crystal, information on how the actual structure deviates from the ideal one, resulting for example from internal stress or from defects, can be determined.
The diffraction of the X-rays, that is central to the XRD method, is a subset of the general X-ray scattering phenomena. XRD, which is generally used to mean can wide-angle X-ray diffraction (WAXD), falls under several methods that use the elastically scattered X-ray waves. Other elastic scattering based X-ray techniques include small angle X-ray scattering (SAXS), where the X-rays are incident on the sample over the small angular range of 0.1-100 typically). SAXS measures structural correlations of the scale of several nanometers or larger (such as crystal superstructures), and X-ray reflectivity that measures the thickness, roughness, and density of thin films. WAXD covers an angular range beyond 100.

X-Ray Diffraction for Determining Atomic and Molecular Structure

Source: Faisal Alamgir, School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA
X-ray diffraction (XRD) is a technique ...

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Growing Crystals for X-ray Diffraction Analysis

Source: Laboratory of Dr. Jimmy Franco - Merrimack College
X-ray crystallography is a method commonly used to determine the spatial arrangement of atoms in a crystalline solid, which allows for the determination of the three-dimensional shape of a molecule or complex. Determining the three-dimensional structure of a compound is of particular importance, since a compound&#39;s structure and function are intimately related. Information about a compound&#39;s structure is often used to explain its behavior or reactivity. This is one of the most useful techniques for solving the three-dimensional structure of a compound or complex, and in some cases it may be the only viable method for determining the structure. Growing X-ray quality crystals is the key component of X-ray crystallography. The size and quality of the crystal is often highly dependent on the composition of the compound being examined by X-ray crystallography. Typically compounds containing heavier atoms produce a greater diffraction pattern, thus require smaller crystals. Generally, single crystals with well-defined faces are optimal, and typically for organic compounds, the crystals need to be larger than those containing heavy atoms. Without viable crystals, X-ray crystallography is not feasible. Some molecules are inherently more crystalline than others, thus the difficulty of obtaining X-ray quality crystals can vary between compounds. The growth of X-ray crystals is similar to the process of recrystallization that is commonly used for purifying compounds, but with an emphasis on producing higher quality crystals. Often, higher quality crystals can be obtained by allowing the crystallization process to proceed slowly, which may occur over the course of day or months.

Source: Laboratory of Dr. Jimmy Franco - Merrimack College
X-ray crystallography is a method commonly used to determine the spatial arrangement of atoms ...