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.

Transcript

The overall goal of this high pressure single crystal diffraction technique is to determine the crystal structure of minerals at the environment of the earth's deep interior. This measure can help answer key questions in geophysics and geochemistry such as determining the completion of earth's mineral and coal, all explaining the assessment of these continuities inside the earth. The main advantage of this technique is that it is mostly direct and a straightforward measure to determine the structure of minerals at high pressures and temperatures.

Begin this procedure with sample preparation as described in the text protocol. Place approximately one milligram of lanthanum hexaboride powder at the rotation center of the diffractometer to collect powder diffraction patterns at several marCCD detector positions. Collect the powder diffraction patterns by clicking the start button on the marCCD EPICS interface.

Use this diffraction pattern to calibrate the detector sample distance and the tilt of the marCCD detector. After completing the detector calibration, remove the lanthanum hexaboride standard from the diffractometer. Place the diamond anvil cell or DAC in the sample holder.

Then put the sample holder on the diffractometer sample stage. To achieve all the motion controls with the EPICS user interface or EUI, first rotate the phi axis so that the sample chamber is perpendicular to the view and zoom camera by setting the phi angle to 120. Then find the sample chamber with the viewing camera at the minimum magnification.

Center the sample's image by changing the sample X, Y, and Z in the EUI. Focus the image of the sample by adjusting the microscope Z in the EUI. Then zoom in to the maximum magnification.

Align the sample chamber'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's access 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 phi angle to 90 in the EUI so that the sample chamber is perpendicular to the incident x-ray beam.

To correct for sample displacement from the center of the instrument along the DAC axis, use the Scan W Software. Scan the DAC position in both horizontal and vertical directions perpendicular to the incident x-ray. Use motorized translations built into the goniometer while collecting transmitted beam intensity data with a photo diode detector placed behind the sample.

The photo diode detecter is mounted on a neumatic actuator and can be moved in and out of the beam remotely from the control station. Find the center position in the collected intensity scan corresponding to maximum transmission using the center function of Scan W.This is the center of the sample chamber. In the EUI rotate the sample using the goniometer phi access by a few degrees and repeat the vertical transmission scan.

Repeat the scan twice at both positive and negative phi offsets. After aligning the sample, collect the single crystal diffraction data with the CCD DC Software. At first, collect a phi scan with a photo diode by clicking the scan button on the Scan W software.

This scan determines the maximum opening angle and the functional shape of the absorption effect of the diamond anvils and backing plates. A wide phi exposure is then performed to cover the maximum opening angle that the DAC allows followed by a series of one degree step phi exposures. To carry out this step, set the total range to the maximum opening angle and set the number of steps to the same number in the CCD DC Software.

Collect wide phi scans at different detector positions by specifying the detector arm position in the delta and neu directions in the CCD DC software. This allows access to more diffraction peaks. Following data processing as described in the text protocol search for the samples diffraction peaks and fit the peak intensities.

To do so open the wide angle phi exposure in the software. Go to the search 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 uranium gasket rings.

Fit the diffraction peaks to their accurate positions and intensities. Search for the sample's diffraction peaks for all the detector positions by clicking the peak search button in the software and save the corresponding peak tables by clicking the save peaks button. Next, reconstruct the diffraction peak's distribution in reciprocal space by opening the peak table for one detector position.

Also, open one image in the step phi 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 scan panel and press the compute profile from scan button.

This step will find the phi angle for each diffraction peak at which the peak intensity is the strongest. Save the resulting peak table pks file. Then repeat this step for all the wide rotation images at different detector positions.

Next, index the diffraction peaks using the RSV software. First, open the first peak table file. Then use the append 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. Open the preliminary UB matrix in RSV by importing the P4P file.

Then refine the UB matrix with the d spacing of each diffraction peak using the refined with d spacing button. If the symmetry of the crystal is known, select the appropriate crystal system constraints. When the refinement converges, the optimized UB matrix and the lattice parameters of the crystal are determined.

Save the optimized UB matrix as a UB file. In the initial peak search process the program might have missed some low intensity peaks that are valuable in the structure determination. To search for these missing peaks, go back to the software and open the wide angle phi exposure image.

In the predict panel, open the UB matrix of the crystal and simulate the diffraction pattern. In the peak's panel search for the observed diffraction peaks and remove the unobserved peaks. Fit the peak positions and intensities of the peaks by clicking the peak fit button.

Save the peak table before exporting the merged peak table as described in the text protocol. The sample chamber is aligned to the rotation center which is carried out by scanning the sample chamber with an x-ray. The sample chamber scans at the x-ray normal direction and phi rotation by plus delta phi and minus delta phi.

Shown here are the x-ray transmission profiles of the sample chamber scans at different phi angles. The offsets of the x-ray transmission profiles are used to calculate the positional correction along the incident x-ray direction. The marCCD detector is then calibrated using the data analysis software.

Shown here is the lanthanum hexaboride powder diffraction pattern which is used to carry out the calibration. The diffraction peak search was performed using the data analysis software. In total 63 diffraction peaks were found in this wide exposure image.

Indexing of the diffraction peaks is performed automatically by the software. Shown here is the UB matrix calculation of the crystal sample using the RSV software. 112 diffraction peaks were found with the same diffraction image using the peak prediction function.

Once mastered, this technique can be done in one to two hours, if it is performed properly. While attempting this procedure it is important to remember to align simple property with the x-ray to get the correct diffraction peak in this case. After watching this video you should have a good understanding of how to carry out high pressure single crystal diffraction experiments.

Other measures like high pressure powder x-ray diffraction can be performed to studies in knowing crystal structures with less experimental time. After its development, this technique paved its way for researchers in the field of mineral effects to explore the structures of minerals in deeper earth's conditions.

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Journal (Chemistry)

Journal (Chemistry)

High Pressure Single Crystal Diffraction at PX^2

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