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Clay Separations focus on separating the clay size fraction, >2um<2um, from the rest of the material. In order to get only that size fraction we prepare the sample in a different way. Do not freeze dry samples waiting for clay separations. If the samples have already been dried the treatments will still work but using fresh, wet samples is easier. Below are outlined various treatments and methods we do on board.
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It may be necessary to dissolve the carbonates in the sediment to better identify the clay minerals. The goal is to remove as much carbonate as possible to isolate the material contained within the carbonate for analysis. There are two standard methods for removing carbonate aboard the JOIDES Resolution: hydrochloric acid (HCl) and acetic acid. Ask the Science party which method they prefer. If there is no preference, use acetic acid.
Hydrochloric Acid Treatment
HCl is the simplest method for removing carbonate from sediment but does have severe drawbacks. Strong acids damage the mineral structure, especially within trioactahedral minerals. Before proceeding, be aware that this treatment may affect clay crystallinity.
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Acetic Acid Treatment
This is the recommended treatment for carbonate removal. The process is slightly more involved than the HCl procedure, but far less damage is done to the mineral structure. The following steps are from Kitty Milliken (UT-Austin).
- Place ~2 cm3 of undried sample into a 50 mL centrifuge tube. This should approximately fill the bottom cone of the tube. Then add 25 mL of a 10% acetic acid solution. Mix well and let sit until the reaction ceases; this may take a few minutes or up to an hour. The samples can sit in the acid overnight with no harm. You may need to stir the sample and break it up with a spatula a few times.
- Periodically shake the sample until the reaction has stopped (i.e., no more bubbles).
- In the Chemistry Laboratory, spin the sample in the centrifuge for 15 minutes at 1500 rpm
- Decant the acetic acid solution into the sink while running water down the drain to flush the acid through the pipes.
- Add 25 mL of DI (nanopure) water to the centrifuge tube and centrifuge again for 15 minutes at 1500 rpm.
- Decant the water.
- Repeat the "wash cycle" (Steps 4 and 5). The water wash should be done at least twice to flush out all of the acetic acid. When the sample stops smelling strongly of vinegar, you can move on to separating clay.
Separating Clay
Hydrochloric Acid Treatment
HCl is the simplest method for removing carbonate from sediment but does have severe drawbacks. Strong acids damage the mineral structure, especially within trioactahedral minerals. Before proceeding, be aware that this treatment may affect clay crystallinity.
- Place undried sample on a glass slide or quartz disk.
- Using a Pasteur pipette, slowly drop 2M HCl on the sample until bubbling/fizzing stops.
- Desiccate and transfer sample to sample holder for analysis.
Separating Clay
There are various methods for separating clay from coarser material involving a series of centrifuging or gravity settling. There are various methods for separating clay from coarser material. Those listed below are methods used onboardon-board.
If you removed carbonates first, start here after your water washes are finished and the water has been decanted. If you did not remove carbonates, take approximately 5 mL of sample material and put into a centrifuge tube.
Suspending Material
Get the sonic dismembrator case and probe power source. Using the dismembrator is a very effective way to fully and randomly suspend the material. Suspended material can then separate out according to size, with the largest grain size on the bottom and the very small clay size fraction on top.
The dismembrator setup is shown on the left in Figure 19. The power source is connected to the probe. The probe fits into the case through a hole in the top. Put the probe into the top clamp and the sample tube into the bottom clamp. Adjust the positions so the probe goes into the tube. The probe should be about half-way into the sample material without touching the sides of the tube. The probe releases a lot of energy, and if it is touches the sides it will heat up the tube and the sample. 
Figure 19 (above): The dismembrator set up. Included is the soundproof box and the Probe with power source.
Figure 20: Dismembrator power source control Panel. (A) On/Off switch (B) Start button (C) Set button (D) Mode button
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- Add ~25 mL of a 1% borax solution into the centrifuge tube. Borax prevents the sample from flocculating. Too much Borax however will increase flocculation.
- Put the tube into the bottom clamp inside the dismembrator case. When satisfied with the positioning, press the "Start" button on the probe power supply (Figure 17B). If the material does not appear to be circulating throughout the whole tube or the tube is heating up, adjust the probe position and start the dismembration over.
- Let samples settle overnight (~12 hours). The next morning, the material should be separated out with the clear liquid filling most of the tube and sediment filling the bottom cone.
"Quick and Dirty" Clay Separation Method: Not for
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Semi-quantitative Analysis
- In centrifuge tube, mix a small amount of bulk sample (~5 mL; fresh, not dried) with 1% borax solution. Use an ultrasonic bath or dismembrator, if necessary.
- Centrifuge the borax solution/sample mix at 1000 rpm for 5 minutes to remove the >2 µm size fraction.
- Decant the borax solution (containing suspended clays) into a new centrifuge tube and spin it at 1500 rpm for 15 minutes to remove the remaining <2 µm clay size fraction.
- Decant the borax solution and wash the clay residue with distilled water.
- Spin-down again at 1500 rpm for 15 minutes. Repeat Steps 4 and 5 as necessary to remove the borax.
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10. The spreadsheet has the calculations already embedded. Remove background (subtract background).
If If you get the RED "ZI correction must be applied" message shows up, you will need to open the Configuration and adjust the home position for the 2Theta drive. If there is no message just save the worksheet under a new name and no more action is needed.
Apply ZI Coorection
Open the Configuration Program on the desktop.
In the left side panel navigate to Motorized Drives > 2Theta. In this window go to Zero Reference - Home of the Axis. Enter the corrected ZI value from the excel spreadsheet into the 'Zero' space.
Select 'File' > 'Save and Download' or click on the red CNF arrow.
the configuration program Motor Drives > 2θ > Zero Refer. Enter the current ZI value in the excel spreadsheet – the Corrected ZI value is what you need to update/change the configurations ZI value to. Save and Download. DO NOT CHECK THE BOX FOR THE PSD CONTROLLER. Downloading the config file to the PSD Controller corrupts the Controller. For more information see the Troubleshooting section. Always backup the config.file on the server. With ONLY the 'Save Configuration' and 'Download Configuration to Diffractometer' boxes checked select 'OK'. The new configuration will take a moment to download to the Diffractometer.
Now that the scan is complete put the Anti Air Scatter Screen back on. Move the y drive to the 360 position and open the front door. Line up the Screen with the screw holes. There is a small divet and you will feel the Screen settle into place when positioned correctly. Then carefully put on the screws. When the Screen is back in place close the door and put the cover back on the base.
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The Endeavor D4 has Endeavor has several safety issues that should be reviewed. Please see the Bruker Manual D4 Endeavor XRay Diffractometer – Introductory User Manual for the list of precautions.
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Save the file under a new name to the path Local Disk C: > DIFFDAT1 > DIFFDAT1_old computer pre March 2013. You can print this file by clicking the "Report" tab at the top the subtree window and then clicking the print icon. Occasionally scientists will ask for a printout of the settings to put in their reports.
Checking Quality of a Scan
A peak should have have a minimum of 5 data points above the halfway up a peak. During an active scan in XRD Commander go to the main 'Adjust' tab and right click in the measurement window. Select 'dots'. The scan changes from a continuous line to the individual data points. Zoom in on a few peaks and count how many dots are above the halfway point on a scan. It is fine to have more than 5 points but less than 5 means the peak shape is not well resolved. If less than five suggest to scientist a longer measuring time.
Troubleshooting
For specific errors or instructions on adjusting or realigning components on the D4 please refer to the D4 hardware maintenance binders in the XRD lab.
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