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Sample preparations are split into two main categories:
A. Bulk powder samples
B. Clay separations
Before running samples, go over the methods with scientists and check for any special sample requests.

Preparing Sample Holders for the D4

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1. Place a small amount of sample powder in the center of a quartz or single crystal quartz disk.
2. Add 2–3 drops of 70 % isopropyl alcohol or distilled water to the sample. Note: Isopropyl dries faster than water.
3. Spread the sample to a thin layer using a glass rod. The slurry should be spread evenly across the disk. If there is not enough material to cover the entire disk, concentrate the sample in the middle of the disk where the X-rays will contact the sample.
4. Place the sample in the desiccator to dry before running in the XRD.

Clay Separations

Clay Separations focus on separating the clay size fraction, <2 µm, 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.

Removing Carbonates before Clay Separation

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.

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).

1. Place sample in centrifuge tube with 25 mL of 10 % Acetic Acid for at least 1 hour to decarbonate (it helps to place the centrifuge tubes on the agitator in the cold room) 
   1. Please note, that sample with a large amount of carbonate (more than 50%) may require more than 1 treatment of Acetic to reach complete decarbonation.
2. Centrifuge for 15 mins at 1500 rpm, decant and wash with 25 mL of nanopure water (3X to remove all 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.

1. Place undried sample on a glass slide or quartz disk.
2. Using a Pasteur pipette, slowly drop 2M HCl on the sample until bubbling/fizzing stops.
3. 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. Those listed below are methods used on-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 in Figure 22. 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.
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Figure 22: The dismembrator set up. Included is the soundproof box and the Probe with power source.

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Figure 23: Dismembrator power source control Panel. (A) On/Off switch (B) Start button (C) Set button (D) Mode button

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1. 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. 
2. 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 20B). 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.

Standard IODP Clay Separation Method: Not for Semi-quantitative Analysis

1. In centrifuge tube, mix a small amount of bulk sample (~5 mL; fresh, not dried) with 1% borax solution. Use agitator or dismembrator, if necessary to suspend particles.
2. Centrifuge the borax solution/sample mix at 750 rpm for 4 minutes to remove the >2 µm size fraction
3. Decant the supernatant liquid (containing suspended clay) into a new centrifuge tube 
4. Centrifuge the <2 µm fraction for 15 mins at 1500 rpm to remove the Borax solution
5. Decant the borax solution and add 25 mL of nanopure water to wash the clay
6. Repeat Steps 4 and 5 as necessary to remove the borax (USGS recommends repeating up to 4-5 times)

Alternative method from Exp. 379

1. Add 25 mL of 1% Borax solution to the clay plug 
2. Dismembrate the sample (machine is auto set on time), to remove the >2 µm clay fraction
3. Centrifuge for 4 mins at 750 rpm, decant the supernatant liquid into a separate centrifuge tube (you should end up with a ~full centrifuge tube of suspended clay)
4. Repeat steps 1–3 on the remaining >2 µm fraction
5. Centrifuge the <2 µm fraction for 15 mins at 1500 rpm to remove the Borax solution 
6. Decant and add 25 mL of nanopure water
7. Centrifuged for 60 mins at 3000 rpm, the liquid decanted before loading onto a zero background silica disk.

Preparing the Mount

Clay mounts are put onto a zero-background silicon disk that fits into a 2 mm steel sample holder (Figure 24). Only put the disks into sample holders that have a hole drilled in the bottom. The hole allows the disks to be taken out, otherwise they are stuck inside the holder. The disk should sit flush with the sample holder. Some of the disks are at different depths, so a quartz insert disk can also be put in the bottom of a sample holder with the silicon disk on top. Do not force the zero background disks into the holder, it may break.

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Figure 24: Steel sample holder with silicon disk

1. Remove the <2 µm size fraction by collecting the uppermost 1 cm of solution with an eye dropper (it helps to add a little isopropanol). If necessary resuspend flocculated clay particles using the dismembrator and add more borax solution.
2. If material is still very suspended, try centrifuging the samples for 4 minutes at 750 rpm. In this instance, the >2 µm size fraction will be the only fraction suspended in the liquid and all the larger grains will be packed in the bottom. Take the suspended material with an eyedropper and put it on the quartz disk.
3. Make an oriented clay mount by placing 2–3 drops (enough to cover the disk) of clay suspension directly onto the silicon disk. If the material is not spreading evenly, add a drop or two of 70% isopropanol and spread the material around with a small glass rod. Once spread, let the sample dry in the desiccator. The clay particles orient themselves as the solution dries on the disc. Note that it can be difficult to determine if there is enough material on the disc for a scan. Sometimes it may appear as if there is no sediment in the upper 1-2cm and thus nothing on the disk. Try scanning in the XRD first, it is surprising what the XRD will return. If the scan is not satisfactory add a few more drops from a bit deeper in the test tube. 
4. Once the sample is dry, you are ready to run it through the D4. If there are additional treatments requested, continue to the sections below.

Additional Clay Treatments before Scanning

Treating with Ethylene Glycol

The following techniques are modified from the U.S. Geological Survey Open-File Report 01-041, A Laboratory Manual for X-Ray Powder Diffraction. Ethylene glycol can be used to expand swelling clays (e.g., smectites, montmorillonite, nontronite, and beidellite), some mixed-layer clays, and vermiculite as an aid to mineral identification. There are two ethylene glycol treatment methods:

1. Vapor
2. Quick

 Vapor Treatment

The advantage of the vapor treatment is less disturbance of the sample and less amorphous scattering of X-rays by excess liquid than in the Quick method.

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Figure 25: Glycolator

1. Find the "glycolator" container (Figure 25) stored in the ICP preparation sink cupboard.
2. Pour ethylene glycol to a depth of ~1 cm in the bottom of the container.
3. Take off the lid and place the samples on the rack inside the glycolator.
4. Place glycolator in an oven (60°–70°C) overnight (~12 hours).
5. Figure 19: Glycolator.Keep samples in the glycolator until ready to run through the D4. Glycolation only lasts for 4 hours after the samples are removed from the glycol atmosphere.

Before placing samples in the D4, wipe all sides of the sample holder with a Kim Wipe to remove any ethylene glycol. Ethylene glycol is sticky and can damage the grabber arm and sample spinner.

Quick Treatment

1. Using a glass rod or eye dropper, apply a drop of ethylene glycol directly to the surface of the sample mount.
2. Samples are ready to be analyzed as soon as the glycol is uniformly absorbed on the sample mount. Excess ethylene glycol may be gently mopped up with a Kim Wipe.

Heating Samples

Several clays have intensity peaks at very similar angles making it difficult to distinguish one clay from another. Heating clays is a way to work around this. We can run a sample through the D4, heat the sample in the muffle furnace, run again, and then compare the scans. For example, kaolinite and chlorite have overlapping peaks, making it hard to differentiate one from another. Heat morphs kaolinite, and it develops an amorphous signal, essentially removing its presence in the scan and leaving only the chlorite signal. The amount of kaolinite and chlorite can be determined by comparing these scans.

1. Prepare an oriented clay mount by adding several drops onto a zero-background Si disk in a sample holder and spreading it out evenly with a glass rod.
2. Put the clay mount in the desiccator until it dries.
3. Put the sample in the muffle furnace in the Chemistry Laboratory.

Different temperatures and heating times are used when trying to identify different minerals. Confer with your scientist to determine the parameters.

1. When the muffle furnace has finished heating and is cooling down, wait until the temperature reaches between 100° and 200°C before removing the sample. The sample can be placed in the desiccator until it reaches room temperature. Once it has completely cooled down it can be run in the D4.

Clay Separation Method for removal of Chlorite

For the double peaks of Kaolinite and Chlorite, heating the sample only suggest that one of the minerals is present, it will not give final and complete results for a sample that contains both Kaolinite and Chlorite. In order to determine which mineral is present, an additional treatment is necessary.

1. Take the <2 µm clay fraction, this should be rinsed and free of any treatments, in centrifuge tube add ~20 mL of 1N HCl
2. Vortex the sample to completely dislodge all material before pouring sample into a 100 mL beaker, add stir bar once sample is in place
3. Set hotplate to 300°C (boiling point of HCl is ~101, but in order to maintain a continuous boil the hotplate needs to be much hotter)
4. Set the stir RPM below 100, this is only to keep the material suspended within the HCl
5. Start time once the samples have come to a complete boil, leave for 2 hours — add more HCl as necessary (DO NOT, let the sample go dry and burn)
6. Once the sample has boiled for 2 hours, turn off hot plate and allow sample to return to room temperature before pouring beaker contents back into a clean centrifuge tube, rinse beaker with DI water to collect all material
7. Centrifuge down for 15 mins at 1500 rpm, decant acid and rinse with 25 mL nanopure (3X)
8. After samples has been washed 3X and is free of HCl, centrifuge for 60 mins at 3000 rpm

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Running Samples in the D4

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