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NOTE: Sample preparation is discussed in more detail under Sample Preparation for XRD Analyses in the main Laboratory Manuals, Guides and Resources>XRD confluence page.
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.
Grinding Solid Samples
There are three primary ways to grind samples:
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Mortar and pestle is the most common method for sediment. Below, each method is outlined. Any sample material remaining once all analyses are complete can be given to the Curator at the end of the expedition to be sent back to the repository. Any sample that has been treated should be disposed of at End of Expedition, when all possible rescans and special treatments are completed.
Drying Samples
Freeze-dry sample(s) for at least 12 hours before grinding. If the samples still feel cold when removed from the dryer, the samples still have moisture in them and need to dry longer.
The freeze dryer is comprised of a sample "bell" chamber and a Labconco freeze-dryer. On the bell are two valves, as shown in Figure 5. Each valve has an "Open" and "Closed" position. The top valve controls the vacuum inside of the bell, and the bottom valve controls the air flow between the cooling coil and bell. A valve parallel with the tube is open and allows air flow; a valve perpendicular with the tube is closed. In Figure 5, configuration A (closed) will hold a vacuum, but configuration B (open) will not.
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Figure 5. (A) Freeze dryer bell valves in closed position. (B) Freeze dryer bell valves in open position.
To freeze-dry samples
- Cut open the sealed sample bags and fold the top edge over to keep the bag open.
- Take the top of the bell off of the dryer and arrange samples in the bell, making sure no sample bags are pinched closed.
- Open the vacuum valves slowly so that you do not cause a large rush of air to blow the samples around. Figure 5A shows the configuration to dry samples and Figure 5B shows the configuration for loading and unloading samples.
- Flip the "On" switch located on the right side of the Freeze Dryer.
- Press the "Auto Refrigeration" button (Figure 6A) and then the vacuum button (Figure 6B). The temperature will start to drop and the vacuum pump will turn on.
- When the temperature drops to –40°C, the vacuum is created in the bell and the pressure drops.
- Expect the temperature to be between –42° and –52°C and the pressure to be ~0.350 mBar.
- The indicator lights (Figure 6D) show how the cooling and pressure reduction are progressing. When all indicator are lights are on the freeze dryer is at its peak performance.
- If there is an error the red "Alarm" light will turn on. Press the "Menu" button (Figure 6C) to view it and clear it if necessary.
- After samples are dry, slowly open the valves to release the vacuum in the bell. Remove the samples from the bell and store them inside the desiccator until they are ready to be ground to prevent reabsorption of moisture.
Figure 6. Freeze dryer control panel.
Mortar and Pestle
Choose the appropriate mortar and pestle size (large or small) and place it on the counter (Figure 8). Obtain a glass slide, a sample holder, and a scoopula (Figure 7). Clean all items after each use with isopropyl alcohol and a KimWipe.
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Figure 7: Mortar and pestle sample preparation set up.
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Mixer Mills
The follow instructions are for two mixer mills, Spex 8000 and the Newer Retsch MM400. Currently the Retsch MM400 is the recommended mixer mill to use and it is located in X-Ray Prep or MBIO area of Chem lab.
Figure 8: Spex 8000 mixer mill. Featured are the safety latch, timer dial, and start/stop button in the middle of the dial.
To operate the 8000 mixer mill, turn the knob to the desired time and press the "Start" button in the middle. That button will also stop the mixer mill. The dial does not move automatically, so if it is turned to 5 minutes it will stay there. The dial does not need be set back to 0 to work.
Grinding Vessels
There are three types of grinding vessels available for the 8000 mixer mill: alumina ceramic, tungsten carbide, and hardened steel (Figure 9). Tungsten carbide and steel vessels are better for more robust grinding, and alumina ceramic is better for minimizing contamination. Check with the Science Party to see which vessel type is preferred.
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Figure 9: Three types of mixer mill grinding vessels.
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Figure 10: Steel vessel components. (A) Lid (B) Container (C) Steel Grinding Ball (D) O-Ring
Figure 11: Tungsten carbide vessel. (A) Vessel container (B) Lid (C) Tungsten carbide grinding ball
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Label the vessel with a small printed label of the sample it holds. After the sample is ground, transfer that label to an 8 or 16 mL snap cap bottle that will hold the powder.
Loading the Grinding Vessel into the Mill
Put your sample inside the vessel. The material should be approximately the size of a pea to prevent any jamming and to ensure all pieces are ground up. Place 1 to 2 grinding balls inside the container. Tungsten carbide and steel vessels can take up to 2 balls. The alumina ceramic vessel is more brittle and 1 ball is recommended. Finish assembling the grinding vessel and open the lid to the mixer mill.
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Figure 13: Inside the 8000M mixer mill. Highlighted is the sample holder clamp that holds the grinding vessels, the primary lock, and the secondary lock.
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Starting the Mill
Set the timer to the desired grinding time. The time will vary depending on sample material. Start with a conservative time, 2 to 3 minutes, check the material, and add more time if the sample still feels gritty. Harder rocks can go up to 10 minutes or higher to grind down to the right sample consistency. When the mill finishes grinding, remove the vessel the same way as it was put into the clamp: hold the vessel firmly against one clamp while unscrewing the primary lock. Keep the vessel straight and hold it firmly. If one of the lids starts to crack open, sample material will spill into the machine. If this happens, clean up the powder with a damp towel. Any leftover powder can get into the motor and damage it.
Transferring Powder
Collect a metal tray, weigh paper (large or small), 8 or 16 mL clear snap cap bottles, a scoopula, Kim Wipes, and isopropyl alcohol. Clean all materials with isopropyl alcohol. Place a piece of weigh paper on the metal tray. Pour the sample material from the grinding vessel onto the weighing paper. Use the scoopula to scrape the sides and lids of the vessel to remove extra material. Transfer the sample from the weighing paper into the sample vial. Label the vial with a small printed label and label the cap with a permanent marker.
Cleaning the Vessels
Clean the grinding vessels with a toothbrush and DI water. In some cases the vials are still dirty or have sample stains on them. If so, take a small amount, approximately 5 mL, of silica sand and grind it in the mixer mill for ~3 minutes. Then pour out the sand (can be trashed in burnables or collected and thrown overboard) and clean the vessel with DI water and a toothbrush or green scrub pad. Lay out cleaned vessel parts on a Kim Towel and dry with a Kim Wipe. The cork rings take a longer to dry, so collect fresh, dry rings before grinding the next sample.
Retsch MM400 Mixer Mill
The manufacturer's manual for the Retsch MM400 can be found here (in Retsch MM400 XRD Lab Notebook). Figure 14 shows the Retsch mixer mill.
Figure 14: Retsch MM400
Figure 15. Agate grinding jars and ball.
Each grinding jar for the Retsch mill (Figure 15) has a main jar, a lid, a ball, and a white teflon spacer. Use the spacer to avoid damaging the agate (Figure 16). The inside of the jar and lid are lined with agate and the ball is of made of agate. Poor the freeze dried soft sediment (not hard rock) grains into the jar. Fill the jar half way to three-fourths with sample. Place one grinding ball in the jar. Clean off any of the sediment sample with a kimwipe that has gotten onto the jars threads and screw the lid on. Be mindful not to cross thread the lid to the jar.
Figure 16. Agate grinding jars with teflon spacer and the bent metal spatula for removing the teflon spacer.
Loading the Jar into the Grinding Mill
Place closed grinding jar horizontally in the clamps. Verify the pin is in closed position (Figure 17) and tighten the clamps by turning the handle until the jar is securely tighten (hand tight is good). Close lid and select desired program to run.
Figure 17. Retsch jar clamp
Starting the Mill
After the grinding jars are secured in the clamps, the pin is in the closed position and the clear cover is closed it is time to select grinding settings (Figure 19). Program 1 (A) is currently set for 12 min at 25 1/s. This setting is good for clay rich material. Softer sediments such as CaCO3 typically need less time. It is important to only grind soft sediments in the agate jars and hard material should be ground in the shatter box. After Grinding cycle has completed turn knob counter clockwise and pull pin up and into its open position (Figure 19A). Unscrew clamp and open jar to verify grind size. If sediment is still too coarse regrind.
Figure 18. A) Preset programs. B) The shaker frequency C) The time grinder is set for D) The start and stop.
Transferring Powder
After grinding is complete remove grinding jar from clamps. Rotate black screw counter clockwise a quarter turn and pull the pin up into the open position (Figure 17). When the pin is in the open position unscrew black knob until grinding gar is loose enough to remove. Unscrew grinding jar, poor powder onto weigh paper or directly into clean and labeled sample bag or sample vial.
Cleaning the Jars
To clean the jars amd grinding ball rinse with DI water and kim wipes until kimwhipes come out clean. Finish cleaning by rinsing with isopropal alcohol and drying with kim wipe. Use the bent metal spatula to pry out the white teflon spacer, we have spares but those can be reused many times.
Shatterbox
Shatterbox vessels are not commonly used for sediment XRD samples. Please refer to the XRD Sample prep for hard rock samples for instructions for using the shatterbox.
Preparing Sample Holders for the D4
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The initial window (Figure 31) will open. The left half of the screen is the file input where you select the files you want to convert. The right half of the screen is where you select the new converted file type and where the files should go.
Figure 30: First window in File Exchange. (A) Input File Type dropdown menu (B) Input DATA folder (C) Output File Type dropdown menu (D) Output DATA folder (E) Convert button
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