lumigen instrument center x-ray crystallographic ... ttk 450 stage xrd_2.pdf · [email protected]...

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Updated: 2020 March 6

LUMIGEN INSTRUMENT CENTER X-RAY CRYSTALLOGRAPHIC

LABORATORY: WAYNE STATE UNIVERSITY

Standard Operating Procedure for the TTK 450 Stage

Contact Manager:

Dr. Cassie Ward Dr. Sameera Perera

[email protected] [email protected]

Office room 061 Chemistry Office room 135 Chemistry

(313) 577-2587

Location

Lumigen Instrument Center X-Ray Crystallographic Laboratory

Department of Chemistry

Wayne State University 050.1 Chemistry Building

5101 Cass Avenue

Detroit, MI 48202

LIC Lab: (313) 577-0518

Safety Requirements for the X-ray Crystallographic Laboratory

Access to the lab will be revoked if you do not follow these safety procedures.

1. While working in the X-Ray Crystallographic Laboratory, researchers are always

required to wear Personal Protective Equipment (PPE). The appropriate PPE include

dosimetry ring, safety glasses, long pants/skirt covering the legs completely, closed-toe

shoes, and gloves. Do not wear gloves while using the computer keyboard or mouse. All

required PPE needs to be supplied by the user. Dosimetry rings must not be removed

from the lab.

2. Food and beverages cannot enter the lab. Never eat or drink inside the phaserlab.

3. Please keep the area around the instruments and prep stations clean. If you use the lab’s

sample holders, clean them after use. Properly dispose glass waste in the appropriate

container. All samples must be properly disposed of in your research lab.

4. Following a spill, please clean it up with a paper towel or broom. If you are unsure how

to clean up the spill, contact the lab manager (Dr. Ward) or the LIC Director (Dr.

Westrick). If the spill occurs after hours with personal injury, please contact WSU police

department (7-2222) and Dr. Westrick, immediately. If samples come in contact with the

eyes, use the emergency eye wash station. Turn on the cold water on high and pull the

knob to the eye wash. Run water to the eyes for 15 minutes.

5. The Standard Operating Procedures (SOPs) are next to the instruments. The users are to

follow what is written in these procedures.

6. You must log the usage time into the appropriate instrument logbook.

7. All researchers working in LIC must complete the EH&S initial course for Laboratory

Safety Training and Radiation (X-ray) Generating Machine training and show proof of

completion. Users whose safety training has expired will not be permitted access to the

laboratory.

8. Users must also sign the Wayne State University Laboratory Specific Training Form

(Appendix L).

9. In case of an instrument malfunction, turn off the instrument and contact Dr. Ward

immediately.

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Be aware that the X-Ray Crystallography Laboratory has a red binder containing the

Chemical and Laboratory Safety Information. It is located on the second shelf above the

dosimetry rings cabinet. This contains the Department of Licensing and Regulatory

Affairs Radiation Safety Section Ionizing Radiation Rules.

Additional Safety Requirements for the D8 ADVANCE XRD

1. In case of an instrument malfunction, turn off the instrument (Figure 1) press one of the

two red buttons. Contact Dr. Ward immediately, or the WSU police (313-577-2222) if

occurrence is after hours.

Figure 1: Picture of the D8 ADVANCE. Highlighted in the red circles are the emergency shut-

off buttons. The blue circle is the Open Door button.

Training and Usage Requirements

Before Training:

1. All users must pass the online EH&S Laboratory Safety Training and Radiation (X-ray)

Generating Machine training (https://about.citiprogram.org/en/homepage/). Print the

certificate after completing the quiz and bring it to Dr. Ward. The two safety trainings

must be completed every Janurary and the printed certificate must be brought to Dr.

Ward.

2. A dosimetry form must also be filled out (http://research.wayne.edu/oehs/pdf/dosimetry-

request-form.pdf) and signed by Dr. Westrick. Bring the signed form to Dr. Ward.

3. You must have an Infinity account and have requested access to the Lumigen X-ray

Laboratory. You must also have an index number assigned to you from your PI.

4. Contact Dr. Ward for training.

After training:

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5. You can reserve time for the D8 ADVANCE using the calendar in Infinity.

6. Dosimetry rings must be worn while working in the lab. The rings are stored in the

cabinet next to the sink.

7. You must write your first and last name legibly and the hours of use into the Logbook

that is next to the instrument.

Overview

1. The TTK 450 Stage is designed for reflective x-ray diffraction (XRD) to determine the

underlying structure, phase, and identification of a powder or polycrystalline material

(bulk or thin-film) under various environmental conditions.

2. The TTK 450 can control the chamber temperature in the range -193°C to 450°C

i. To reach < 120°C or >300°C, the vacuum (10-2 mbar) pump must be used.

ii. To reach < 20°C, liquid nitrogen is required. (A vacuum or dry nitrogen is

recommended due to condensation inside the stage when below room temperature.)

iii. The chamber can be filled with other gases in the temperature range -120°C (with

the liquid nitrogen) to 300°C. The stage can only hold ~2.9 psi. It is up to the user

to provide the gas and a regulator.

Sample Preparation

1. The TTK 450 Stage is shown in Figure 2, which the temperature is controlled through

the TCU 110 Temperature Control Unit (Figure 3).

2. To open the instrument door, push the Door Open button on the right of the door (Figure

1, blue circle) and pull open the glass door.

Figure 2: TTK 450 stage for heating >300°C or cooling samples below room temperature in

vacuum.

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Figure 3: TCU 110 temperature controller box.

3. Inside the TTK 450 Stage is shown in Figure 4. The sample holder is removed by

unplugging the PT100 then slide the holder out towards you.

4. Check the paste on the bottom of the holder and the stage where the holder was to ensure

the paste is still soft. If necessary, remove the dried paste with a cloth and alcohol. Then

apply more heat conducting paste (in the blue box on the shelf above the computer) to the

bottom of the sample holder by placing some paste on a glass slide and move the sample

holder over the paste until covered uniformly.

5. Using the sample holder pictured in Figure 5:

i. Add powder samples to cover the entire rectangular area and level with a glass

slide.

ii. For bulk or thin-film samples, set the sample onto the holder. The height of the

sample holder is 0.8 mm and bulk sample taller/shorter will need to be adjusted. It

is suggested by Anton Paar to not measure bulk or thin-films under vacuum due to

heat transfer problems.

iii. Caution: Bulk/thin-film samples are difficult to measure because of irreproducible

thermal transfer. This stage also does not have a computer controlled z-position, so

XRR or GI-XRD will not be very accurate. It may still be possible to determine

film thickness or phase identification.

6. Place the sample holder in the sample slot, Figure 4. Connect the Pt100 before closing

the chamber.

7. The sealed chamber will look like Figure 2 if a vacuum is needed. The chamber does not

need to be completely sealed if running from 25 to 300°C in air.

8. The water cooling circuit needs to be turned on (Figure 14).

9. Turn on the TCU 110 controller and push the heater button next to the display.

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Figure 4: Inside the TTK 450 chamber.

Figure 5: Sample holder for the TTK 450.

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10. If needed, turn on the vacuum and/or liquid nitrogen (Figures 12 and 15). The nitrogen

Dewar pressure gauge is already set to 0.6 bar. It is important that the clamp to the

siphon is closed so the pressure can build up inside the Dewar to push the liquid nitrogen

into the cryostat of the sample chamber.

11. The cooling button on the TCU 110 controller turns off the cooling device (Figure 3).

12. It is recommended to use the vacuum or dry nitrogen to illuminate condensation onto

your sample when running low temperatures.

13. The TTK 450 stage can be operated with inert gases in the temperature range -120°C

(with the liquid nitrogen) to 300°C. An adaptor with a Teflon tube and a ¼” NPT will

connect to a ¼” MNPT. Use the other Swagelok fittings to connect to a gas line.

14. Before changing the temperature, run the sample at room temperature to ensure the

sample is correctly in place and at the right height. If the height needs adjusted, loosen

the two screws on the base place. Then loosen or tighten the screw shown in Figure 6 to

move the stage down or up, respectively. Height adjustments shift the peak positions in

the diffraction pattern. Alternatively, peaks can be shifted after a measurement using

EVA for post-data processing.

Figure 6: The TTK 450 closed without the vacuum tubing when running samples from room

temperature to 300°C. The arrow is pointing at the set-screw for sample height adjustments.

Operating the Instrument

This SOP will cover how to use the software with this stage and how to perform Bragg-Brentano

geometry.

1. Open the program pinned to the task bar at the bottom called DIFFRAC.COMMANDER

(has “XRD” in the icon). If there is a communication error, close the program and double

click the Measurement Server icon on the desktop to initiate communication with the

instrument. Then re-open the DIFFRAC.COMMANDER program.

Height

Adjustment

Set Screw

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Figure 7: Screen shot of the DIFFRAC.COMMANDER program in the Commander Tab

2. Under the Commander Tab in the program (Figure 7), the first section is called

Instrument Components, which controls the Goniometer parameters (the theta angles of

the x-ray source and detector), and the Twin Optics. If there is nothing listed under the

Commander Tab, then there may be a connection problem. Go to File and click on

Connect. Hit CONNECT. Do not change the IP address.

i. The program is usually opened and operating. However, if the program was closed,

upon opening the program, instead of green check marks, as shown in Figure 8,

there will be yellow ‘!’. Click the check boxes to the Theta and Detector (Figure 8)

and hit the Initialize All Checked Drives (label 2 in Figure 8). Every parameter

should now have a green check mark as shown in Figure 8.

ii. Initialize Component (labeled 1) will move the detector and/or radiation source to a

given value (Figure 8) when the box is checked.

iii. Twin-Primary is the motorized slit on the x-ray source and will most likely be set to

0.681 mm*.

iv. Twin-Secondary is the motorized slit on the detector side and can be set to 4.988*

mm (fully open) for a high number of counts.

v. *These are the suggested shutter values for novice users. To change a value, enter

the desired slit width and hit Apply New Value to the Instrument Settings (label 3)

3. The next section is the X-Ray Generator (Figure 9)

i. The voltage needs to be high enough to produce enough ejected electrons to hit the

target material (Cu or Mo) to generate x-rays.

1. For Cu x-rays, voltage needs to be 40 kV and current is 40 mA.

2. For Mo x-rays, voltage needs to be 50 kV and current is 30 mA.

ii. The Tube (Cu or Mo) will automatically be selected based on which tube source is

installed. If the source tube needs to be changed, please notify Dr. Ward at least

24 hrs in advance.

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Figure 8: Screen shot of the Instrument Components section. The icon labeled 1 is the Position

All Checked Drives, which activates any of the parameters that are checked. The icon labeled 2

is the Initialize All Checked Drives, which should only be clicked when first opening the

program. The icon next to label 3 is Apply New Value to the Instrument Settings.

4. In the TCU 110 Controller section, the temperature can either be fixed at one temperature

during a scan (as shown in Figure 9) or changed to Set Temperature with Rate. To

change the temperature, enter in the value and check the box and click on “Apply new

value(s) to the instrument settings” (label 1).

5. Detector should be set to LYNEYE_EX_T (1D mode for powder sampled, 0D mode for

thin-films). In the properties button, the check mark button to the right of the Detector

pull down menu, make sure that High Resolution is selected for 1D mode.

Figure 9: X-Ray Generator menu and TCU 110 Controller menu in the

DIFFRAC.COMMANDER program. Label 1 is “Apply new values(s) to the instrument

settings”.

1

3

2

1

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6. In the Scan Setup section (Figure 11)

i. Scan type select Coupled TwoTheta/Theta.

ii. Scan mode select Continuous PSD fast for powder samples.

iii. Adjust the Time (integration time) and the range of the scan in the two boxes

labeled 1 and 2 in Figure 11 in the row 2Theta (°). Set the Increment step size,

which is labeled 3 in Figure 11. The 2Theta scan range for powder samples is 3-

129°.

Figure 11: Scan Setup menu.

7. After the scan is completed, save your data in the correct extension you need. Make

sure to take your saved data with you when finished. The Crystallographic Laboratory is

not responsible for storing and maintaining your data.

8. Remove the sample only when the chamber temperature reads 25°C. If the chamber is

under a vacuum, very very slowly start to crack open the chamber. If the chamber is

opened too quickly your sample will be blown everywhere and you will have to clean out

the entire inside chamber.

Standard Reference Materials

1. LaB6 standard can be used in the TTK 450 stage in the temperature limits of this stage.

i. Preparation of LaB6 NIST Standard (660c)

1. A bottle of LaB6 is provided in the lab and can be prepared by the user.

2. The reflection indices and peak position for LaB6 using the Cu x-ray source

can be found on the NIST website https://www-

s.nist.gov/srmors/view_cert.cfm?srm=660c

3. The following table is data collected from this instrument with the Mo source

at two temperatures, 25° and 230°C (Dec 2017), and the NIST values using a

Cu source.

4. The sample holder surface is made of Cr-plated copper and may appear in the

sample’s diffraction pattern. Ni and Pt peaks have also appeared in the

diffraction patterns. A background scan of the empty sample holder could be

performed to help identify peaks contributed from the sample holder.

https://www-s.nist.gov/srmors/view_cert.cfm?srm=660c

https://www-s.nist.gov/srmors/view_cert.cfm?srm=660c

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Removing the TTK 450 Stage

2. Removing any of the stages should be performed only by Dr. Ward.

3. In the program, move both the source (Theta) and the detector to 20°.

4. Close the program. Turn off the TCU 110 unit. Turn off the vacuum pump (Figure 12).

Figure 12: Vacuum pump for the TTK 450 behind the instrument.

5. Shut off the instrument using the instructions located on the instrument (Figure 13). If

you are not sure how to do this, please ask before proceeding.

6. Turn off the water to the stage (directly behind the instrument, Figure 14). Double check

that you turned off the valves for the TTK 450 water lines. Also, make sure the liquid

nitrogen tank is closed (Figure 15), if used.

LaB6

h k l NIST (Cu) 25°C (Mo) 230°C (Mo)

1 0 0 21.358 9.79 9.79

1 1 0 30.385 13.86 13.86

1 1 1 37.442 16.98 16.99

2 0 0 43.507 19.65 19.64

2 1 0 48.958 21.98 21.98

2 1 1 53.990 24.13 24.11

2 2 0 63.220 27.92 27.91

3 0 0 67.549 29.65 29.64

3 1 0 74.747 31.30 31.28

3 1 1 75.846 32.87 32.84

2 2 2 79.872 34.37 34.35

3 2 0 83.847 35.83 35.80

3 2 1 87.794 37.23 37.20

4 0 0 95.673 39.90 39.87

4 1 0 99.645 41.19 41.16

3 3 0 103.663 42.45 42.41

3 3 1 107.752 43.67 43.63

4 2 0 111.936 44.86 44.82

2θ

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Figure 13: Front of the D8 ADVANCE with the turn on/off instructions in the red circle.

Figure 14: Ball valves for the water lines to the TTK 450 stage in the ON position.

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Figure 15: Liquid nitrogen tank next to the computer in the closed and open position.

7. Figure 16 shows the source when the power is on. Neither of the lights on the source

should be on when removing or replace a stage. Follow the instructions on the

instrument to turn it off.

Figure 16: X-ray source. The yellow light indicates the instrument is ON.

8. Remove the vacuum tube. Pull out the two water lines quick disconnects and unplug the

liquid nitrogen connector, the heater and temperature sensor connector, and the

temperature controller box connector (Figure 4).

9. Take out the 3 screws (Figure 17).

10. Rotate the stage counter-clockwise until the two red dots are aligned, and pull the stage

out.

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Figure 17: TTK 450 stage showing the 3 screws to remove the stage.

Connecting the TTK 450 Stage

1. Make sure the power to the x-ray source is off (Figure 13).

2. Insert the TTK 450 Stage with the two red dots aligned and rotate the stage clockwise

until the three screw holes are aligned.

3. Tighten down the three screws (Figure 17)

4. Connect the two water lines quick disconnects, the liquid nitrogen connector, the heater

and temperature sensor connector, and the temperature controller box connector (Figure

4).

5. Turn on the water (Figure 14).

6. Turn the power to the instrument back on (Figure 12).

7. Turn on the TCU 110 (Figure 3). Push the heater button next to the display on the TCU

110.

8. Depending on the desired temperature, turn on the vacuum (Figure 12) and the liquid

nitrogen dewar tank (Figure 15).

9. Open the DIFFRAC.COMMANDER program.

Basic Principles of XRD

1. X-ray radiation is produced by applying a high voltage (5-40 kV) across a filament to

discharge electrons focused at a target. Specifically, this target is either made of Cu or

Mo, which produces x-rays with a wavelength of 1.54 Å or 0.71 Å, respectively.

i. You must ask Dr. Ward to have the x-ray source changed.

ii. To run thin-film samples for GI or XRR, the Cu tube must be used (parallel beam

geometery).

2. The x-ray beam is directed at the sample at an angle theta (θ). When the x-rays encounter

an atom (or electron density), they can be absorbed, reflected, or transmitted. If the x-rays

are reflected/scattered at an angle θ, then Bragg’s Law is obeyed, and maximum intensity

results (Figure 18) and you get a diffraction pattern.

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3. The atoms in a powder or polycrystalline material are arranged in a periodic fashion such

that the diffracted waves will consist of sharp constructive interference peaks. The

position and intensities of these peaks are used to identify the underlying structure.

Figure 18: Example of a crystal lattice where the black circles represents atoms (or lattice points),

the purple arrows are the incoming and scattering x-ray radiation at wavelength λ, n is an integer,

d is the distance between crystal lattices, and θ is the angle of the incident/scattered radiation.

Bragg diffraction only occurs when the scattered radiation constructively interferes, which is

described by the conditions stated in Bragg’s Law.

4. Determining the identity, structure, or indices of a sample from the collected diffraction

pattern can be accomplished using the EVA or TOPAS programs, which are on the same

computer controlling the XRD.

5. The appropriate sample types include crystalline organic or inorganic solids, such as

metals, oxides, clay minerals, soil, rocks, cement, and synthetic materials. XRD is a non-

destructive technique, so most samples can be recollected after the measurement.

References

1. Bruker. (2010). D8 ADVANCE/D8 DISCOVER: User Manual Vol. 1, Karlsruhe,

Germany.

2. “Instruction Manual: TTK 450 Low-Temperature Chamber with TCU 110 Temperature

Control Unit” (2014) Anton Paar.

Appendix: Additional Information

1. The TWIN optics installed on the D8 ADVANCE are automated (computer controlled) to

switch between parallel-beam geometry (Göbel mirror) and Bragg-Brentano parafocusing

geometry. The Göbel mirrors will only reflect Cu radiation, so Mo cannot be used in

parallel-beam geometry.

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2. The LYNXEYE XE-T detector functions as a digital monochromator, removing sample

fluorescence, Kβ radiation, and background scattering. We do not need to use Kβ filters,

Ni mirrors, or monochromators.

Above is a figure of the XRD with all the components labeled for user’s reference.

lumigen instrument center x-ray crystallographic ... ttk 450 stage xrd_2.pdf · [email protected]...

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