lumigen instrument center x-ray crystallographyic … xrk 900 stage xrd.pdf · powder or...

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Updated: 2020 March 6

LUMIGEN INSTRUMENT CENTER X-RAY CRYSTALLOGRAPHYIC

LABORATORY: WAYNE STATE UNIVERSITY

Standard Operating Procedure for the XRK 900 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 lab.

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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10. 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.

2. Do not touch the stage after a temperature measurement until it has reached 25°C.

3. Do not use corrosive, poisonous, or explosive materials or gases in the XRK 900 stage.

4. The windows of the XRK 900 stage reaction chamber are made of beryllium, which is

toxic if inhaled. Do not touch or puncture the windows. If the windows are broken,

evacuate the room and call WSU police.

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.

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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:

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 XRK 900 Stage is designed for reflective powder x-ray diffraction (XRD)

measurements to determine the underlying structure, phase, and identification of a

powder or polycrystalline material (bulk or thin-film) under various environmental

conditions.

2. Thin-films can be measured in this stage. The stage is equipped with a computer

controlled z-position translator, so XRR or GI-XRD can be performed.

3. The XRK 900 can be pressurized from 1 mbar up to 10 bars (0.01-145 psi). A vacuum

pump is provided for low pressure measurements, and tubing from the stage to the gas

regulator is provided. It is up to the user to provide the gas cylinder with the appropriate

regulator. The stage can hold reducing, oxidizing or inert atmospheres.

4. The XRK 900 can control the chamber temperature in the range 25-900°C.

Sample Preparation

1. The XRK 900 Stage is shown in Figure 2, which the temperature of the stage is

controlled through the TCU 750 Temperature Control Unit (Figure 3).

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Figure 2: XRK 900 stage.

Figure 3: TCU 750 located behind the front panel of the instrument. The top temperature is the

temperature of the sample holder, while the bottom is the temperature of the chamber.

2. There are two sample holders for the XRK 900 stage reaction chamber (Figure 4). An

“open” sample holder is used to allow a reaction gas to pass through the sample, hence

the holes in the holder (Figure 4). For measurements in a vacuum or with stationary gas,

the “closed” sample holder has to be used. The sample holders are made of Macor (a

glass-ceramic material), which is necessary to run above 600°C, but are extremely fragile

and should only be handled by Dr. Ward.

3. The powder sample can be added to the holder, while the holder is on the stand (Figure

5a). Make sure the height of the sample is level with the sample holder’s outer ring using

a glass slide. There is an anti-scattering shield and retainer that sits on top of the sample

holder to reduce background scatter. It is recommended for low 2θ values. They can be

found in the accessary box above the computer station.

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Figure 4: Picture of the closed and open sample holders

Figure 5: A) Sample holder in the stand. B) Inserting the sample holder into the XRK 900

reaction chamber.

4. 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.

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5. Insert the sample holder into the XRK 900 stage reaction chamber (Figure 5b). The

sample holder is inserted into the stage from the bottom and secured by the four fixing

screws.

6. To measure the XRD pattern of a thin-film material, place the thin-film material on the

sample holder. There is a Macor disk that fits inside the sample holder that should be

used to prop up the thin-film so that the height of the film is above the sample holder

ledge.

7. Once the sample holder is securely locked in place, connect the gas inlet from the sample

holder to the stage and connect the thermocouple cable to the stage (Figure 6).

Figure 6: XRK 900 Reaction Chamber Stage with all the connectors labelled.

8. On the diffractometer, when running powder samples, it is usually not necessary to

include a divergence slit, but Soller slits are necessary to help collect and collimate the

scattered x-rays.

9. For thin films, see the XRR or GI-XRD SOP to set up the diffractometer.

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

sample is correctly in place and at the right height (which is adjustable in the program,

next section).

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Operating the Instrument

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

geometry. To use this stage with a thin-film sample in parallel-beam geometry, use the GI-XRD

or XRR SOP.

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.

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 sample number and the Goniometer

parameters (the theta angles of the x-ray source and detector). 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 (red box in

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).

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.

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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 Z_XRK900 will adjust the height of the sample for accurate peak positions (when

using a known standard).

Figure 8: Screen shot of the Instrument Components section of the DIFFRAC.COMMANDER

program. 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.

Figure 9: X-Ray Generator and TCU 750 Controller sections

4. 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

3

2

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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.

5. The TCU 750 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).

6. Detector should be set to LYNEYE_EX_T (1D mode). 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.

7. In the Scan Setup section (Figure 10)

Figure 10: Scan Setup menu.

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 10 in the row 2Theta (°). Set the Increment step size,

which is labeled 3 in Figure 10. The 2Theta scan range for powder samples is 3-

129°.

8. 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.

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

under a vacuum or pressure, slowly open the gas/vacuum seal. 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 is provided by the Crystallographic Laboratory.

i. Preparation of LaB6 NIST Standard (660c):

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

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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 for Mo sources (Dec

2017) at two temperatures, and the NIST values using Cu. If the peaks are

shifted, the sample height can be automatically changed using the Z_XRK900

input in the Instrument Components section (section 7.b.iv).

Removing the XRK 900 Reaction Chamber Stage

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

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

3. Close down the program. Make sure the vacuum pump is off (Figure 11).

Figure 11: Vacuum pump behind the instrument.

4. Shut off the instrument using the instructions located on the instrument (Figure 12). If

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

LaB6

h k l NIST (Cu) 25°C (Mo) 230°C (Mo)

1 1 0 30.385 13.88 13.87

1 1 1 37.442 17.00 16.99

2 0 0 43.507 19.65 19.64

2 1 0 48.958 21.99 22.00

2 1 1 53.990 24.12 24.12

2 2 0 63.220 27.91 27.90

3 0 0 67.549 29.63 29.62

3 1 0 74.747 31.26 31.25

3 1 1 75.846 32.84 32.82

2 2 2 79.872 34.33 34.31

3 2 0 83.847 35.79 35.77

3 2 1 87.794 37.18 37.14

2θ

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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5. Turn off the water to the stage (directly behind the instrument, Figure 13). Double check

that you turned off the valves before removing the water lines connected to the XRK 900

stage.

Figure 12: Front of the D8 ADVANCE with the turn on/off instructions in the red circle.

Figure 13: Ball valves for the water lines to the XRK 900 stage in the ON position.

6. Figure 14 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.

7. Remove the sample holder and place it on the sample holder stand.

8. Disconnect the computer cable, the vacuum or gas line, thermocouple to TCU 750

connector, heater connector, and the water lines (Figure 6). Make sure the sample holder

has been removed before removing the stage.

9. Take out the 3 screws on the stage plate to the goniometer. Rotate the stage counter-

clockwise until the two red dots are aligned, and pull the stage out.

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Figure 14: X-ray source. The yellow light indicates the instrument is ON.

Connecting the XRK 900 Stage

1. Make sure the power to the x-ray source is off (Figure 14).

2. Insert the XRK 900 Stage with the two red dots aligned and rotate the stage clockwise

until the three screw holes are aligned. Tighten down the three screws.

3. Connect the computer cord, the vacuum or gas line, thermocouple to TCU 750 connector,

heater connector, and the water lines (Figure 6).

4. Open the ball valves to the water (Figure 13).

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

6. Turn on the heater to the TCU 750 (button next to the display, Figure 3).

7. (Optional) Connect the vacuum line to the Teflon line with the vacuum adaptor and

Swagelok ¼” screw on the two ends (Figure 15) or if gas is being used, connect the

provided Teflon line to the gas tank and the other end to the ¼” Swagelok inlet.

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Figure 15: Connecting the vacuum hose to the Teflon tube with the vacuum adaptor to the

¼” Swagelok inlet at the 900 XRK stage.

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 at low angles, the Cu tube must be used.

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 16) and you get a diffraction pattern.

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 16: 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

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

Germany.

2. “Instruction Manual: XRK 900 Reaction Chamber” (2014) Anton Paar, Graz, Austria.

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.

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 crystallographyic … xrk 900 stage xrd.pdf · powder or...

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