LUMIGEN INSTRUMENT CENTER X-RAY ... Flip Stick Stage XRD.pdfDr. Cassie Ward Dr. Sameera Perera...

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Updated: 2020 March 6

LUMIGEN INSTRUMENT CENTER X-RAY CRYSTALLOGRAPHIC

LABORATORY: WAYNE STATE UNIVERSITY

Standard Operating Procedure for the Flip-Stick 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.

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.

Quick Overview

1. The Flip-Stick Stage is used for reflective x-ray diffraction (XRD) measurements of up to

nine samples.

2. The Flip-Stick can also spin samples.

Sample Preparation

1. The Flip-Stick Stage is shown in Figure 2, which can accommodate up to nine samples,

and it can also spin a sample.

Figure 2: Flip-Stick stage for using up to nine samples

2. Use a circular sample holder, an example is shown in Figure 3. Place a small amount of

sample on the holder, making a 1 cm diameter (~0.5-1 g). Make sure the height of the

sample is level with the plastic outer ring of the holder by using a glass slide.

i. Some of the sample holders have a height-adjustable middle region. Adjust the

height of this middle region based on how much sample will be used.

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Figure 3: Example of a powder sample in the round holder

3. To measure the XRD pattern of a bulk material, place the material in the middle of the

sample holder, and make sure the height of the sample is level with the sample holder’s

outer ring using a glass slide. Make height adjustments to the middle region, pushing it

up or down. The sample does not need to be adhered to the holder. If the sample height

is higher than the sample hold then the z position of the stage can be changed by

performing a z scan in 0D detector mode.

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

2, blue circle) and pull open the glass door. Place the sample holder in one of the nine

sample slots, Figure 4.

Figure 4: Sample in the sample position 2 (1A02).

1. On the diffractometer, it is usually not necessary to include a divergence slit, but Soller

slits are necessary to help collect and collimate the scattered x-rays.

Operating the Instrument

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

geometry.

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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.

2. Under the Commander Tab in the program (Figure 5), 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 nothing is 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.

Figure 5: Screen shot of the DIFFRAC.COMMANDER program in the Commander Tab

Figure 6: Screen shot of the Instrument Components section of the DIFFRAC.COMMANDER

program. Select the Sample Position using the drop down menu, labeled 1. The icons labeled 2

is “Load Selected Sample into the Instrument”, 3 is “Unload Sample from the Instrument”, 4 is

2 3 4 1

5 6

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“Initialize Component” (activate the sample to be measured), 5 is “Position All Checked

Drives”, and 6 is “Initialize All Checked Drives”.

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 6,

there will be yellow ‘!’. Click the check boxes next to the Theta and Detector and

then hit the “Initialize All Checked Drives” (label 6 in Figure 6). Every parameter

should now have a green check mark as shown in Figure 5.

ii. In the “Sample Pos.” row, select the sample number to run (1A01 through 1A09).

Figure 6 shows a sample loaded in 1A02 (label 1).

iii. To load the sample, hit the “Load Selected Sample into the Instrument” label 2 in

Figure 6.

iv. Then hit “Initialize Component” to move the sample into the position to be

irradiated. Icon labeled 4 in Figure 6.

v. Synchronous rotat can be checked if spinning the sample is desired.

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

0.681 mm*.

vi. 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.

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

the desired slit width, check the box next to the new value, and hit Apply New

Value to the Instrument Settings next to the checkmark box.

Figure 7: X-Ray Generator menu in the DIFFRAC.COMMANDER program.

3. The next section is the X-Ray Generator (Figure 7)

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.

iii. 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.

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4. In the Scan Setup section (Figure 8),

Figure 8: 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 is 3-129°.

5. After the scan is completed, save your data. Make sure to take your saved data with you

when finished. The Crystallographic Laboratory is not responsible for storing and

maintaining your data.

Standard Reference Materials

1. Two standards are provided by the Crystallographic Laboratory.

2. Corundum (Alumina (Al2O3)) NIST Standard (676a). Do not touch the surface of the

corundum. This sample should be handled by a trainer.

i. Stored inside the instrument’s cavity is the corundum standard (Figure 9). The

reflection indices and peak position for corundum using the Cu x-ray source can be

found on the NIST website. https://www-

s.nist.gov/srmors/view_cert.cfm?srm=676A

Figure 9: Corundum sample.

ii. The following table is data collected from this instrument using both Cu and Mo

sources (Oct 2017) and the NIST values.

https://www-s.nist.gov/srmors/view_cert.cfm?srm=676A

https://www-s.nist.gov/srmors/view_cert.cfm?srm=676A

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3. Preparation of LaB6 NIST Standard (660c)

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

ii. 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. The following table is data collected

from this instrument using both Cu and Mo sources (Oct 2017) and the NIST

values.

Al2O3

h k l NIST (Cu) Cu Mo

0 1 2 25.574 25.57 11.69

1 0 4 35.149 35.14 15.97

1 1 0 37.773 37.77 17.13

1 1 3 43.351 43.30 19.57

0 2 4 52.548 52.55 23.51

1 1 6 57.497 57.49 25.58

2 1 4 66.513 66.51 29.23

3 0 0 68.203 68.21 29.90

1 0 10 76.873 76.86 33.25

1 1 9 77.233 77.22 33.40

2 2 3 84.348 84.35 36.00

0 2 10 88.994 88.98 37.64

1 3 4 91.179 91.18 38.40

2 2 6 95.240 39.70

2 1 10 101.070 41.60

2θ

LaB6

h k l NIST (Cu) Cu Mo

1 0 0 21.358 21.36

1 1 0 30.385 30.38 13.88

1 1 1 37.442 37.44 17.00

2 0 0 43.507 43.50 19.66

2 1 0 48.958 48.96 22.00

2 1 1 53.990 53.99 24.14

2 2 0 63.220 63.22 27.93

3 0 0 67.549 67.55 29.66

3 1 0 74.747 74.74 31.31

3 1 1 75.846 75.85 32.88

2 2 2 79.872 79.87 34.38

3 2 0 83.847 83.84 35.83

3 2 1 87.794 87.79 37.24

4 0 0 95.673 39.92

4 1 0 99.645 41.19

3 3 0 103.663 42.45

3 3 1 107.752 43.67

4 2 0 111.936 44.86

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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Removing the Flip-Stick 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°. Initialize the

component to sample (1A01). Follow steps in Section Operating the Instrument 2.i-ii.

This moves the stage inward for easier handling.

3. Close down the program.

4. Shut off the instrument using the instructions located on the instrument (Figure 10). If

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

Figure 10: Front of the D8 ADVANCE with the turn on/off instructions in the red circle.

5. Figure 11 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 11: X-ray source. The yellow light indicates the instrument is ON.

6. Take off the knife edge (Figure 12).

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7. Remove the computer cable.

8. Take out the 3 screws (Figure 12).

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

out.

Figure 12: Flip-Stick stage. In the picture, 2 of the 3 screws can be seen. The third is below the

sample holder.

Connecting the Flip-Stick Stage

1. Make sure the power to the x-ray source is off (Figure 11).

2. Insert the Flip-Stick 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 12)

4. Connect the computer cord.

5. Turn the power to the instrument back on (Figure 10).

6. Open the Measurement Server program to initiate communication before starting 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 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 13) and you get a diffraction pattern.

Set-screw for knife edge

2 of the 3 screws

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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 13: 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. “D8 ADVANCE.” Bruker. https://www.bruker.com/products/x-ray-diffraction-and-

elemental-analysis/x-ray-diffraction/d8-advance/technical-details.html. Accessed Oct.

2017.

3. Manning, B.; Ichimura, A.; (2006) Bruker D8 ADVANCE Powder XRD Instrument

Manual and Standard Operating Procedure (SOP). Retrieved from

http://files.instrument.com.cn/bbs/upfile/20087511723.pdf

4. Molecular Structure Laboratory, University of Wisconsin. (2016). Powder Diffractometer

Operation Instructions D8 ADVANCE with a Cu Kα Sealed Tube and Lynxeye. Retrieved

from http://xray.chem.wisc.edu/Documents/Powder_XRD_operation_notes.pdf

5. “Powder Diffraction SRMS.” (2016) NIST. https://www.nist.gov/programs-

projects/powder-diffraction-srms. Accessed Oct. 2017.

https://www.bruker.com/products/x-ray-diffraction-and-elemental-analysis/x-ray-diffraction/d8-advance/technical-details.html

https://www.bruker.com/products/x-ray-diffraction-and-elemental-analysis/x-ray-diffraction/d8-advance/technical-details.html

http://files.instrument.com.cn/bbs/upfile/20087511723.pdf

http://xray.chem.wisc.edu/Documents/Powder_XRD_operation_notes.pdf

https://www.nist.gov/programs-projects/powder-diffraction-srms

https://www.nist.gov/programs-projects/powder-diffraction-srms

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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 ... Flip Stick Stage XRD.pdfDr. Cassie Ward Dr. Sameera Perera...

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