digilab fts 7000 fourier transform …...5. power up the fts 7000 system (power supply module on the...

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STANDARD OPERATING PROCEDURE:

DIGILAB FTS 7000 FOURIER TRANSFORM INFRARED SPECTROMETER WITH UMA 600 MICROSCOPE

Purpose of this Instrument: Analyze chemical composition of micro and macro samples; quantitatively identify molecules and functional groups in a molecule.

Location: Engineering Research Building (ERB) Room 211

Primary Staff Contact: Dr. Weiqiang Ding 304-685-1938 Office: ESB G75D [email protected]

SPECIFICATIONS

IR Sources: Tungsten-Halogen Near-IR Source 25,000 – 2,100 cm-1

Mid-IR Duraglow Source 7,900 – 375 cm-1 Beam Splitters:

Near-IR Quartz 20,000 – 2,800 cm-1 Potassium Bromide (KBr) 7,500 – 375 cm-1

Mylar 6.25 m 470 – 50 cm-1

IR Detectors: Linearized MCT (Mercury Cadmium Telluride) 10,000 – 450 cm-1 (FTS 7000 & UMA 600) DTGS (Deuterated Tri-Glycine Sulfate) 10,000 – 150 cm-1 (FTS 7000) FPA (Focal Plane Array) 4,000 – 900 cm-1 128×128 pixel 350×350 mm sample area (UMA 600)

The Shared Research Facilities are operated for the benefit of all researchers. If you encounter any problems with this piece of equipment, please contact the staff member listed above immediately. There is never a penalty for asking questions. If the equipment is not behaving exactly the way it should, contact a staff member. NOTE: The purpose of this manual is for general measurements with the FTIR. For more advanced measurements or measurements with accessories (e.g., specula reflectance accessory, focal plane array (FPA), attenuated total reflectance (ATR), etc.), please contact Materials Fabrication and Characterization Facility staff members or refer to the FTS 7000 spectrometer manual and Digilab Win-IR Pro software & FTS 7000 training course material, which are located on top of the FTIR system workbench.

mailto:[email protected]

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START UP

1. Log in on the FOM and write down your name and other information on the logbook.

2. Turn on the computer and the monitor if they are off.

3. Turn on power switch and the cooling switch on the front control panel of the water chiller (Figure 1a) on the floor beside the FTIR work bench.

4. Check the temperature setting (position of the temperature setting knob) on the front control panel of the chiller. It should be set at 25 oC. If not, set the knob to 25 oC.

5. Power up the FTS 7000 system (power supply module on the floor under the bench).

6. Power up the UMA 600 infrared microscope if you will use it (power button in the rear).

7. Open the top cover of the FTS 7000 system. Check the beam splitter currently being used (default: KBr beam splitter). If you want to use another beam splitter, replace it and store the other in the storage chamber (Figure 1b).

NOTE: Handle and insert beam splitters gently. Aggressive handling or “slamming” beam splitters into place may reposition beam splitters and ruin the system alignment. Such damage will require a service visit to realign the FTIR.

Figure 1. (a) Water chiller; Top view of (b) the FTS 7000 system and (c) UMA 600 microscope.

8. Get liquid nitrogen with the 4L dewar from the liquid nitrogen tank in the room beside the optical microscope bench. CAUTION: Liquid nitrogen could be dangerous if not properly handled. It can cause injury if it comes in contact with your skin. Always wear the apron, the gloves and the face shield while handling liquid nitrogen.

9. Open the top cover of the FTS7000 spectrometer (Figure 1b). Remove the black plug for the MCT detector dewar port (Figure 1b). Insert the funnel (located on the workbench beside the FTIR, Figure 1c) and position the hole on the funnel stem AWAY from you. CAUTION: Liquid nitrogen will gush out from the hold when the dewar is full. Always position the hole away from yourself and other users in the room.

10. Carefully fill liquid nitrogen to the detector dewar until liquid nitrogen starts gushing out from the hole on the stem of the funnel. Highlight important safety notes in red.

Beam splitter chamber

Beam splitter storage

MCT detector dewar port

MCT detector dewar port

(b) (c)

Funnel

(a)

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11. Fill liquid nitrogen to the MCT detector dewar on the UMA 600 microscope if you plan to use the microscope. There are two dewars on the microscope and the one for MCT detector is the left side one when you view it from the back of the microscope (Figure 1c). Use the step ladder to access the dewar on top of the microscope from the back.

12. Allow about 20 minutes for the dewars to come to thermal equilibrium.

13. Top off the dewars with liquid nitrogen. Put the plugs back and close the spectrometer cover. NOTE: Liquid nitrogen in the dewars will last for about 6 hours. Please make sure that there is liquid nitrogen there during your entire session. You may need to top off the dewars again during your session. Not enough liquid nitrogen in the dewars will cause signal degradation and data collection errors.

14. Start the Varian Resolution Pro program on the computer desktop. If the software program could not start, contact a Materials Fabrication and Characterization Facility staff for help.

SETTING RAPID SCAN PARAMETERS

Activate Rapid Scan window from the drop down menu Collect > Rapid Scan. Set the operation parameters for the rapid scan as follow:

1. Electronics Tab

Typical scan parameter setting:

Speed: 20 KHz (for MCT detector) 5 KHz (for DTGS detector)

Filter: 5 KHz (for 20 KHz speed) 1.2 KHz (for 5 KHz speed)

UDR (Under Sampling Ratio): 2 (for mid-IR) 1 (for near-IR)

Resolution: 8 cm-1

or 4 cm-1

for solids and liquids; 2 cm-1

or better for gases

Sensitivity (Gain): 1 (default) (Options: 1, 1.5, 2, 3, 4, 8, 16)

Scans to Co-add: The number of scans to add together to form the spectrum. Co-adding improves the signal-to-noise ratio in the spectrum. Recommended value: 16 or more.

Range: Mid-IR 4000 - 400 cm-1

Near-IR 15000 - 3300 cm-1

Figure 2. Electronics tab setting.

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2. Optics Tab

Select the IR source, Beam, Detector, Beam Splitter, Aperture (and microscope operation mode).

IR Source: select the source to illuminate the sample. Available sources: Mid-IR and Near-IR.

Beam: select the path for sample beam. Internal for FTS7000 system, External for UMA600.

Detector: select the detector to use for data collection. DTGS and Linearized MCT for FTS7000 system, UMA600 (left: FPA right: Linearized MCT)

Beam Splitter: NIR Quartz (20,000– 2,800 cm-1) KBr (7,500–350 cm

-1) Mylar 6.25 m (470 – 50 cm-1)

Aperture: select the aperture being used and select the aperture diameter. Available options: Open, 2 cm-1, 0.25 cm-1, 0.1 cm-1. The aperture setting determines the optical resolution, the smaller aperture size results in higher available resolution. For example, at 4000 cm-1 wave number, the available resolution for Open aperture setting is 4 cm-1, the available resolution for 2 cm-1 aperture setting is 2 cm-1.

Typical Setting for Measurements with FTS 7000 System

IR Source: Mid-IR Beam: Internal Detector: Linearized MCT Beam Splitter: KBr Aperture/Source: Open

Figure 3. Optics tab setting options.

3. Advanced Tab

Interferogram Symmetry: asymmetric for single-sided data collection (default)

Delay before Start: enter number of seconds to wait before starting the data collection

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Enable Gain Ranging: activate amplification outside the Gain Ranging Radius

Gain Ranging Radius: the number of data points around the center burst on which amplification does not occur. Select 40 for mid-IR and near-IR; select 200 for far IR.

Figure 4. Advanced tab settings.

4. Background Tab

New Background:

Scans to Co-add: The number of scans to add together to form the spectrum. Co-adding improves the signal-to-noise ratio in the spectrum. Recommended value: 16 or more.

NOTE: the number of background scans should be at least as large as the number of sample scans set in the Electronics Tab.

5. Computations Tab

The computations page defines a set of operations to perform after the data collection. The operations above the Stop bar in the active method are automatically performed. You can view the results of each operation by using the Reprocess (see Data processing section).

Post-Collect Operations:

a. Drag STOP bar to the desired endpoint (e.g., below truncate).

b. Click on any function to modify its parameters as follow:

(a) Compute dialog box:

General page:

Apodization Function: select NB Medium

Zero Filling Factor: select Auto (default)

Advanced page: select Use Standard Processing (default)

(b) Ratio dialog box:

Ratio To: select Absorbance (default)

% Noise Level Ratio: select Auto (default)

Background File Name: CURRENT (default)

Use Current: Checked (default)

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ALIGNING AND CALIBRATING THE SPECTROMETER

1. Check that the beam splitter is properly seated.

2. Close the sample compartment purge shutters on FTS 7000 by pulling them out (knobs in the “out” position, Figure 5).

NOTE: Purge shutters should be used whenever the bench compartment is open.

Figure 5. Shutter knobs in the “out” position.

3. Open the sample compartment cover and remove any sample or accessory from the compartment chamber.

4. Place one attenuator screen (metal wire mesh screen) over the sample compartment beam entrance port located on the right hand side of the compartment chamber (Figure 6).

Figure 6. Interior of sample compartment chamber.

5. Open the sample compartment purge shutters (the knobs in the “in” position).

6. Press the Setup button at the bottom of the Rapid-Scan dialog box to display the Setup Spectrometer window that shows the alignment interferogram (Figure 7).

7. Press the Align button to start the automatic alignment.

Shutter knob Shutter knob

Purge shutter

Attenuator screen

Sample holder

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8. Verify that the peak magnitude is less than 10 V zero-to-peak (normally around 6-9 V). If peak

voltage is clipped (higher than 10 V or lower than 10 V), first decrease the gain by reducing the Sensitivity parameter (on the right side of the program screen, Figure 5) and if necessary insert more metal wire mesh screens over the sample compartment beam entrance port (on the right side of the compartment chamber, Figure 6).

Figure 7. Typical alignment interferogram.

9. Press Calibrate button to calibrate the grain ranging radius (GRR) circuitry and grain range amplification system.

10. Press OK button to save the alignment and calibration data.

NOTE: You should re-align before using the spectrometer for the first time or after changing a source, beam splitter or detector.

You should re-calibrate after changing UDR or Speed on the Electronics page or Filter on the optics page, or after changing the detector or any accessory.

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DATA COLLECTION MODES

There are three commonly used operation modes of the FTIR system (detailed below):

1. FTS7000 in transmittance mode

2. UMA600 in transmittance mode

3. UMA600 in reflectance mode: for non-transparent samples or samples on non-transparent substrate

NOTE: You need to record the scan parameter settings in your own lab notebook for future reference.

MODE 1: TRANSMITTANCE MODE WITH FTS7000

1. Scan Parameter Setup


Optics Tab (Typical Setting)

IR Source: Mid-IR

Beam: Internal

Detector: Linearized MCT

Beam Splitter: KBr

Aperture: Source Open

Optics Mode: Transmittance

2. Background Spectrum Collection

A reference spectrum (Figure 8) must first be collected in order to correct for the contributions from

water vapor (2,0001,300 cm-1 and 4,0003,500 cm-1), CO2 (2,350 cm-1 and 670 cm-1) and protective coating of the KBr windows (three bands around 2,900 cm-1, if you are using the KBr beam splitter) from the final spectrum.

(1) Check the sample compartment to ensure that there is no sample on the holder.

(2) Press the Background button at the bottom of the Rapid Scan window to start collecting a background.

(3) After the data is collected, the background spectrum will be displayed on screen.

(4) Name and save the data file.

(5) Label the background file in the spreadsheet under the spectrum.

Note: If you enter a new number of Scans, you must press the Enter key to activate the new number of Scans.

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Figure 8. Typical background spectrum with KBr beam splitter in UMA 600 transmission mode.

3. Sample Loading

(1) Close the two purge shutters for the sample compartment (knobs in the “out” position).

(2) Open the sample compartment cover.

(3) Place the sample on the sample holder (Figure 6) with the area of interest aligned with the round opening on the sample holder.

(4) Close the sample compartment cover. Open the purge shutters (knobs in the “in” position).

4. Data Collection

(1) Open the Rapid Scan window at Collect > Rapid Scan menu.

(2) Press the Scan button to start collecting a spectrum.

(3) Once the spectrum is collected, it will be automatically processed based on the setting in the Computations Tab.

(4) The processed spectrum will be displayed on screen and be saved in the same document as the collected background.

(5) You can rename the file by clicking on the file name and type in a new name in the spreadsheet under the spectrum window.

NOTE: If you enter a new number of Scans, you must press the Enter key to activate the new number of Scans. The number of Scans should be less or equal to the “scans to co-add” set in the Background tab.

NOTE: Users should make sure that they copy all their data out from the computer in a timely manner. The Shared Research Facilities is a multi-user facility and therefore cannot guarantee that the saved file will not be modified or deleted.

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MODE 2: TRANSMITTANCE MODE WITH UMA600 MICROSCOPE




IR Source: Mid-IR

Beam: External

Detector: UMA600

Beam Splitter: KBr


Microscope/Detector: Right (Linearized MCT)

Optics Mode: Transmittance

2. Background Spectrum Collection

(1) Check and ensure that the observation hole on the microscope sample stage is not covered.






3. Sample Loading

(1) Mount your sample on top of the microscope sample stage with the area of interest above the observation hole on the stage.

(2) Cover the sample with the plastic protective enclosure over the objective lens.

4. Data Collection




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NOTE: If you enter a new number of Scans, you must press the Enter key to activate the new number of Scans. The number of scans should be less or equal to the “scans to co-add” set in the Background tab.


MODE 3: REFLECTANCE MODE WITH UMA600 MICROSCOPE




IR Source: Mid-IR

Beam: External

Detector: UMA600

Beam Splitter: KBr


Microscope/Detector: Right (Linearized MCT)

Optics Mode: Reflectance

2. Sample Loading and Focus

(1) Mount sample on the gold mirror substrate (gold mirror is stored in the first drawer under the FTS 7000 work bench).

(2) Mount the gold mirror (with sample) on the microscope sample stage.

(3) Cover the sample area with the plastic protective enclosure over the objective lens.

(4) Click on the Scope Setup button at the bottom of the Rapid Scan window.

(5) Select the Reflectance Mode in the Microscope Tab in the Scope Setup window (Figure 9a).

(6) Select Detector #2 (Linearized MCT) in the Microscope Tab.

(7) Focus on the gold substrate surface with the microscope focus knob.

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Figure 9. (a) Scope setup window; (b) scope setup adjustment knobs.

(8) Adjust the aperture size with the rotation knob on the microscope control panel (Figure 9b) or with the Rotation buttons in the Aperture Control section of the Microscope tab window (Figure 9a).

(9) Adjust aperture orientation with the aperture size adjustment knob on the microscope control panel (Figure 9b) or with the Field Stop buttons in the Aperture Control section of the Microscope tab window.

(10) Click on OK to return to the Rapid Scan Setup window.

(11) Click on the Setup button at the bottom of the Rapid Scan window to display the Setup Spectrometer window that shows the alignment interferogram (Figure 7).

(12) Adjust the focus of the optical microscope to maximize the signal intensity displayed on top of the interferogram window.

(13) If necessary, select a proper Sensitivity number in the Setup Spectrometer window to maximize the signal intensity (less than 10 V zero-to-peak).

(14) Click on OK to return to the Rapid Scan Setup window.

2. Background Collection

(1) Check to ensure that the beam is focused on the gold mirror substrate without sample coverage.





(a) (b)

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4. Sample Spectrum Collection

(1) Focus on the sample surface on the gold substrate surface the microscope focus knob.

(2) Click on the Setup button at the bottom of the Rapid Scan window to display the Setup Spectrometer window that shows the alignment interferogram (Figure 7).

(3) Adjust the focus of the optical microscope to maximize the signal intensity displayed on top of the interferogram window.






NOTE: If you enter a new number of Scans, you must press the Enter key to activate the new number of Scans. The number of scans should be less or equal to the “scans to co-add” set in the Background tab.


DATA PROCESSING

NOTE: Below lists four basic data processing procedures. More advanced manipulation may be found in the FTIR manual located on the instrument work bench or by contacting a Materials Fabrication and Characterization Facility staff member.

1. Data Reprocess

(1) Select the spectrum file you want to reprocess from the spreadsheet under the spectrum window.

(2) Activate the reprocess function from drop down menu Operation > Reprocess.

(3) In the Transform window shown on the right side of screen, drag the red STOP section behind the desired processing step. The corrected spectrum will be shown below the original spectrum.

(4) You can replace the original file with the reprocessed one by clicking on Replace button or save the reprocessed file under another name by clicking on Add button.

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Figure 10. Data reprocess example.

2. Spectral Subtraction

(1) Select the first spectrum file in the spreadsheet.

(2) Activate subtraction function from drop down menu Transforms > Spectral Subtract.

(3) Select the spectrum to be subtracted and press OK. The display shows the original spectrum and the spectrum to be subtracted together in the top window and the subtraction resultant spectrum in the bottom window.

(4) You can replace the original spectrum with the subtraction result by pressing the Replace button or save the subtraction result under another name by clicking on Add button.

3. Peak Picking

(1) Open the spectrum file.

(2) Activate peak pick function from drop down menu Operations > Peak Pick.

(3) Select a proper Sensitivity value (sensitivity of 1 will pick the fewest peaks; 8 the most).

Figure 11. Peak pickup example at sensitivity of 2.

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4. Baseline Correct

(1) Open the spectrum file.

(2) Activate baseline correct function from drop down menu Transforms > Baseline Correct.

(3) Select a proper correction type: Linear or Spline.

(4) Use left mouse click to select baseline points on the original spectrum. The Corrected spectrum will show in the bottom window.

(5) You can replace the original spectrum with the corrected one by pressing the Replace button or save the corrected result under another name by clicking on Add button.

Figure 12. Baseline correct results of a transmittance spectrum.

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SHUT DOWN

Sample Unloading for the FTS 7000 System

1. Close the two purge shutters for the sample compartment (knobs in the “out” position).

2. Open the sample compartment cover. Remove the sample.

3. Close the sample compartment cover. Open the purge shutters (knobs in the “in” position).

Sample Unloading for the UMA600 Microscope

1. Raise the plastic protective enclosure above the objective lens.

2. Unload your sample from the microscope sample stage.

System Shut Down

1. Save your experiment data. Copy the data off the FTIR computer.

2. Exit the Varian Resolution Pro program.

3. Turn off the UMA 600 microscope. The power switch is in the back of the microscope.

4. Turn off the FTS 7000 spectrometer. The power switch is on the power supply module under the FTS7000 workbench.

5. Turn off the power switch and the cooling switch on the front control panel of the water chiller.

6. Log off your session on the FOM.

7. Sign out on the log book. Report any problem in the comment section and fill out the Service Request Form.

8. Clean up the working area before leaving the room.

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EMERGENCY PROCEDURES

If a user ever has a problem, even if slightly unsure about, ASK someone who knows and can help. There are no penalties for asking for help but there may be for not reporting damage to the equipment that may delay or prevent others from working. If, at any time, the user needs to contact someone for help, call or locate the following staff of the Materials Fabrication and Characterization Facility (MFCF):

Weiqiang Ding Office: ESB G75D Phone: (304) 685-1938 cell

Harley Hart Office: Hodges 240 Phone: (412) 443-1514 cell

If no one is available and the FTIR is not acting as expected, the user should do the following:

Turn OFF the FTS 7000 system power (on the floor under the bench)

Turn OFF the UMA 600 microscope power (on the back of the microscope)

Exit the Varian Resolution Pro program

Shut down the computer Then, if possible, the user should stay with the FTIR while trying to contact the above individuals. If it becomes necessary to leave the instrument then the user should leave a large, legible note on both the FTIR and at least one of the above individuals’ offices, stating:

The problem (describe what happened and steps taken)

When it occurred (date and time)

User name and phone number

If a dangerous situation is evident (smoke, fire, sparks, etc.), ONLY if it is safe to do so, the user should press the green power button on the power strip located on the floor behind the FTIR workbench to turn OFF power to the entire FTIR system and notify the proper emergency personnel. In any case, the user should leave the facility and contact emergency personnel as soon as possible from a safe place.

digilab fts 7000 fourier transform …...5. power up the fts 7000 system (power supply module on the...

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