CHE 450G: Practical Inorganic Chemistry

U of KY Dept of Chemistry

FT-IR Instruction Sheet

This handout explains how to use the Mattson Galaxy 5020 Fourier Transform Infrared spectrometer to collect your data. This is an actual research instrument, not 450G laboratory equipment. Please follow these instructions exactly.

• How do I obtain a spectrum?
• How do I obtain a solution spectrum?
• How do I manipulate the spectrum and massage the data?
• How do I generate a peak list?
• How do I annotate the peaks on my spectrum?
• How do I plot my spectrum and/or peak list?
• What do I do to run additional samples?
• I'm done. How do I leave the instrument?

How do I obtain a spectrum?

1. Prepare the instrument for a background/sample scan:
   1. Sign in on the instrument logbook. Use your last names and "CHE 450G".

   2. Turn up the nitrogen flow (upper black knob located at the middle of the bench. Do not adjust the lower black knob).
      Dry nitrogen gas is continually purging the optics and sample compartment of the instrument. The flow is turned down to a minimum when the instrument is not in use to conserve nitrogen.

   3. If you are using a reference sample (i.e. solution IR etc.), open the sample compartment and place it in the sample holder. Close the lid.

   4. If the instrument is in "Standby" mode, the Mirror Stopped and Standby lights will be lith. Press the Standby button to take it out of this mode.
      There is a mirror inside the instrument that is continuously moving back and forth. By placing the instrument in Standby mode, the mirror is stopped, saving wear on the optics.

   5. After pressing the Standby button, the instrument will do a self test and then the Data Acquisition, Ready and Reference lights will come on (Acquisition will be blinking; this is normal). The display will read "** Ready to collect spectrum**"

2. Turn on the computer and start the WinFIRST software:
   1. Turn on the computer, printer and monitor (if switched off). DO NOT touch any keys until it has booted and Windows has started.

   2. The computer should go into Windows automatically.

   3. In the Program Manager the WinFIRST directory will usually be open. Double click the WinFIRST icon to start the program.

      Note: If the icon is not visible you will have to open the WinFIRST directory.

3. Call up the Acquisition Control Panel.
   1. This will normally open automatically. If not you can click on the fourth icon from the left in the toolbar at the top of the screen (it looks like a squiggly line).

   2. The Control Panel will open. It can appear as a large box or a small box depending on whether Options has been clicked. If the box is small, click Options to make it large.
      Note: The default value for scans is 16 scans at 2 cm^-1 resolution. The default scan range is 600 - 4000 cm^-1. Please do not change these values.

   3. Click on the button Load Method.... You will be presented with a dialog that asks you which method to use. Click on CHE450G method and then click OK.
      This tells the instrument to save your data in the CHE 450G folder in the Data directory. Be sure to pick the proper folder or you may save into someone else's directory! Note: If you are running multiple samples you only have to Load Method the first time.

4. Perform a Background Scan
   1. Click on the Background radio button on the Control Panel if it is not already selected.

   2. Click on the big green Scan button.

   3. The computer will say "Please Prepare for a Background Scan". Click OK when you are ready to proceed (usually you would like the sample compartment to purge for at least a minute after you close the sample compartment door).
      If nothing happens (i.e. no data collection) then try again from step 2.

   4. Acquisition of the background begins. You will see a status report in the window and in the lower right it will say "xx% complete".

   5. When the computer is done, it will ask for a data file name. Enter something no longer than 8 letters/numbers as you are constrained by DOS. Do not use any file extensions (periods) in your name. Click OK.
      NOTE: It is highly recommended that you name your files by your initials and notebook page. For example: Rob Toreki would have a sample RT22A.

      You can use the same data file name for background and sample scans (they have different file extensions so it's OK).

   6. You will then be prompted for a title. Since this is a background scan, it does not really matter what you type. Click OK.

      The background file is always saved. This is good if you want to run several samples but not rerun the background each time. In usual practice you can throw away the background files (*.bkg) when you are done.

   7. Your Background scan will appear. It typically contains a broad curve and may or may not have large peaks due to CO₂ and water depending on how long you purged the sample compartment.

5. Collect Sample Data
   1. Open the sample compartment and put in your sample. Let the compartment purge for roughly the same amount of time you did for the background.

   2. Click on the Control Panel if it is visible. If not you can click on the multicolored icon in the lower left that says "Control Panel" or on the fourth icon from the left on the toolbar.

   3. Select Sample by clicking on the radio button on the Control Panel.

   4. Click the big green Scan button.

   5. As before, messages will appear and the % complete will be displayed.

   6. You will be prompted with a filename. Enter something no longer than 8 letters/numbers as you are constrained by DOS. Do not use any file extensions (periods) in your name. Click OK.

   7. You will be prompted for a title. It is best to erase everything that is there and put a short description of the sample, date, time and notebook page. Include whether it was a Nujol mull, pellet, solution (and solvent) etc. since you may not remember this information months from now.

   8. Your spectrum will now be displayed. You can enlarge it to full screen size by clicking on the up arrow in the upper right hand corner of the sample window.

How do I obtain a solution spectrum?

1. Obtain a spectrum of your solvent using the procedure outlined above, save it to disk and then close the file.

2. Obtain a spectrum of your solvent + sample as above. Be sure to use the same cell (or a matched cell). You can reuse the same background, so no need to recollect that.

3. Under the File menu select Load Reference.... Select the name of your solvent file and click OK.

4. We now want to subtract our reference (pure solvent) from our sample (sample + solvent). To do this, go to the Math menu and choose Subtract....

5. You will see three spectra. The bottom one (in white) is the difference spectrum. Move the slider bar or type a number in the box (something close to 1.0 usually works best) until the difference spectrum is flat as possible in the regions where your solvent peaks normally occur. Be careful not to "oversubtract" when, for example, you have CH peaks from your compound superimposed on the CH peaks of your solvent.
   • Sometimes the difference spectrum will run off the screen while you are subtracting. If so, simply click the Re-Scale button and continue your adjustments.

6. When everything is to your satisfaction, click Done. You may want to change the text header on your file to include "solvent subtracted" and then save the file under a new name.

How do I manipulate the spectrum and massage the data?

Left mouse button -- by clicking and dragging you can make a box. When you release the button whatever is in that box will be enlarged to full screen size. If you simply click without dragging, then the full spectrum will be displayed.

Right mouse button -- clicking on this will bring up a dialog box where you can change things like the number of spectra displayed at once, colors of various spectra and the range you want to display. Please don't change any of these settings!

Baseline Correction -- You can do this in two ways, both found under the Math menu.

1. You can try an Auto Baseline which will usually give you a reasonable spectrum unless you have large negative peaks (from doing solvent subtraction, for example).

2. If this is not satisfactory you can do a Baseline... correction manually. When you choose this selection, your spectrum will be displayed, the cursor will be a crosshair and a dialog box will say "Choose a new baseline"

   Move the cursor to a (high) point on your spectrum that you want to be at approximately 100% transmittance. Then click on other points in your new baseline -- a series of lines will join these points.

   When you are done, click "OK" and the baseline will shift. Click in the spectrum with the left mouse button to see the whole spectrum.

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How do I generate a peak list?

You can get a listing of peak positions and intensities for the entire spectrum at once or blow up selected regions. There is also more than one way to label the peaks directly on your spectrum (see "How do I annotate the spectrum?" for the best way).
1. Select the region where you want a peak list

2. Under the Math menu, select Peaks...

3. A dialog box will come up. Ignore the options/boxes and click OK.

4. A red box with "Pick two points for the threshold" will appear and the cursor will be a crosshair.
   What you are doing now is setting a threshold, just like on the NMR machine. By clicking two points you are drawing a line -- only peaks crossing below this threshold will be reported.

   Notice that only peaks with wavenumbers between your two points will be reported, not everything on the screen.

5. The program will then open a new window and title it something like "WinFIRST Report #1". It will contain the peaks that were below your threshold in the specified wavenumber range.

6. To get back to your sample, either click on its window or pull down its name from the Window menu.

7. You will see that your peaks are now labeled on your plot as well.

8. Repeat the above steps for each region of interest. Each time, the new list of peak data will be added to the end of the list in the Report window.

9. Note: Sometimes the peaks overlaid on your plot will crowded/superimposed. We can erase these by going up to the Tools window and selecting the Annotator if it is not already displayed. The icon in the lower right corner of the Annotator palette erases all the numbers/text superimposed on your spectrum.

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How do I annotate the peaks on my spectrum?

If the peaks labeled on your spectrum are not satisfactory (too crowded, off the screen) from using the Peaks... command you can use the Annotator palette to place the peak labels precisely where you desire.
1. If the Annotator palette is not visible, then select Annotator from under the Tools menu.

2. As with every other icon in WinFIRST, when you place a cursor over an icon, there is a description of the icon's function in the lower left hand corner of the window. To see what each icon/button does, refer to the corner.

   Three of these buttons are particularly useful:

   Annotate a data peak writes the cm^-1 value directly under the peak that you select. This is only good for isolated peaks and ones that aren't near the bottom (where they can get cut off).

   Annotate a data peak and value labels the peak with cm^-1 and intensity and lets you move the label to wherever you want. You have to select twice -- once for the peak and once for where you wish to place the label. A line is drawn between the label and peak.

   Erase Annotations gets rid of all the annotations on the plot.

3. Blow up the region of interest (if you desire) and click on the desired button on the Annotator palette. YOU HAVE TO CLICK THE ANNOTATOR EACH TIME YOU WANT TO LABEL A PEAK -- clicking a button on the Annotator palette does not "turn on" a continuous labeling mode.

4. Keep in mind that peak labels spaced far apart in a blown up view may be overlapping when you display the full spectrum.

5. If you wish to get rid of your peak labels then you can select "Erase all Annotations" from the Annotator palette.

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How do I plot my spectrum and/or peak list?

To plot your spectrum:
1. Display the area you wish to plot.

2. Select Plot... from under the File menu.

3. In the upper left corner of the screen that is displayed, click on your filename (it will end in .ras). Your spectrum should now appear in the box in the middle of the screen. This is a print preview.

4. Hit the Plot button.

5. After the Print Manager is done, hit the Done button to return to your IR spectrum.

   If you wish to plot a blowup of your spectrum, display that area on the screen and repeat steps 1-5.

To plot your peak list:
1. Do everything as above, only select the WinFIRST Report #x instead of your spectrum. It will be displayed in the window etc. ...As far as I can tell, there is no easy method for plotting peak lists that run off the screen, although you can Export to the Clipboard and print from a different application

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What do I do to run additional samples?

If you want to use the same background (i.e. you are running several KBr pellets), all you have to do is put your sample in, let it purge and then collect Sample data. It will use the last collected background as background.

You can take a new background each time, but this is generally unnecessary.

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I'm done. How do I leave the instrument?

1. Exit the WinFIRST software. Select Exit from the File menu.

2. Leave everything else on. NEVER SHUT OFF THE IR INSTRUMENT!!
   We leave the IR on all the time for two reasons. First, the heat generated by the IR filament helps keep moisture from condensing on the beam $plitter and optic$. Second, turning the source on and off puts thermal stress on the filament which can shorten its life span.

3. Remove your sample from the instrument.

4. Turn off the upper black knob on the nitrogen supply. The flowmeter should read 50. Do not touch the lower knob.

5. Put the instrument into Standby mode: Press the Standby button once. The display will tell you to press the button one more time to put it into Standby. Please do. The lights by Mirror Stopped and Standby will be come on and the LCD panel will tell you the instrument is in Standby Mode.

6. Clean up any mess you've made!

7. Sign out on the logbook. Note any problems/errors/kudos.

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This page was last updated and is copyright 1996-2000 by Rob Toreki. All rights reserved.