FT-IR Operation Instructions

ThermoElectron 6700 FT-IR

(Last updated 9/09/07)

I. Using the FTIR Computer

II. Collecting a Spectrum

(i) collect a background spectrum

(ii) apply sample to ATR accessory

(iii) collect sample spectrum

III. Manipulate the Spectrum

(i) height and width of your spectrum

(ii) autobaseline adjustment command

(iii) find peaks command

(iv) label important group frequencies

(v) save your spectrum

IV. Clean Up

I. Using the FTIR Computer

NOTE: The Dell computer is a locked computer. That means that when the computer is restarted, it reverts to its original configuration, erasing any data that any user has stored on its hard drive. Therefore, it is imperative that you save your data to a drive other than the Dell¹s hard drive!

II. Collecting a Spectrum

a) Start the Omnic software by clicking on its icon on the desktop. You will immediately get a dialog box asking which accessory you will be using (see Figure 1 below). The Smart Orbit accessory is the default and the accessory we will use so just click the OK button.

Figure 1: A screenshot of the initial dialog box of the Omnic software.

b) When you click OK, you will be presented with a blank spectrum labeled [Window1] (see Figure 2 below). Many of the tasks that you will have to perform can be done by clicking on the appropriate button on this screen. Some things to note on this screen are:

(i) The Experiment box has Smart Orbit in it. This is the ATR accessory we are using.

(ii) Below this is a row of buttons broken into five groups. The most middle group of 6 buttons are commands to manipulate the spectrum once it has been collected.

(iii) Below the buttons is another box, presently with No spectra selected. This box will have the title of your spectrum once you obtain it.

(iv) The largest section of the window is a blank spectrum. The y-axis has %transmittance (%T) on it (0% to 100%) and the x-axis has the frequency designation (4000 cm^-1 to 600 cm^-1).

(v) Finally, the bottom of the screen has 6 round buttons (these are cursor tools), 4 arrow buttons (to allow the spectrum to be expanded, contracted, increase %T, or decrease %T), another blank window (that will show a low resolution version of the entire spectrum), and move right and move left buttons.

If you hold the cursor over any of the tool bar buttons, you will see the name/function of the button.

Figure 2: Screenshot of a blank Omnic window.

c) The first task is to collect a background spectrum. Both water and carbon dioxide present in the atmosphere absorb in the IR region. In addition to the components in the atmosphere, we want to subtract out any absorption bands due to the accessory that we will be putting the sample on. To collect a background, click on the Collect Background button, the second from the left on the toolbar. The instrument is configured to run preview scans as soon as you click the button. After a moment you¹ll see a spectrum of the window substrate, water vapor, and carbon dioxide (see Figure 3 below). This preview scan will continue to refresh itself until you press the Start Collection button to the right of the spectrum title bar. The Start Collection command will prompt the instrument to collect 32 scans of the background. Every few scans, the screen will be updated. When the 32 scans are completed, a Confirmation dialog box will appear (Figure 4). Since you DO NOT want to look at this background spectrum, select No in the dialog box, i.e., you do not want it added to Window1.

Figure 3: Screenshot half way through the collection of the background spectrum. Fifteen of the default 32 scans have been collected.

Figure 4: This is the Confirmation dialog box that appears after the 32 background scans have been obtained. Select No, since you don¹t want to look at the background.

d) The next task is to collect the sample spectrum. Click the sample collection button on the toolbar (that is the 3^rd button from the left on the top, see Figure 2). A confirmation dialog box will appear asking you to Please prepare to collect the sample spectrum. (Figure 5) This means that you must now apply your sample to the instrument.

Figure 5: The Confirmation dialog box that appears when you click the sample collection button on the toolbar.

e) Preparation of the sample: You will need approximately 2 milligrams of a solid sample (or about 1 drop of a liquid sample). Using a microspatula, apply the solid sample to the 3 mm clear circle (the window) in the middle of the ATR accessory stage. Be sure to completely cover the 3 mm circle. Then swing the vertically mounted press to directly above the window and screw the larger (of the two) dial on the press to bring the press tip down, making contact with the sample. The sample is now prepared.

f) You can now press the OK button in the Confirmation dialog box illustrated in Figure 5. The OK button prompts the instrument to begin the preview scan mode. If after a moment, you do not see a spectrum, you may have to tighten the press on to the sample. The larger dial has a clutch, so if you tighten the press all the way, it will then turn easily, indicating that you can not tighten it any more. Now look at your spectrum. Can you see absorption bands? If you need to apply still more pressure with the press, you can turn the small dial on the press from the yellow dot toward the blue dot. You should see a spectrum appear in the preview mode. An example with a ziplock plastic bag as the sample is shown in Figure 6 below.

Figure 6: Preview mode of a ziplock baggie as sample. Notice that in preview mode that the number of scans is 1/1.

g) You are now ready to collect your sample spectrum. Generally, you collect as many sample scans as background scans. The instrument is set to collect 32 background and sample scans. Click the Start Collection button to the right and above the spectrum (see Figure 6). After a few scans, you should see your sample s spectrum. When the 32 scans are complete, a dialog box will appear asking you to name your spectrum (Figure 7). The title you chose should be informative as it will be included on the left hand side of your spectrum. Note: This is not saving your spectrum and the title does not have to be the same as the Save As name. As an example, I¹ve chosen to give the test sample an informative name followed by a naming code. The code I recommend, and require for saving the spectrum, is your initials, the unit that you are working on, the page # of your lab notebook where you have talked about running an IR of that sample. As an example of the proper naming scheme, let us say that the spectrum is the second compound in Unit 2, so the name would be htu27b (ht for my initials, u2 for Unit 2, 7 for page # 7 in my laboratory notebook, and b for the second spectrum of that unit). For this tutorial, I¹ll describe the sample as polyethylene baggie, and I¹ll save this test file as HT-IRtest-2 (note this is not the proscribed naming scheme). Once you have named the spectrum, click OK in the title dialog box and another Confirmation dialog box, exactly the same as Figure 4, will prompt you to decide whether this sample spectrum should be added to Window 1. Click Yes and you will have your spectrum (see Figure 8).

Figure 7: The title dialog box.

Figure 8: A sample spectrum that has been named (not with the correct naming scheme!) and added to Window1. Note the informative title.

III. Manipulate Your Spectrum

a) Height & Width of your spectrum: The height and width of the spectrum displayed in Window1 can be adjusted either from the menu bar or by using the four arrow tools at the bottom left of Window1. Pressing the double-headed horizontal arrow tool will cause the spectrum to expand horizontally. Try it. (Note that the mini spectrum on the very bottom shows you the entire spectral region that you recorded and indicates the expansion that you have just performed. See Figure 9.) The next set of arrow tools allows you to heighten or contract the absorption bands (the peaks in the spectrum).

Figure 9: Manipulating the spectrum with the expand/contract tool bar buttons found below the spectrum. Note that the original spectral region appears in the mini spectrum at the very bottom right with the expanded region in white and the region we can¹t see in the main window in gray.

b) Automatic Baseline Correct: In some cases a spectrum will appear slanted. To correct for this slant, first type control A. This will switch the y-axis from % transmittance to absorbance units. (Note that the bands now go up instead of down.) Once in absorbance mode, you can click on the Automatic Baseline Correct button on the upper toolbar. (It is in the middle set of 6 tool bar buttons, just to the right of the middle, and it has two spectra on it, one that looks slanted and another that looks good.) You will now have 2 spectra in the active window, your original and this adjusted spectrum, with the new adjusted spectrum as the selected one. (The active spectrum is always in red. This new spectrum also has an asterisk in front of it, indicating that it has been manipulated. If you perform another manipulation, the new spectrum will have two asterisks in front of it s name.) If you like the new one, click on the original one and clear it (either from the edit menu or by typing control delete). You can now type control T to get back to a % transmittance spectrum.

c) Find Peaks: You will need to identify absorption bands by noting where they occur (at what wavenumber) and how intense they are. One way to do this is by using the Find Peaks tool bar button. It is the furthest right button of the middle set and has an absorbance spectrum with 4 green arrows pointing at peaks. When you press it, a horizontal threshold line appears in the middle of the main window and a vertical slider appears on the left (see Figure 10a and b). You are now in a sub-program and you will be prompted to either replace your original spectrum with what you have done in this sub-program, or to exit out of the sub-program without any changes. Any peak extending below the threshold will be labeled. You can adjust the threshold line by clicking higher on the spectrum, this gives you more peaks, or lower, less peaks.

When you are happy with how the spectrum looks, click the Replace button to the right of the title bar. This will give you a dialog box asking if you want to replace your original spectrum with this new peak-annotated spectrum (see Figure 11). Click Yes, if you want to, No, if you want to revert to the original.

Figure 10: (a) The Find Peaks button puts you into a sub-program with a threshold line and a slider on the left. (b) If you click above the initial threshold line, you¹ll have more peaks picked. Note that any peak below the threshold line gets picked.

Figure 11: Confirmation dialog box to accept the
labeling from the Find Peaks sub-program.

d) Label Important Group Frequencies: The instrument does not know which absorption bands are informative and which are not. You have to decide that. Some peaks are very small, yet very informative. So you need a way to mark important peaks, if the Find Peaks command does not tag them. You can do this quite easily, manually. Click the Annotate Cursor tool (it is the one with a T on it at the bottom left of the spectral window). The cursor should now be a T. Move the cursor to the band you want to label and click down on the mouse button. The position of the cursor will appear with a line connecting the peak with the numerical position (in wavenumbers). Before letting go of the mouse button, you may want to drag the numerical position to a less cluttered spot on the spectrum. Try it. I have used the Annotate Cursor tool to mark the 4 major bands in the spectrum of the ziplock baggie in Figure 12.

Figure 12: Major absorption bands marked with the Annotate Cursor.

e) Saving Your Data: It is imperative that you save your spectrum to a device other than the hard drive of the FTIR computer, because as soon as the computer is restarted, the data will be gone! Save your valuable data to your thumb drive.
(i) Plug your thumb drive into the USB cable on top of the CPU box and save a copy of your spectrum to it (see Figure 13a). The thumb drive will show up as the removable dive (E). Give your spectrum a name that follows our convention (i.e., htu27b).
(ii) To be able to import your spectrum into a report or to look at it at home, paste the spectrum into a Word document. To do this, select the Export function from the File menu and TIFF as the file type. You can save the TIFF file on your thunb drive and at a later date, open it and then paste it into a Word document. I recommend that you always save a MicroSoft Word document with your spectrum pasted into it, be sure to add the saved name, on your thumb drive in addition to the Omnic file of your spectrum.