5.3.1: Instructions for using the Nicolette iS50 FTIR

You will use a Nicolet iS50 FT-IR Fourier Transform Infrared (FTIR) Spectrometer to collect FTIR spectra. Below are instructions for its use.

Note on Collecting Data

This is a single-beam instrument: there are two steps for collecting any sample spectrum.

1. Record a background interferogram of the gas cell containing only air.
   A fast Fourier transform (FFT) will be applied to obtain the background transmittance spectrum.
2. Introduce your gas sample into the same cell and record a new interferogram.
   The software will perform FFT analysis on this interferogram to obtain the transmittance spectrum of your sample. To calculate the sample’s transmittance spectrum, this spectrum is then ratioed against the single beam background spectrum. The absorbance spectrum of your sample will be calculated by the instrument software, and displayed.

Setup the FTIR Instrument

1. Check the sample holder in the spectrometer to make sure there is nothing blocking the path of the infrared beam.
2. Mount the sealed gas cell on the gas cell holder (it should contain only air).
3. Close the cover and allow the sample compartment to be purged with dry, CO₂-free air for at 2 minutes, noting the time so that the purge time is reasonably accurate. While the chamber is purged, set up the software.
4. The Omnic software may already be loaded. If not, load it by clicking the icon on the Windows desktop. As the software loads you will see a blue light turn on at the top front right side of the instrument.

   

   Figure \(\PageIndex{1}\): The Omnic Button Bar. (CC-NC-BY-DUKE CHEM)

5. Click the Experiment Setup from the toolbar (Figure \(\PageIndex{1}\)), and go to the Collect tab (Figure \(\PageIndex{2}\)). Enter the appropriate settings. The settings for your first set of scans is below:
   • No of scans: 16 scans
   • Resolution: 8 cm^-1 
   • Final Format: Absorbance
   • Experiment Title: CHEM301L, 8/cm
   • Experiment Description: Enter whether it is a Background or Sample of HCl

     

     Figure \(\PageIndex{2}\): The Collect Pane of the Experiment Setup Window. (CC-NC-BY-DUKE CHEM)

   • Click on the Bench tab (Figure \(\PageIndex{3}\))and wait for the interferogram to appear. The Max signal should be around 4 when the cell is in position. Record a screen shot of the Bench tab for your notebook.  Click OK.

     

     Figure \(\PageIndex{3}\): The Bench Pane of the Experiment Setup Window. (CC-NC-BY-DUKE CHEM)

6. Select Collect Background from the Collect menu (or with the Col Bkg button, see Figure \(\PageIndex{1}\)).
   • Click OK when you see the Confirmation box. It will take about 4 minutes for the background scan to complete. Part way through, the background scan will be displayed on the main software screen.
   • Once complete, add the spectrum to the window when prompted.
   • Note the presence of water vapor, CO₂, and the polymer coating on the in the spectrum (Figure \(\PageIndex{4}\)). This arises from the atmosphere surrounding the cell (Remember: you gas cell is evacuated at this point).
   • Capture a figure of the background for your ELN using Edit\(\rightarrow \) Copy or using the Snipping Tool software.
   • Save your background data file:
   • Go to File \(\rightarrow \) Save as. Save the file in your course data folder using the file name format YYYYMMDD_8cm_background_GROUPNAME.

     

     Figure \(\PageIndex{4}\): A Typical Background Spectrum collected at 8 cm\(^{-1}\) resolution. (CC-NC-BY-DUKE CHEM)

Collect Sample Spectrum

7. Remove the evacuated gas cell from the sample compartment. Under the supervision of your instructors, and following the instructions provided, carefully introduce a gas sample into the cell.
8. Replace the gas cell on the sample holder, and close the door of the sample compartment. Allow the sample compartment to purge for the same time as in the background spectrum.  While you wait, do the next step.
9. If the most recent background spectrum was collected for your cell, then you my skip this step.  Otherwise you must specify which background file should be used for this sample:
   Go to Experiment Setup  and in the Background Handling options box, select "Use specified background file".  Then use the Browse button and choose the background file that you collected earlier.  Then, press OK when your background file is selected.

   

   Figure \(\PageIndex{5}\): Copy and Paste Caption here. (Copyright; author via source)

10.  Select Collect Sample from the Collect menu (or use the Col Smp button). You can enter a title or leave the default date/time when prompted. Click OK, and OK again in the Confirmation box to start the run.
11. When the scan is complete, add the scan to the window and you will see both sample and background displayed.
12. Save the spectrum data file (File \(\rightarrow \) Save as). Use the data file format YYYYMMDD_ HCl_8cm_GROUPNAME
13. Save the spectrum again using Save as and choose the .csv file format. (You need this one for data fitting!)

    

    Figure \(\PageIndex{5}\): Overlaid Background and FTIR Spectrum at 8 cm \(^{-1}\) resolution. (CC-NC-BY-DUKE CHEM)

14. Click on the background scan to make it the active scan (red) and select Hide Spectra from the View menu to remove the background spectrum from view.

    

    Figure \(\PageIndex{6}\): The Sample Spectrum (background is hidden). (CC-NC-BY-DUKE CHEM)

15. Zoom in on the region around the peaks \(\PageIndex{7}\). You can do this using the left mouse button to click, drag a box around, and click again to zoom in on a specific region. You can also use the zooming tools at the bottom of the window.

    

    Figure \(\PageIndex{7}\): Enlarging the peaks region. (CC-NC-BY-DUKE CHEM)

16. Select Find Peaks from the Analyze menu or click the button (Figure \(\PageIndex{8}\). Move the horizontal threshold bar down so that it captures as many of the peaks as possible without getting into the noise at the baseline (see Figure \(\PageIndex{8}\) below). You can also adjust the sensitivity slider at the left of the screen to fine tune the peak selection. When you have a good selection of peaks, do the following:
    • Capture an enlarged view that contains all of the peaks and peak labels, put this in your ELN.
    • Click the Clipboard button to put the peaks table into the Windows Clipboard.
    • Open Excel and paste the clipboard into a spreadsheet (Ctr1 + V).
    • Save the spreadsheet containing the peaks in your data folder.
    • Make sure you've saved a screenshot (as already instructed) and that you have saved the excel file containing the list of peaks. Find these files on the computer and open them to be sure you have them and the contain the expected information.
    • Click Replace at the top right of the screen to bring you back to the active window.

      

      Figure \(\PageIndex{8}\): The find peaks result shown in enlarged view for a spectrum taken at 8 cm resolution. Peaks are labeled using the Find Peaks option. A list of found peaks can be copied to the clipboard using the Clipboard button at the top left of the window while "Find Peaks" is active. (CC-NC-BY-DUKE CHEM)

17.  If you wish to record the spectrum of a new sample, repeat steps above (repeat background collection if you are collecting data at a different resolution!).

Remove the gas cell and Shutdown the Instrument

7. Simply CLOSE THE OMICS SOFTWARE!
   When you are done with the instrument and all of your work is saved, close the software. You will notice the blue light on the instrument turn off as the instrument goes into standby mode.
8. Remove your sample from the sample compartment and close the cover.
9. Follow the instructions for safely cleaning and storing the cell to prevent damage.