5.3: Experimental and Instructions

Note

The ELN and other files for this experiment are here: Shared Files for Duke Students

Part 1A: Computational prediction of vibrational frequency

On your computer's internet browser, please navigate to Entos Envision  (https://envision.entos.ai), a free online computational platform. Use your duke email address to register a new account or log into your account. Type "HCl" in the text entry box and press "search".

The molecular structure of hydrochloric acid (HCl) is already calculated and available in Entos's database. Capture a snapshot of the HCl model.

From the lefthand menu, choose "IR Spectra". Record the calculation basis set (listed as "method"), the Frequency of vibration (and units), and a snapshot of the simulated IR spectrum. Comment on whether the simulated spectrum matches your prediction from the pre-lab assignment.

Next, measure the calculated bond length. To do this, click on "Energy" on the lefthand menu, then go to the righthand icon menu and choose the "Measure Bond Lengths and Angles option (). Then click on each atom of the bond and note the measured bond length.

Part IB: Preparation of sample and collection of FTIR spectrum

Preparation of Gas Sample Cell

• Gaseous HCl will be introduced into an IR gas cell. Note that because natural chlorine is a mixture of two isotopes \( \ce{^{35}Cl} \) and \( \ce{^{37}Cl} \) (in a ratio of 3 to 1), this sample is a mixture of two different gases, each with a distinct spectrum.
• Hydrogen chloride is a colorless, pungent, and corrosive gases that fume in air. Contact will cause burns to the skin, severe burns to the eyes and burns to the respiratory system if inhaled. A vacuum line will be used to transfer the gases from their high-pressure containers to an evacuated IR cell.
• When not in use the IR gas cell must be stored in the desiccator. The cell is constructed of a glass body with KBr windows at each end. Ensure that the salt windows are kept free of moisture at all times. Please do not touch these windows.

Vacuum-Line Start-Up

Most of the following will be completed by the TA before the lab period.

1. Check that all external valves on the working and main manifold are closed to the outside atmosphere.
2. Attach an empty N₂ trap to the main manifold. Hold this trap in place until a vacuum has formed.
3. Turn on the floor vacuum pump to start generating a vacuum.
4. Turn on all valves in the manifold that are connected to gages (marked with purple tape).
5. Turn on the diffusion pump.
   • Ensure that the floor pump is on BEFORE the diffusion pump. Otherwise, the diffusion pump will generate heat and the oil within the pump will oxidize, causing long-term damage to the diffusion pump.
6. Turn on Digivac electronic monitor. Use this to actively monitor the pressure at the end of the main manifold.
7. Check the analog pressure gauge on the diffusion pump to ensure the pressure is stable.
   • Throughout the experiment, the pressure should remain below 30 mtorr if the system is closed and stable.
8. Fill a 4L dewar with liquid N₂ from the shared Chemistry department supply.
9. Place a second dewar underneath the N₂ trap and fill with liquid N₂ from the 4L dewar such that the N₂ trap is submerged in liquid N₂
10. Check the level of N₂ as the experiment progresses. Refill if necessary to ensure the trap remains cold.
11. Check to ensure the pressure at the end of the main manifold is below 30 mtorr before proceeding.

Transferring HCl to gas cell

1. Remove gas cell from the desiccator and attach to the middlemost section of the working manifold shown below in Figure \(\PageIndex{1}\).

   

   Figure \(\PageIndex{1}\): Vacuum line set-up: working manifold and main manifold

2. Evacuate the back of the gas cell and introduce a vacuum to the interior of the cell.
3. Remove cell from manifold, bring it to the FTIR instrument, and take a background spectrum (see "Obtaining an FTIR Spectrum using the Nicolet iS50" below).
4. Replace the gas cell onto the working manifold and open it to vacuum.
5. Connect the pressurized HCl cannister to the working manifold via a vacuum-rated line. This line should contain its own needle valve that may be closed to separate the cannister from the rest of the working manifold. Introduce a vacuum to the line and to the pocket between this needle valve and the main valve on the cannister. The HCl cannister should remain closed at this time. Close the needle valve once this pocket has been evacuated.
6. Close the working manifold off from the main manifold.
7. Introduce a small amount of HCl gas to the pocket between the cannister and the needle valve by turning the cannister's main valve 180 degrees open briefly, and returning 180 degrees to close the cannister once more.
8. After ensuring the HCl cannister is closed, open the needle valve to release HCl into the working manifold. Use the mercury pressure gauge on the working manifold to monitor this process.
   • If the pressure rises such that it threatens to expel mercury from the pressure gauge, open the working manifold to the main manifold to release pressure.
9. Slowly release HCl from the working manifold using the valve to the main manifold until the pressure in the gas cell reaches 10 mmHg.
10. Close the gas cell off from the working manifold and open the working manifold to the main line to release any excess HCl from the rest of the system. (Remember to include the pocket between the needle valve and the HCl cannister!)
11. Record the FTIRl spectrum using "Obtaining an FTIR Spectrum using the Nicolet iS50" below.
12. Once all data has been collected, return the gas cell to the working manifold and safely evacuate all remaining HCl.
13. Close and remove the evacuated gas cell and return it to the desiccator.

Vacuum Line Shutdown

1. Turn off the diffusion pump. Wait 5 mins for the pump to cool.
   • The pump should be cool before any oxygen is introduced to the system to prevent oil in the pump from oxidizing.
2. Close all valves with purple tape.
3. Turn off Digivac monitor.
4. Turn off the floor pump.
5. Pick an external valve and open it to release the vacuum and open both the working manifold and the main manifold to the air.
   • Do this quickly after step 4. The system should not be left under vacuum without an active vacuum pump.
6. Remove N₂ trap and transfer it to the fume hood to safely evaporate excess HCl gas.
   1. Do this quickly after step 5. Leaving the N₂ trap cold after the vacuum has been released may cause liquid O₂ to condense, which is highly volatile.

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Obtaining an FTIR Spectrum using the Nicolet iS50

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, as so you'll collect a background spectrum first, then subtract that background from the spectrum of your sample.

• Begin by recording a background interferogram of the evacuated gas cell. A fast Fourier transform (FFT) will be applied to obtain the background transmittance spectrum.
• Next, introduce your gas sample into the same gas 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. Finally, the absorbance spectrum of your sample will be calculated and displayed.

Setup the Experiment and Collect a Background Spectrum

1. Check the sample holder in the spectrometer to make sure there is nothing blocking the path of the infrared beam.
2. Mount the evacuated gas cell on the gas cell holder.
3. Close the cover and allow the sample compartment to be purged with dry, CO₂-free air for at 5 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 scan are below:
   • No of scans: 8 scans
   • Resolution: 8 cm^-1 
   • Final Format: Absorbance
   • Background Handling: Collect background after 200 minutes. (This is the time that the background is considered useful and after this time you will need to collect a new background spectrum)

     

     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 4.5. 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 8cm_background_DDMMYYYY_initials.

     

     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 guidance of your TA, introduce about 1 cm Hg pressure of HCl gas into the cell. You must be careful to avoid the introduction of air into the cell. 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.
8.  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.
9. When the scan is complete, add the scan to the window and you will see both sample and background displayed.
10. Save the spectrum data file (File \(\rightarrow \) Save as). Use the data file format HCl_8cm_YYYYMMDD_initials
11. 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 HCl FTIR Spectrum at 8 cm \(^{-1}\) resolution. (CC-NC-BY-DUKE CHEM)

12. 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)

13. Zoom in on the region around the HCl 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)

14. 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 an HCl 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)

15.  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!).

Shutdown the Instrument and Store the Gas Cell

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. Re-evacuate the gas cell to remove your sample and store the evacuated cell (with stopcocks closed) in the desiccator.

Data Analysis for HCl FTIR spectrum for Part I 

After collecting your first spectrum, please email your results to yourself, your group, and your instructors. Then assemble your group and begin group discussion and analysis of the data. The files linked at the top of this page will guide you to analyze the spectrum, derive mathematical models to fit the data, and calculate molecular parameters from the fits. (links copied here for convenience: Shared Files for Duke Students). Your instructors will be on hand to help guide you if you get stuck.

Part II: How does instrument resolution effect the certainty of derived parameters?

In Part II, you will collect the same spectrum of HCl at different instrument resolutions to determine how instrument resolution affects the error in your results. If you are finished with part I early, you may be able to collect this data in the first lab period. Otherwise, data collection for Part II will happen in the second week of this module.