Taking an IR
This web page contains step-by-step instructions for the collection of IR data.
Contents
 What is an IR?
Collecting the background.
Preparing the Sample.
Collecting the Spectra and Peak Picking.
The Final Spectra.
What is a FT- IR Spectrometer?
A fourier transform infared (FT-IR) spectrometer is a machine that is commonly used to identify functional groups by measuring the vibrational frequencies of molecules when they are scanned with a infared light. The picture shows a typical FT-IR spectrometer that you will find in your lab. From left to right, the equipment shown is a printer, the FT-IR spectrometer, and a monitor, keyboard, mouse and computer. The FT-IR located in your lab may be slightly different, however, the software and general instructions will remain the same for each machine.
There are three basic steps towards the collection of a FT-IR spectra: collecting the background, collecting the spectra, and peak peaking. A background spectrum is scanned first, in order to eliminate peaks that would "contaminate" your spectra, such as atmospheric CO2 and H2O. After that is done a sample is placed within the IR spectrometer and scanned. After a fourier transform calculation that is done by the computer, the background spectrum is subtracted from the sample spectra, leaving a corrected spectrum of your sample. The last step is to find and label the major peaks to help you correctly analyze the spectrum. This is known "peak picking". After these steps have been done, you are ready to print a copy of your spectra for analysis at home. The following steps detail the steps needed to collect a FT-IR spectrum.
Open the program "Omnic FTIR" by double clicking the icon located on the Windows desktop. This will open the program that you will want to use to collect your spectra. Once the program is open, the screen will be similar to the picture shown below. The experiment should be automatically set for "Transmission E.S.P.". If it is not, click the scroll down bar and choose it.
| Collecting the background
Click the left-mouse button on the "Col Bkg" button (6th button from the left).
| The following confirmation window will pop up. Click "OK" and proceed.
At this point, it is important to be patient while the spectrometer finishes scanning the background. The spectrometer will take 16 scans at a 4 resolution. This should be good enough for most samples you will need to do.
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| After the first block of 4 scans, a preliminary scan is shown upon the window. You must let the spectrometer finish all of the scans before opening up the chamber of the spectrometer or starting any new functions on the program. A progress meter at the bottom left of the window will show you the amount of time left in the scan.
| When the background scan is finished, the following confirmation window will pop up. Click "Yes" and proceed.
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| Your finished background scan will similar to the one below. The large doublet peak at ~2350 cm-1 is the peak given by CO2. Flushing the chamber with N2 gas can eliminate this peak, but for our purposes we will not typically do that in lab.
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Preparing the Sample
The picture below shows equipment that you will use to prepare your sample. At the far left is a desicator, an airtight chamber that has a drying agent at the bottom to absorb moisture. A desicator is used for storage of items that should be kept dry. The next item is a salt plate holder (the black and silver object), used to hold salt plates upright while your spectra is being scanned. The clear disks to the right of the salt plate holder are salt plates. There are two slat plates on the paper, and they are a little difficult to see.
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Salt plates are used to mount the sample in the IR. While there are many methods for mounting samples (Teflon tape, KBr pellets, etc...), we will be using salt plates, as they are easy to use. You should be careful with these plates as the are fragile and scratch easy. You should store salt plates in a dry environment, such as a desicator.
The white cylinder is a container that salt plates are stored in before being placed in the desicator. In the back row are bottles of acetone and methylene chloride. The salt plates are cleaned with acetone in between use and before storage.
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Two types of samples you may have to take an IR of are solids and liquids. There are two (slightly) different techniques for mounting the samples onto the salt plates. Typically, liquid samples are sandwiched between two plates, while solid samples are spread in a thin film onto a single plate.
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To mount a solid sample onto a salt plate, you need to dissolve the sample in a liquid before mounting. Methylene chloride is a good solvent to dissolve samples in because of its low boiling point and it does not have a carbonyl functional group to that would appear in your spectra. You do want to be careful to avoid skin contact with methylene chloride. To mount your sample upon the salt plate, drip your sample dissolved in methylene chloride in the middle of the salt plate. Carefully blow on the plate to evaporate the solvent. Try to keep the sample in the middle of the plate. When the methylene chloride evaporates, a thin film of the solid will form on the plate.
| If your sample is a liquid, then a small amount of "neat" (pure) liquid should be dropped in the center of the plate. A second salt plate should be placed on top of the first plate, sandwiching the liquid sample in-between the two plates.
After your sample is mounted, remove the silver cap on the holder and slide the salt plate(s) into the black tube. Once the plate(s) are flat against the bottom of the tube, replace the silver cap to tightly hold the salt plates in place. The solvent is allowed to evaporate, leaving the solid compound on the plate.
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| To the left is a view of the inside of a FT-IR spectrometer. A triangular bracket is located in the middle of the spectrometer. This holds the salt plate holder in place while your spectra are being scanned.
Insert the holder into the bracket (upper right) so that the silver tube is positioned in the center of the chamber. Slide the holder to the bottom of the bracket (bottom right).
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You should be aware that breathing into the chamber while you are placing your sample could saturate the chamber with CO2, which would show on your scanned spectrum. Your sample is now ready to be scanned. Be careful not to exhale directly into the chamber. Once the sample is in place, close the lid and turn the locking knob to secure the lid.
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Collecting the Spectra and Peak Picking
At this point, the computer screen should still have the background spectra in the open window. Click on the "Col Smp" button (5th from the left) to begin the scan upon your sample.
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Once the "Col Smp" button is clicked, this pop-up window will come into view. A date is given by default, but can be replaced by the name of the compound or the lab experiment number. This title is not the name of the file, but it will be listed on the printout, so it is good to have an identifying name. After you give your spectrum a title, click "OK".
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| In this example, we are preparing an IR spectra of ethyl acetate, so that is the title it is given.
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| The following confirmation window will pop up. Click "OK" and proceed.
At this point, it is important to be patient while the spectrometer finishes scanning the sample. The spectrometer will take 16 scans at a 4 resolution. This should be good enough for most samples you will need to do.
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After the first block of 4 scans, a preliminary scan is shown upon the window. You must let the spectrometer finish all of the scans before opening up the chamber of the spectrometer or starting any new functions on the program. A progress meter at the bottom left of the window will show you the amount of time left in the scan.
| When the background scan is finished, the following confirmation window will pop up. Click "Yes" and proceed.
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| At this point the display (below, left) shows both the background spectrum, in blue, and the spectrum, in red.
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| If you remember, the purpose of the background was to remove contaminating peaks from the spectra of your sample. The program does this automatically, by subtracting the background peaks from your spectrum.
It is not necessary to keep the background unless you are going to take more spectra. If that is the case, save the file, and prepare a new sample. If you only need a printout, follow the instructions as given below.
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On the printout, you will want to remove the background from the screen. Left-mouse click on the background spectra. This will turn your spectra gray and the background red.
| A picture of the screen is shown to the right. Click the left-mouse button on Edit, Clear to delete it from the screen.
The only spectrum that should be visible is the one of your sample. If the background is the only spectrum visible, you deleted the wrong spectrum. An "undo" option is available under Edit, Undo.
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| If you successfully removed the background from view, then you will want to find the peak values before printing. Click the left-mouse button on Analyze, Find Peaks, as shown to the left, to "peak pick". This function will label the major peaks shown on the screen.
If the whole spectrum is not visible at this point, you may want to left-mouse click on the "Full Sc" button (11th button from the left). This will bring the whole spectrum into view.
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Typically, these are all of the steps you will need to do to prepare a spectrum for printing. On occasion, you may need to adjust the baseline (adjust a sloping baseline of a spectrum), or other processing. These items will not be discussed now, but are available under Process. Your teaching assistant can help guide you if you need to perform any advanced processing.
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The Final Spectra
At this point your spectrum should look similar to the one shown below. The background has been removed, and the major peaks are labeled with their wavenumbers. As you can see on the example spectrum of ethyl acetate, the major peaks at 2984-2908 cm-1 are C-H stretches, and the peaks at 1447 and 1374 cm-1 are C-H bends. The ester carbonyl (C=O) peak is clearly visible at 1735 cm-1, and the major peak at 1243 cm-1 is a (C=O)-O stretch. You are now ready to print your spectrum. Left-mouse click the "Print" button (3rd button from the left). Your spectrum should print now.
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| Before you leave, you must clean your sample from the salt plate. Remove the salt plate holder from the IR chamber and close the lid. Remove the salt plate and rinse the plate with acetone, collecting the acetone in a beaker. Dispose the acetone wash into the "Used Organics" jug, and place the dry salt plates into the desicator. It is important to clean the salt plates, as any left over sample would contaminate the next spectrum taken.
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