Fourier Transform Infrared spectroscopy (FTIR spectroscopy) is a useful and exquisitely sensitive technique used to identify and quantify unknown compounds, as well as study fine molecular details.

However, to obtain a meaningful IR spectrum, it is not only important to prepare the sample correctly but also to learn how to clean the apparatus that houses your (liquid) sample. Only through proper sample preparation and cleaning of the apparatus can you have clean, meaningful and reproducible data.

But First, How Does FTIR Spectroscopy Work? (Briefly)

FTIR spectroscopy produces an IR spectrum from a sample, whether solid, liquid, or gas.  The sample is exposed to infrared wavelengths (longer wavelengths and lower frequency than visible light). The sample can absorb light and produce a pattern of measurements or a “molecular fingerprint.”

The technique is advantageous, because it can be used to collect high-resolution data over a variety of wavelengths in seconds to minute’s time (much like a UV/vis spectrophotometer). These molecular vibrations correspond to specific chemical bonds, which are unique to each molecule and, therefore, each compound absorbing the variety of wavelengths.

The Apparatus

Liquid samples are much easier to prepare and involve using a liquid cell apparatus. The liquid sample is held together in place between two windows made of specific, suitable materials that do not interfere with the IR absorbance of the specific application.

However, in between the two windows lies a spacer. This Teflon spacer provides a specific path length for the light to shine through and allows a quantitative measurements according to Beer’s Law:

(Absorbance = concentration * path length* extinction coefficient)

The windows are sandwiched between a pair of metal plates held together by 4 screws, which are mounted in the IR chamber, similar to the way the UV/vis chamber holds a cuvette.

In FTIR spectroscopy, keeping the windows clean is just as important as the sample preparation. Below is the protocol I use to keep calcium fluoride windows essentially spotless.

Acid Washing/Cleaning Calcium Fluoride Windows

You will need your personal protective equipment (PPE) such as:

Additional requirements for washing a pair of CaF2 windows:

  • Large glass beaker halfway filled with water
  • 50 mL corning tubes halfway filled with water (2 per window)
  • Small 100 mL beaker (put no more than 20 ml Sulfuric acid)
  • Forceps


  1. Dissolve a few crystals of potassium permanganate (KMnO4) (generally no more than 5 semi big crystals) into a beaker of sulfuric acid (no more than 20 mL). Be careful, because this is a very strong oxidant that will cause fire (and a possible explosion) if you are not mindful of what you are doing. The color should be green but not dark green.
  2. Use forceps to gently put the calcium fluoride window, one at a time, in the permanganic acid. Wash for no more than 10-15 seconds.
  3. Remove the window being very careful not to scratch it or drip acid all over. Put the window in a corning tube halfway filled with water. The water should turn slightly pink-purple.
  4. Repeat for the second window. Remove both windows and place them in another corning tube with water to prepare for rinsing.
  5. Dilute the acid: pour all of the contents of the first corning tubes and the permanganic acid into the larger beaker.
  6. Use soda ash to carefully neutralize the contents of the larger beaker.
  7. Rinse the windows carefully using deionized water and dry them using pressurized air. Use the windows immediately or store them in a safe place to prevent them from getting dirty or scratched.

You may not need to rinse with permanganic acid before every experiment. In fact, it may not be a good idea to rinse each time, because rinsing with permanganic acid can cause pitting of the windows. As long as you immediately rinse with deionized water and dry it completely after experimenting, then using permanganic acid is just a great back-up tool to ensure the windows are clean.


To collect the best IR data, get trained by someone who has prepared IR samples and run the instrumentation previously, but also pay close attention to cleaning and storing the cell apparatus windows properly

FTIR is not a simple technique to learn, and is highly sensitive, making this technique even more challenging to use. But if you start with clean windows, the results should be clear.

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  1. Hey, I think this is relevant only to your particular type of “window”.
    In my lab we use a KBr crystal as a ‘mount’ for our liquid sample.

    We clean it with cotton wool soaked with either 100% ethanol or another alcohol (I think its propanol… but I don’t have my notebook near) if the sample is dried on the crystal.

    Anybody else does something similar?

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