FTIR Transmittance should be 100% maximum since the logic is that it absorbs the same amount of radiation as the reference, which cannot be beyond 100%. In my knowledge, a baseline correction might be needed.

Unfortunately, instruments may show some drift which means that the reference spectrum should be recorded newly every once in a while. A baseline correction is certainly possible, but the drift is not necessarily constant with regard to wavenumber. What are you actually using as a reference? Note that in infrared spectrophotometry it is generally not a good idea to measure either an empty or a cuvette filled with the pure solvent as reference...

Normally, if you run a background you don't get more than 100% transmittance, unless you have malfunctions in the optics of the instrument itself.

Do you focus the beam at the middle of the cell, and use an aperture? If you make incidence parallel light (NA>0) into the transmission cell, and the refractive index of the sample in higher than air, the light intensity of the sample may become larger relatively. As the result, there is some the possibility the baseline may be higher than 100%.

The absence or wrong done baseline correction is a typical reason for you observation. The other reason might be luminescence of your sample in the IR region, which is less probable. Jiri

Instrumental settings may cause this. If the IR source is close to it's final days, you may see hot spots developing which can drive your transmittance > 100%. This will be unpredictable. A fresh background scan can help for individual spectra.

If you have mercury cadmium telluride (MCT) detector that is saturating (too much light; the aperture may be open too much), this can also cause the effect you describe This is often in the form of an asymmetrical peak in the low frequencies. Inspection of the single beam background would show negative values in the low frequencies.

I think the simple way to diagnose the problem is to compare the raw single channel spectra (the IR light intensity convolved by the instrument elements) of the sample against that of reference. Then look at where intensity of the sample spectra is larger than that of the reference. Where is the location? At long wave length ? or is it periodic? A question: what is your reference? Is it the empty cuvette or filled with the pure solvent ? Or nothing?

Baseline correction, sample luminescence, and spectrometer software design (esp if those intensities are found at higher wavenumbers and bands are distorted) could be the cause.

hello , please tell me why do i get low transmittance sometimes when i scan sample i.e of 6% and when i match the same spectra with standard it shows purity if of 99%, as I am using instrument Make SHIMADZU FTIR - DRS assembly

A low transmittance would be a function of concentration or pathlength. Ideally the strongest peak does not go lower than 10% transmittance (or absorbance of 1.0). Try to make your sample either thinner or reduce the concentration.

Virendra Singh : I agree with Joe Van Gompel . Can you tell us more about the form of your sample (thin film, pellet, liquid...), substrate/cuvette etc?

Thomas Mayerhöfer : I am using DRS technique with disc holder instrument - Shimadzu FTIR and follow the procedure by taking Background by grinding KBr and after background for sample preparation, titutating KBr (100mg) along with powder samples (5mg) in mortar and pestle and put it in to small circular disc after that i put sample scan button so i had file of that spectra

If you are performing Diffuse Reflectance Spectroscopy (DRS), how do you end up with transmittance? And what kind of sample do you have (organic or inorganic material)?

Actually, your spectrum does look quite ok, but I still do not understand how you end up with transmittance from a DRS measurement..

If you are collecting your spectra as diffuse reflectance, then the appropriate y-axis units are Kubelka-Munk or KM units. THe equation is

f(R) = (1-R)2 /2R = 2.3 ac/s where R–absolute reflectance of the layer,

a-absorptivity

s–scattering coefficient

Diffuse reflectance is highly dependent on particle size and packing.

What this all means is that if the spectrum is displayed in the units inappropriate to the sampling method, the spectrum will be distorted. So make sure the software is set up to provide the proper units for the y-scale.

More information can be found here.

https://www.piketech.com/files/pdfs/PIKE_Diffuse-Reflectance-Theory-Applications.pdf

Most software packages have a KM function. I'm sure it is a simple y-axis conversion.

i am using lab Solutions for FTIR - SHIMADZU as server based 21CFR data base management software please help me for doing KM Fuction

https://www.shimadzu.com/an/ftir/support/ftirtalk/talk1/intro.html

This talks about diffuse reflectance in general and is a good introduction. You will have to investigate the Help section of your Shimadzu software to apply the KM function.

please Thomas Mayerhöfer , I want much more explanation about "what is the problem of attaching ATR unit and collecting the data as "transmittance"?

normally, I do this, then I convert transmittance to absorbance by the software.

ATR means "attenuated total reflection", which means that you measure in reflection mode (without sample, reflectance is unity, therefore total reflection, with an absorbing sample, reflection is attenuated). The reflectance spectrum looks a bit like transmittance spectra if the oscillator strength of the vibrations is not too strong. Therefore, to some extent, you can set absorbance A = -lg (R/R0) a bit like in case of transmittance where A = -lg (T/T0). Actually the first should be called "reflectance absorbance" and the second "transmittance absorbance" because they are only approximately equivalent and only for vanishing oscillator strength. In any case, absorbance is a quantity that is not conform with Maxwell's equations, therefore usually ill-defined and mostly useless, except for gases...

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Thank you very much @ Thomas mayerhöfer for your valuable illustration. On the same topic, I have attached a graph of FTIR spectrum of 25 mixture of two components. We have submitted a manuscript containing this spectrum and we got these reviewer comments

- transmittance spectra-how was possible to obtain transmittance spectra after ATR measurements.

- The values at Y axis- 135 % of transmittance?

Can you help me by illustration of this problem and what is the appropriate reply, also, do you recommend me to repeat this measurements again ?

Thanks

I don't know which kind of spectrometer you have, but I guess you have to adjust manually what kind of resultant spectrum you get. No problem here, since the spectrum is calculated in the same way. However, if I were you, I would repeat the measurements and record (much) more often the reference spectrum, this should prevent you from getting over 100 % (and, also, should avoid the non-linear change I see concerning the baseline).

Thanks again dr. Thomas Mayerhöfer . I will take your advice and repeat the whole measurement.

I am working on Shimadzu IRAFFINITY-1 device loaded with IRsolution software and I have also "The Unscrambler X software".

Concerning the non-linear changes, I have done several pre-processing steps before chemometrics calculations, these steps are baseline correction then "Detrending".

I have attached the Detrended spectrum, I want to know what do you think about it, as i get "reviewers comments" that dislike it.

Also,

Is there a "protocol" to choose the preprocessing steps of FTIR charts?

thanks

I have to admit that I also don't like those spectra. From a theoretical point of view, you simply should obtain a flat line at 100 % without sample. If you have a sample, in the spectral region were you don't have absorption you still should get a flat line at 100 %... or at 0 % if you convert ithe spectra to reflectance absorbance. In case of those spectra it seems as if you don't have a flat baseline but an undulating one...

I agree with Thomas that you should take backgrounds more frequently. I also note that your % T is low at higher wavenumber values. This is due to scattering and should not be a surprise given the sampling technique. It is very important to have consistent sample preparation. Unfortunately that means a great deal of time preparing new backgrounds, and these must be consistent as well, else your high wavenumber baselines will fluctuate up and down.

ATR spectra are recorded incorrectly, therefore the reviewer has the right objections. Unfortunately, the registration of all spectra should be repeated. Good luck :)