A same targeted product A and B synthesized in two different way and produced FTIR data shows same bands for A and B. But the transmittance is varying as B>A . Can we say that A is pure than B?
FTIR transmittance follows the Lambert-Beer law, so the absolute values depend both on sample thickness and concentration. You didn't tell weather your used solid samples (like KBr pellets) or a cuvette for liquids. For KBr very often the quality of sample preparation (weights of KBr and sample, homogenization of sample) influence the transmission. No need to say that the concentrations should be the same for A and B.
Normally, differences in band allocation and/or peak ratios indicate differences in quality.
I agreed with the Thomas Fischer, It is possible to quantitate the compound by using FTIR; if you take area of the particular band against quantity of the sample. you can predict which one is in pure form.
Yes, the halides have only one IR-active vibration which is well below 1000 cm-1... since this vibration is very strong, reflectance spectra are certainly more suitable...
The IR active compounds can be correlated with compound purity when compared with the same standard pure compound, generally used in pharmaceutical industry to check their compound purity
In FTIR, we cannot quantify as this is just qualitative except for some other substances like Malathion, etc. The purity of any substance can be checked by using known reference standards like USP, EUROPEAN, JAPANESE PHARMACOPOEA, etc. There are IR chromatograms available in the library where you can compare your sample chromatograms. Mr. Fisher is right about Beer- Lambert's law, but this is most common in UV/VIS and Atomic absorption spectrophotometer.