The FTIR spectrum of biomass consists protein (60%) and lipids (8%) shows amide I and amide III but does not show the amide II peak at 1510 and 1580 cm-1. What is the possible reason could be?
Dear Puhazh,
It will be helpful to see your spectrum for anyone to figure out the possible reason for missing peaks or other issues.
On your spectrum, Amide I is annotated as band 9 and Amide II as band 10.
Dear Puhazh,
An enlarged spectrum and precise band positions would help a lot. As far as I can see band 10 is located below 1500 1/cm, so this band is not the amide II band.
The Amide II band can shift to as low as 1450 cm-1 depending on protein structural conformation. To me, Band 9 on your spectrum looks to be at roughly 1470-1480 cm-1. Although, I do agree that band positions and a higher resolution spectrum would help a lot.
Also, how have you prepared your sample for analysis?
Article Infrared spectroscopy of proteins
As stated above it is not easy to see the band positions. However the spectrum is dominated with the band about 1400 cm-1 typical of inrorganic carbonate, supported by the presence of your bands labelled 1,2, 3 and 13. What is band 7 and why so strong? Given the strength of the OH at approx 3400 cm-1 and the relatively flat baseline I suspect this may be a distorted spectrum. How was the spectrum recorded and have you applied a correction to the background ?
Band 7 could be due to carbon dioxide v3 modes. I agree with Geoffrey that we need more details on how you have collected and processed the spectra since it does not fit the typical profile one would expect from biomass.
Dear all,
I agree, band 7 is definitely due to CO2. Furthermore, contamination by inorganic carbonate will be likely as bands 10 and 13 appear to be typical for carbonate salts.
An amide II band below 1500 1/cm, however, will be found only if the protons of the solvent are replaced by deuterons, i.e. if H/D exchange takes place. Only in these cases the amide II band (now called amide II') will be found between in the 1450 -1480 1/cm region. I personally have my doubts that band 10 is indeed an amide II' band.
As usual, it all depends on how the samples have been prepared and how the spectra have been processed. Unless we are provided with this additional information then it is hard to deduce why this biological spectrum looks abnormal.
For example, if the sample has been treated harshly and the proteins are far from their physiological pH then it is possible that their secondary structure can take on a more unzipped, beta-sheet-like structure, which would give rise to a red-shifted Amide II band.
Alternatively, it could be that your sample has been contaminated with external components during processing.
Another explanation could be that your spectrum is saturated. If you are analysing your sample as a dried film on an ATR-FTIR instrument then I would suggest that you dilute your sample at least two-fold in water and see if this solves your problem.
I am intrigued to know exactly what has happened to this spectrum.
Article Charge-Induced Unzipping of Isolated Proteins to a Defined S...
Dear all,
Sample preparation includes drying the biomass and make it to powder by grinding. After that the FTIR spectrum is recorded by KBr pellet method.
Moreover I agree with the Geoffrey Dent's and Peter Lasch comment that the sample contains inorganic carbonate.
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