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Advice- discrepancies with spectroscopic nomenclature on FTIR spectra

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FTIR_help:
Hi,

I'm an archaeologist who uses FTIR to do analyses on ancient burnt bone. I was writing a report up for the PI of the lab I am working in, and she notified me that I am not using standard spectroscopic nomenclature when discussing the likely functional groups of the peaks I mention in my methodology. I was a bit confused, as I had been copying all nomenclature from archaeological papers. I showed this to her and she mentioned that I should research why archaeologists were not using standard spectroscopic nomenclature- and that she was busy, it was a job for me to find out!

I entered archaeology through the art history field and have very little training in chemistry. All my spectroscopic training has been self-taught. I thought I may throw the question here to see if there was an easy answer to this discrepancy. If there is not, perhaps there is literature that may be recommended?

I am putting a summary of my issue here, I would really appreciate if anyone has any insight!

Table. 1: My peak identification

Peak height (cm-1)Likely functional group 874 cm-1 CO32- v2 1028-1100 cm-1 PO4 3- v3
1st Comment by chemist: "Strange nomenclature here, does not make chemical sense to me. The groups are CO3 (-2) and the phosphate group is PO4 (3-), so not sure what you have here".

2nd Comment by chemist (after demonstrating that this is what the likely functional groups are labeled as in archaeological literature): "It is chemically misleading. If your audience knows it you may keep it, but add a sentence relating it to standard spectroscopic nomenclature..."

What I have researched so far: To me, I think the issue may be with putting the charges in the functional groups, and perhaps something to do with the ions? I have no issue moving forward with the nomenclature suggested by the PI, but I can not independently evaluate the nomenclature.

Thank you so much for your time. I would be happy to share the citations of the archaeological literature if that would be useful, or answer any other relevant questions.

Borek:
I know my answer will be of little direct use, but I strongly suggest you start with some basic text on IR spectroscopy. IR is more about detecting bonds than functional groups. It happens that detecting some bonds is almost equivalent with detecting some functional groups, but that's not a rule.

Plus, check what chemists mean when they talk about functional groups: https://en.wikipedia.org/wiki/Functional_group - you won't find the anion CO32- there.

wildfyr:
I agree with Borek. FTIR peaks correspond to specific bonds, not whole molecules or ions.

The wavenumbers you identify are for C-O and P-O, but a similar peak could occur in other C-O or P-O containing molecules.

If you look at the whole spectrum for Sodium carbonate http://lisa.chem.ut.ee/IR_spectra/paint/fillers/1472-2/ you can see there are other characteristic peaks, especially the one at 1409-1424. This is probably the C=O. Seeing both in a spectrum lends the most credence to a conclusion of carbonate being present, but also you are assigning each peak to a bond, rather than a whole ion.

FTIR_help:
Hello!

Thank you for your replies- yes, that does make sense that the peaks are assigned to a bond rather than a whole ion, and how seeing many characteristic bonds in a spectra strengthens the likelihood of a compound being present.

My methodology actually includes measuring 14 peaks from the bone spectra, including (what is labeled in the archaeological literature as): PO43- v1 (960 cm-1), PO43-v2 (471 cm-1), PO43- v3 (1028-1100 cm-1), PO43-v4 (565,605 cm-1), CO32- v2 (874 cm-1), CO32- v3 (1400-1550 cm-1). I also am looking at peaks for Amide A+B, Amide II-VII, Aromatic compounds, and HPO42- v2 bending.

I quickly wanted to ask a follow up question, if you happened to have time. Since I am technically identifying bonds, what would be the preferred nomenclature for me to include in the text of my report from the position of a chemist? Perhaps archaeologists list the ions because it is a known component of bone, but I would like to label my tables and figures properly. If I understand correctly I still should not use CO3(-2) and PO4 (-3) as the chemist suggested. Would it be simplified to  'CO3 v2' for example?

I appreciate your time in response, and thank you for the helpful link.

wildfyr:
A chemist would show the actual spectrum, tag the relevant peaks, say what bond they correspond to (i.e. P-O, or C=O) then conclude that the presence of those bonds adds up to this molecule.

In the actual text, I would write, "the presence of strong peaks at 1410 (C=9) and 870 cm-1 (C-O) are characteristic of carbonate"

In fact.... Here is a paper I wrote so you can see an example of what I'm talking about!

https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.201506253

Looking back I think I actually made a mistake in assignment of sulfur oxygen peaks, but at the time I couldn't have known the difference. IR isn't very clean cut.

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