August 13, 2020, 03:48:33 AM
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Topic: Advice- discrepancies with spectroscopic nomenclature on FTIR spectra  (Read 405 times)

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Offline FTIR_help

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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.



Offline Borek

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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.
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Offline wildfyr

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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.

Offline FTIR_help

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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.

Offline wildfyr

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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.

Offline FTIR_help

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Hello!

Thank you so much for providing an example- I now understand the steps I should take and have started looking up what bonds the peaks I have identified are assigned to.

With this information, I would like to make a figure that both combines the identification of bonds/ peak correspondence with the inferred ions. I have done much research since reading your comment and have found a large amount of literature supporting the identification of these spectral peaks in bone with v1,v2,v3, and v4 of the PO43- ion and the v2 and v3 of the CO32- ion (noted to be derived from curve fitting analysis, their assignments, peak deconvolution, and supplemental ultrastructural studies).

As the point of my analysis is measuring these peaks strictly in a known material (bone) for inferring the degree of heat transformation, and not the identification of the substance, I think it is reasonable to make a single figure that communicates the whole package. Previously I suppose archaeologists just directly labeled the spectra with the inferred ions, and this was the nomenclature I became familiar with.

If anyone has an additional moment, I would like to ask advice on the best way to create this figure concisely so it can be understood by both a Chemistry and Archaeological audience.

My original figure in my report looks like figure 2 from Paschalis et al. (1996) -https://link.springer.com/content/pdf/10.1007/BF00369214.pdf.

Ideally I would like to create one figure of a complete spectra with: wavenumbers (cm-1), the identified bonds corresponding to peaks, and the inferred ions. I am thinking of stacking the information above the spectra, with a side bar identifying the chemical bonds and inferred ions (the PO43- ion and the CO32- ion with their vibrational modes). I have not seen a figure like this in my literature review.

I am having trouble thinking of the language I would use to identify the ions- "Attributable ions"? I have seen in the literature authors pointing to the "CO32- v2 band" for example, but I do not know if this is the correct way to use 'bands', as my understanding now is that the characteristic bands are functional groups seen through the intensity and position of peaks.

I really appreciate your patience and time. This has been extremely useful for me, and definitely will be following up on basic IR texts after I complete this report with a new figure and adjusted language in my text and tables. Really, thank you, all!

Offline wildfyr

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I'll try to answer your question when I get to a computer for better typing, but I really admire your thoroughness in trying to be clear and concise across disciplines. It exemplifies the best impulses of a scientist and communicator.

Offline wildfyr

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I think the example you noted is quite useful. Honestly, no chemist would be confused by that image.

In chemistry, sometimes to be specific, we describe the actual molecular motion that corresponds to an FTIR peak. For instance, there is asymmetric and symmetric stretching, breathing modes, wagging, bending, and so on. That's what the v1, v2, etc is for a single bond. At the bottom of this document you can see how these describe some of these in water http://www.ifsc.usp.br/~lavfis2/BancoApostilasImagens/ApLuminescencia/Infrared%20Spectroscop1.pdf


If the paper is based on deconvoluting a complex IR spectrum, this specificity is very useful information. Your paper is now a good reference material for sorting out FTIR peaks. If IDs are clear cut, that level of detail probably isn't necessary, and you can just point to the peaks and say "All these are C-O peaks."

Here is what I might do, draw your image like the example, except instead of CO3 or PO4, write out C-O or P-O v1, v2 etc. v1=symmetric stretch, v2 and v2’=bending, v3=asymmetric stretch. Then draw a line from these single bonds to the ID of the molecule.

I've attached a horribly simple example of what I have in mind. FYI the two peaks around 2800 for aldehyde C-H isn't actually two separate vibration modes, its Fermi resonance which is another can of worms, but I spent 20 minutes on it so you'll just have to accept it as an example :).


Offline FTIR_help

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Hello!

This is incredible!!! Thank you! Thank you so much for putting the time and effort into helping illustrate this figure for me. It's so much more that I could have expected- and I definitely can replicate it with my spectra.

Also, thank you for your kind words. So much of archaeology borrows from other sciences- which, sometimes, is a really interesting strength, but also means that I am only have basic training in other disciplines. Especially with FTIR, I know I was utilizing aspects of spectroscopy and chemistry that I only had basal knowledge of, but did not know what was missing. I was so nervous to be  incorrectly identifying/labeling my spectra, and did not want to disrespect the lab who so graciously let me use their instruments.

I really was having difficulties on my own, and your support and continued responses has really cleared up my next steps in terms of using FTIR as well as move my research and understanding forward.

Hope this message finds you safe and well!


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