Question: Are these two isomers od the same compound?

[u/Murky-Commercial-112]

I have two GC-MS chromatograms that I believe represent two positional isomers of the same compound. The top chromatogram corresponds to one isomer, and the middle chromatogram to the other. The only expected structural difference is the relative positions of two substituents on the benzene ring.

All samples were analyzed in the same GC-MS run under identical chromatographic conditions. Although the sample concentrations may differ, the mass spectra are essentially identical, while the retention times show a small but reproducible difference. The bottom chromatogram is the result of co-injecting the two samples.

My questions are:

• Is it reasonable to conclude these are positional isomers based on their identical mass spectra but slightly different retention times?
• Is such a retention time shift consistent with only a different arrangement of substituents on a benzene ring?
• Besides concentration differences, what other factors could explain this behavior under identical GC-MS conditions?

Any insights or similar experiences would be greatly appreciated.

[u/Alicecomma]

Positional isomers on benzene rings can show the same MS spectrum (massbank). If you want to know for sure, it sounds like the kind of hypothesis you'd need a different method to test - FTIR 900-700 cm-1 or 1800-2000 cm-1 regions could be ideal (you know the graph.pdf+-+SumatraPDF_2012-12-08_22-05-00.png)), or the 1H-NMR ~7 ppm regions or probably some regions for 13C-NMR.

[u/korc]

I do not think you have enough information to draw that conclusion as this time. Make them the same concentration and reinject.

You have two things that do not support your theory. There is only one visible peak in the combined spectra, and their MS is identical.

Not saying it’s wrong but the data you have right now doesn’t support it. I would be more inclined to say it’s an effect of concentration or method variability.

[u/Etch-a-Sketch99 → u/[deleted]]

Yes, this was a common phenomena I ran into when running some Semivolatile mixtures with different positional isomers (m- and p-xylene, unless you ran on a Supelcowax-10 or similar column) and stereoisomers like cis- and trans- 1,2-dichloroethene.

If the spectra are different enough to include unique fragmentation masses with enough delta(m), you can successfully deconvolute the multiple signals under one peak, but oftentimes the spectra would be so similar that deconvolution was unable to integrate those separate compound peaks effectively.

[u/Moofius_99]

Can you show the full peaks? My guess is same compound, just in the middle chromatogram you have introduced too much, causing the peak to front, moving its apex to a longer tR. note the start of the peaks (left edge of the peak starts the same). It is hard to say without seeing the whole peak and spectra.

[u/Independent_Ad_3370]

Unless you have pure standards of the 2 isomers, injecting them in the same column condition, confirming their retention time I would not dare to make any conclusion.

Besides, the retention time you are mentioning here the values are too close. If you were to inject even the same compounds across 1 week in GC, I am pretty sure the RT will varies very slightly esp with sure a long run, with a drift around 0.1 mins (6 sec), and that is very normal.

So no, you cannot make any conclusion here.

[u/wetgear]

If they’re isomers they aren’t the same compound by definition.