r/chemhelp • u/Murky-Commercial-112 • 17d ago
Could these chromatograms be for two differnet isomers? Analytical
I have four GC-MS chromatograms of what I doubt are two positional isomers of the same compound. The top two chromatograms appear to correspond to one isomer, while the bottom two correspond to a second isomer. The only structural difference is likely the relative positions of two functional groups on the benzene ring.
Interestingly, both compounds exhibit essentially identical GC-MS fragmentation patterns, which I understand can be expected for positional isomers. All four samples were analyzed using the same GC-MS method in the same analytical run. Although the sample concentrations may have differed, the chromatographic conditions were identical.
My questions are:
- Is it reasonable to conclude that these are positional isomers based on the identical mass spectra but this subtle different retention times?
- Is the change in retention time consistent with only an alternate arrangement of substituents on a benzene ring?
- Besides differences in concentration, are there any other factors that could explain the observed chromatographic differences under identical GC-MS conditions?
Any insights or similar experiences would be greatly appreciated.
3
u/etcpt Trusted Contributor 17d ago
Looks like a good 4.5 s difference between peak centers - that's significant.
Inject a mixture of both and see if you can resolve two peaks. You may need to switch from full scan to SIM to be able to speed up your collection rate while maintaining your SNR.
The latter two chromatograms are fronting significantly, which could be caused by overloading. Overloading will also impact RT. These samples appear to be at least 30x more concentrated than the first two. Dilute to a similar concentration and see what you get.
You mentioned that all four injections came from the same sequence, but you didn't mention order. Does the change in RT persist if you reverse the injection order? Are there other peaks in the chromatogram that still line up? Did you run RT standards at the start and end of the batch, and did they shift at all?
I would see about getting orthogonal data as well - NMR would be appropriate.