Hello,
we have synthesised a compound that has been previously published in the literature and 1D C13 NMR line up reasonably well (up to 1 ppm difference) for small molecule. However, our 1D 1H NMR spectra do not line up. In particular we observe shifts with greater than 0.5 for one instance and 0.7 for another peak value in the range of 2.9-4.1. We have tested different solvents, including the one used to obtain the literature spectrum as well as anhydrous DMSO-d6 but always end up with 2 vastly different shift values of a total of 6 values compared to the reference spectrum (only one in literature).
We have done some literature survey and some literature (Dumas et al. 2019) claim that an error of 5% may be acceptable for the same compounds in different 1D 1H NMR experiments for the same compound in different laboratories (the compound tested was not similar to the compound that we are working with however). Therefore for a value of an expected value of 3.0, a delta of 0.15 may be considered acceptable. However in our case the deltas are >15%, or even >20%. Would this suggest that we have not obtained the literature compound and that we have produced another molecule? Or are there other, more obvious explanations.
We have done 2D C13 1H HSQC experiments and are fairly confident about our structure. Unfortunately, 2D was not performed for the literature spectrum. Are the discrepancies shift values above (1D 1H NMR) sufficient make the claim that literature has a different molecule present? We think that this would be a big claim, so if we did submit this finding to a journal - what are experiments that may be suggested/required by referees to unequivocally proof that the obtained compound is not the one in literature, for which no 2D NMR was performed?
Any thoughts would be highly appreciated.
Thanks,
Karl
1H chemical shifts can vary more than 13C chemical shifts. Temperature, pH, solvent can affect the shifts. Exchangeable protons from OH or NH moieties are specially sensitive to changes.
The coupling constants and patterns on the other hand should be recognizable if you indeed have the same compound. If you have run a HSQC, did you also colelct a HMBC and if yes do the connectivities make sense for the proposed molecule?
Dear Clemens,
thank you very much for your reply and insights, I appreciate your help and have noted your affiliation.
Yes, we have recorded HMBC, albeit in a different solvent (D2O). The connectivities check out for our compound. HSQC was also performed in D2O and also agrees with our structure. We're very confident about our structure, but we are unsure if we have a new compound when comparing to literature.
The literature compound was only recorded 1D 1H and 1D 13C in deuteriated methanol, hence we have repeated the HSCQ for our compound in the same solvent. Literature does not disclose temperature, so we assume room temperature was used, which we also adopted (25ºC). This is where we observe some >15-20% differences in the proton NMR peak values when comparing to literature.
Our compound is a relatively simple mono carbohydrate derivative and has several OH residues, which make the comparison difficult.
I have followed your advice and compared the proton J coupling values. Unfortunately our compound in methanol only provides one reliable J coupling value, whereas literature provides all but one J coupling in text format. Our single J coupling value is not found in the literature - Of course it could be that this is the missing one in literature, so this does not allow to rule the structure out.
1) In any case, our J values closest literature fit deviates by ~0.9 Hz (see below); would this be considered significant for supposedly the same compound in the same solvent and same temperature (RT)?
2) Our 1D 1H NMR was recorded on a Bruker machine at 800 Mhz, but we were not able to extract patterns as reliably as reported in literature, hence most of our assignments are multiplets, whereas literature claims resolution of several dd or t. We think we can "match" a single peak at 4, (d, J=8.4) in our structure with 4.08 (d, J=9.3 Hz) in the literature. Or would these J values incompatible?
I was surprised to learn that 13C NMR data should be more reproducible. Our compound shows some "minor" differences, when acquired in the same solvent. There are some issues assigning identities for the literature compound because no 2D was performed. However two values are unique enough. One at 51.1 (lit), which for our compound comes out at 53.4.
3) Would this delta of 2.5 be indicative of a different compound?
I have also simply ranked 13C values from low to high and found that the differences between each peak value to the next are not identical, so there doesn't seem to be a systematic error/effect, which we do observe if we acquire our spectra on a different day or for longer periods for the same compound in otherwise identical conditions (i.e. all 13C values are shifted by ~1.5ppm).
Again, thank you very much for your help.
Best Regards,
Karl
Could you tell which device was used in the reference you use to compare with your spectrum? Was your sample prepared the same way? What about the processing parameters?
Dear Eduardo,
thank you for your interest in this problem.
The reference spectra were recorded on a Bruker 300 MHz. Nothing else but the solvent selection (MeOD) was disclosed in the literature. We do not know the sample concentration, neither the exact temperature (we assume RT, 25ºC). The literature 13C spectrum was recorded at 75 Mhz. We assume that the literature 1H spectrum was recorded at 300 Mhz.
What exactly do you mean by processing parameters?
Best Regards,
Karl
Karl,
Since you mentioned that your compound is a carbohydrate derivative, I wonder if the difference in chemical shifts can be attributed to different stereochemical configuration in one of the present chiral centers ? So perhaps you compare NMRs of two different diastereomers ...
I often notice that mistakes in stereochemistry (both in drawing and configuration assignment) are not uncommon, and certainly happening more often than mistakes in NMR description.
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