I have recently isolated an unknown compound with molecular weight of 522 (m/z value = 523). The UV absorption was observed at 263 nm. I have accessed the database to search for any known compound, but i could not identify any. I am speculating the possibility of flavonoids with such UV chromophore. I am hoping to get some suggestion about the possible identity of my compound to figure out its novelty.
The NMR showed 16 carbon atoms from 13C NMR data, but the molecular formula obtained from HRMS suggested the presence of 30 carbons due to the compound is symmetrical. I would like to know if the problem exist during my NMR measurement or any error which led to the mismatch between NMR and MS spectral data?
Any suggestion or advice from RG professionals and members would be greatly appreciated. Thank you in advance!
Dear Chung,
It would be most helpful if you could provide us with some more data. All of this is like a wild goose chaise. There could be a number of reasons why your 13C-NMR lacks signals, of course, one of them being molecular symmetry. Information on the source of your compound (biological origin if such), copies of the actual spectral data (NMR and MS) are necessary. Did you isolate anything else from that source? What was it? Was it similar in polarity (eluted close) with the unknown? On the other hand, even if you purified your compound to a level of higher than 99%, the high m/z fragments could come from an impurity. Consider other m/z values as possible molecular ions. All in all it is difficult to say anything without having more data...
Best regards,
Niko
It would be interesting to know what 1H NMR said on this compound, also IR for functional groups rather than just relying on two conflicting pieces of information.
Dear Mr Lim,
The best way to establish the structure of an unknown compound is to make its full spectral characterization. You should, apart from the MS, 13C NMR and UV, record also IR and 1H NMR. Flavonoid compounds, being polyphenols should give the IR band around 3600 cm-1 (-OH valance vibrations), the large band around 1200 cm-1 (C-O valance vibrations) and -OH deformations vibr. between 1300-1200 non-assoc. and 1400-1300 assoc. You can also use the Raman spectrum, which is more simple in a case of phenols.
On 1HNMR you should analyze exactly the aromatic region 8-6 ppm and correlate it with 13C NMR signals.
Apart from this above, I will suggest you (if you are not sure what compound you've got) to perform the elemental analysis - you'll get the answer which elements EXACTLY are in your compound and what is the % elemental composition.
To help you more, I should see spectra and all required analysis results.
Good luck
Jarosław Lewkowski
One possibility is it could be a dimer. DId you check the HMBC , HSQC and H-H COSY, evaluation of those spectral data will give you more information about the structure, Since you have done a HRMS, it will help you to see about the isomers available. How about the H NMR, is this an aromatic compound. If spectra are available, I can help you more.
Thanks for all of the suggestions and comments. Now, I am in the midst of determining the structure through NMR spectral data interpretation. I will try my best to follow all the given advice and to elucidate the structure of this compound.
I would like to express my greatest gratitude to all the help and advice given by RG professionals to solve my doubts.
Please double check for possible dimerisation (insitu, mass spect) caused by slightly concentrated sample. Although the compound itself is not a dimer.
It happened in my experiment a lot.
Are you observing the 5-OH signal above 12 ppm which is common in most flavones unless alkylated or arylated?
The apparent presence of 16 carbon peaks in the 13C spectrum of a symmetric C30 compound suggests that one might be due to an impurity. A common impurity peak in natural products occurs at about 29.6 ppm in CDCL3, corresponding to the internal methylene carbons of a long chain fatty acid. These compounds commonly co-elute with other compounds. Without knowledge of the 1H and 13C spectra, it is difficult to make an informed comment. However, a symmetric C30 compound could be a symmetrically substituted derivativeof squalene, probably with oxygen substituents. A number of years ago, we isolated a symmetric derivative of squalene, glabrescol which had a string of 5 THF rings in the middle (Tetrahedron Lett, 36, 9137 (1995)) with molecular weight close to your value. They are not the same since glabrescol was not UV-active. However, this might give clues about possible structures.
Thanks Dr. William F Reynolds for your kind explanation. I will check the purity of my compound again to confirm whether there is presence of impurity prior to re-measurement of my NMR spectra. Also, I am greatly appreciate for suggestion of your paper for my reference. I will refer to your previous paper to get some information about the possible structure.
Thank you very much for the advice and suggestion provided.
i ve same prob in one symmetrical flavonoid dimer, i think +1 or -1, in molecular weight is not so big problem, but the extra two carbon is problem, you need 2DNMR for further confirmation, as we solved the problem through HMBC and HMQC corelation, you can see my publish paper in BMCL as well,
“Methylenebissantin: A rare methylene-bridged bisflavonoid from Dodonaea viscosa which inhibits Plasmodium falciparumenoyl-ACP reductase”, Bioorg. Med. Chem. Lett. 2012, 22, 610–612.
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