evilmastermind Posted May 19, 2012 Posted May 19, 2012 Hi, I'm a chemistry student and I'm having a lot of trouble understanding how to interpret NMR spectra... We were given an unknown molecule that we have to identify. I have done 13C , 1H, COSY, HQMC and HSQC nmr measurements and also an infrared spectra and mass spectra... and even with all these I can't figure out what my molecule is!! Here are the spectra: http://s294.photobuc...14/freya-freya/ So far from the 1H and 13C I think I have 6 carbons and 14 hydrogens, and I think there might be an N in there somewhere... But the mass says 387.1 (?!?!) (and I'm not even sure that's my base peak - how can you tell which peak is the base peak anyway?). I think the infrared shows an NH and a C=CH2 at around 3000cm-1.. Also, there are a few peaks in the H nmr spectrum around 7... I thought those were aromatic ring shifts, but integration says that they're CH2 groups... I just have no idea how to figure out its structure... I've spent about 3 whole days non stop trying to understand the spectra and I'm not getting anywhere... Some help would be appreciated if anyone has time to spare... Thanks!
hypervalent_iodine Posted May 20, 2012 Posted May 20, 2012 A few general comments to start with. The big question I have is, do you have any inclination as to what kind of compound this is at all? Where did it come from? This will make it much easier to narrow down. Secondly, what is this for? If it's for a research group, you may want to check with your supervisor that he's okay with you sharing data publicly like this. And finally, are you absolutely sure this is a pure sample? Have you run it through HPLC or even a GC at all? So far from the 1H and 13C I think I have 6 carbons and 14 hydrogens, and I think there might be an N in there somewhere... But the mass says 387.1 (?!?!) (and I'm not even sure that's my base peak - how can you tell which peak is the base peak anyway?). I think the infrared shows an NH and a C=CH2 at around 3000cm-1.. Also, there are a few peaks in the H nmr spectrum around 7... I thought those were aromatic ring shifts, but integration says that they're CH2 groups... I just have no idea how to figure out its structure... I've spent about 3 whole days non stop trying to understand the spectra and I'm not getting anywhere... Some help would be appreciated if anyone has time to spare... Thanks! I'll split this up for you to make it easier to read. 1H and 13C 1D NMR The peak on your 1H NMR that you identified as acetone is perhaps not correct. Acetone pops up at ~1.96 ppm in d-MeCN, not 2.06 ppm. As it happens, you have a peak at 1.96 ppm, but the splitting pattern makes it unlikely to be either acetone or residual d-MeCN. Your residual solvent peak should also crop up at 1.96 ppm, which makes me wonder if the peak you've indicated as being acetone is your solvent peak and you just haven't calibrated it. On that note, why did you use d-MeCN over CDCl3? The multiplet at 1.96 ppm is very curious. The splitting is very clear and would suggest being next to 4 protons, possibly 2 x -CH2 or 1 x -CH and a CH3, though there is nothing else in your spectra that appears to be coupled to it. Again, I would say it's your solvent, but d-MeCN shouldn't be split like that (which makes me question purity). I can't comment too much on the other two peaks without seeing the integration. What makes you think the peaks in the aromatic region are CH2 groups, by the way? You haven't given any integration on the spectra that I can see, but they seem very much like aromatic CH protons to me. I'm assuming you're having issues with the multiplicity of the aromatic peaks you circled with a question mark? The one at 6.53 ppm is a doublet of doublet of doublets (and a very nice one at that), which indicates some kind of long range coupling. The peak at 6.94 ppm looks like it also has or wants to have some fine splitting, but it's hard to tell. I think you may need to scale down the concentration and run your proton NMR again on a machine with more power (a 400MHz or 500MHz would work if you have access to one) to see it. You should also see the splitting on the little triplet at 7.24ppm become more resolved and less lumpy. The larger triplet has a coupling constant of about 9 Hz, which indicates ortho coupling rather than the para coupling you've written on the spectra. That in conjunction with the splitting would place it in between two aromatic protons (most likely the the two doublet systems at 6.53 ppm and 6.94 ppm). You may therefore have a meta substituted phenyl ring, although this would put into question your singlet at 7.01 ppm and to some extent, the smaller triplet at 7.24 ppm (neither of them appear to be due to any common solvents). I've noticed you also have a peak at about 8.25 ppm. It's a rather featureless hump, but could possibly indicate the presence of an enol (which I doubt as you should see some indication of the keto form in the IR) or maybe have something to do with the nitrogen you think is in there (more likely). I think the carbon spectra you have there is a DEPT spectra? It doesn't look like it's been run long enough or phased properly; I would run it again either with higher concentration or with more scans. When you analyse it, compile a report with an overlay of your normal 13C spectra so you can see where there are meant to be peaks and if there are any quaternary carbons. If it isn't meant to be a DEPT, run a DEPT and phase your carbon spectra properly. 2D NMR (COSY, HMQC and HSQC) The external projections on your HSQC, COSY and HMQC look a little odd and I wonder if maybe this was run at a different time to when you ran your original proton spectra? In your original proton spectra, you had some nice splitting at 1.96 ppm which now appears to have disappeared. The splitting in your aromatic region has also become quite a bit different and the shifts are all off. You may want to look into this. In the meantime, I would question your interpretation of the COSY spectra. You've penciled in a line where you have your one and only cross peak from an aromatic proton to a peak in the ~2 ppm range, but you've drawn it as coming down to the wrong aromatic peak. The cross peak clearly sits above the singlet in the middle of all the aromatic peaks, so why have you then drawn it as coming down to the lower field peak? It's curious as well that the peak at just above 7.25ppm isn't coupled to anything. This would be the peak corresponding to the tiny triplet at 7.24 ppm in your original spectra, although again I am dubious of reading too much into it until I know why your projections are so different to your 1H NMR. Your HSQC and HMQC both seem to use different projections on the 1H axis and both look different to your 1D spectra. It's not much good commenting on these until I know why some peaks are missing and the splitting is different, so I'll reserve my analyses until then. IR With your IR, is it possible to change the view window so that you can incorporate the entire spectra? As it is, it does look like you have some kind of amine. The peaks just above 3000 cm-1 are reminiscent of aromatic peaks, which contradicts what you said about the proton NMR. You also appear to have some aromatic breathing peaks, though it's hard to say without the peaks being labelled. Mass spec I'm assuming your mass spec was low res? It looks like something you might get off of a GC-MS run, which typically use quite harsh conditions. If it was run on a proper LRMS machine, you have to consider what ion mode it was run in and take into account the mass of sodium ions, etc. Have you done a high-res mass spec on it? You should get a molecular formula from that. If you can't do that and, try doing a micro analysis on it (CHNO test) or see if you can get some x-ray crystallography done on it (if it's crystalline, of course). As for the spectra itself. There are a lot of peaks at the base line, which makes it hard to figure out if there is a molecular ion peak in there or if so, where it is. I would, as I suggest above, run a high res and see what you get out of that. How temperature sensitive is your compound, out of curiosity? Also, you assume that you absolutely will get a molecular ion peak out of MS. This is not always the case. Some compounds are temperature sensitive and will decompose under the conditions used to collect data. Other times, your compound will form dimers and you'll see a lot of 2M peaks. And in some cases, you might have a very minor impurity in your sample that ionises much more readily than your compound. The result of this can be a near complete masking of m/z peaks from your compound.
evilmastermind Posted May 20, 2012 Author Posted May 20, 2012 (edited) A few general comments to start with. The big question I have is, do you have any inclination as to what kind of compound this is at all? Where did it come from? This will make it much easier to narrow down. Secondly, what is this for? If it's for a research group, you may want to check with your supervisor that he's okay with you sharing data publicly like this. And finally, are you absolutely sure this is a pure sample? Have you run it through HPLC or even a GC at all? I'll split this up for you to make it easier to read. 1H and 13C 1D NMR The peak on your 1H NMR that you identified as acetone is perhaps not correct. Acetone pops up at ~1.96 ppm in d-MeCN, not 2.06 ppm. As it happens, you have a peak at 1.96 ppm, but the splitting pattern makes it unlikely to be either acetone or residual d-MeCN. Your residual solvent peak should also crop up at 1.96 ppm, which makes me wonder if the peak you've indicated as being acetone is your solvent peak and you just haven't calibrated it. On that note, why did you use d-MeCN over CDCl3? The multiplet at 1.96 ppm is very curious. The splitting is very clear and would suggest being next to 4 protons, possibly 2 x -CH2 or 1 x -CH and a CH3, though there is nothing else in your spectra that appears to be coupled to it. Again, I would say it's your solvent, but d-MeCN shouldn't be split like that (which makes me question purity). I can't comment too much on the other two peaks without seeing the integration. What makes you think the peaks in the aromatic region are CH2 groups, by the way? You haven't given any integration on the spectra that I can see, but they seem very much like aromatic CH protons to me. I'm assuming you're having issues with the multiplicity of the aromatic peaks you circled with a question mark? The one at 6.53 ppm is a doublet of doublet of doublets (and a very nice one at that), which indicates some kind of long range coupling. The peak at 6.94 ppm looks like it also has or wants to have some fine splitting, but it's hard to tell. I think you may need to scale down the concentration and run your proton NMR again on a machine with more power (a 400MHz or 500MHz would work if you have access to one) to see it. You should also see the splitting on the little triplet at 7.24ppm become more resolved and less lumpy. The larger triplet has a coupling constant of about 9 Hz, which indicates ortho coupling rather than the para coupling you've written on the spectra. That in conjunction with the splitting would place it in between two aromatic protons (most likely the the two doublet systems at 6.53 ppm and 6.94 ppm). You may therefore have a meta substituted phenyl ring, although this would put into question your singlet at 7.01 ppm and to some extent, the smaller triplet at 7.24 ppm (neither of them appear to be due to any common solvents). I've noticed you also have a peak at about 8.25 ppm. It's a rather featureless hump, but could possibly indicate the presence of an enol (which I doubt as you should see some indication of the keto form in the IR) or maybe have something to do with the nitrogen you think is in there (more likely). I think the carbon spectra you have there is a DEPT spectra? It doesn't look like it's been run long enough or phased properly; I would run it again either with higher concentration or with more scans. When you analyse it, compile a report with an overlay of your normal 13C spectra so you can see where there are meant to be peaks and if there are any quaternary carbons. If it isn't meant to be a DEPT, run a DEPT and phase your carbon spectra properly. 2D NMR (COSY, HMQC and HSQC) The external projections on your HSQC, COSY and HMQC look a little odd and I wonder if maybe this was run at a different time to when you ran your original proton spectra? In your original proton spectra, you had some nice splitting at 1.96 ppm which now appears to have disappeared. The splitting in your aromatic region has also become quite a bit different and the shifts are all off. You may want to look into this. In the meantime, I would question your interpretation of the COSY spectra. You've penciled in a line where you have your one and only cross peak from an aromatic proton to a peak in the ~2 ppm range, but you've drawn it as coming down to the wrong aromatic peak. The cross peak clearly sits above the singlet in the middle of all the aromatic peaks, so why have you then drawn it as coming down to the lower field peak? It's curious as well that the peak at just above 7.25ppm isn't coupled to anything. This would be the peak corresponding to the tiny triplet at 7.24 ppm in your original spectra, although again I am dubious of reading too much into it until I know why your projections are so different to your 1H NMR. Your HSQC and HMQC both seem to use different projections on the 1H axis and both look different to your 1D spectra. It's not much good commenting on these until I know why some peaks are missing and the splitting is different, so I'll reserve my analyses until then. IR With your IR, is it possible to change the view window so that you can incorporate the entire spectra? As it is, it does look like you have some kind of amine. The peaks just above 3000 cm-1 are reminiscent of aromatic peaks, which contradicts what you said about the proton NMR. You also appear to have some aromatic breathing peaks, though it's hard to say without the peaks being labelled. Mass spec I'm assuming your mass spec was low res? It looks like something you might get off of a GC-MS run, which typically use quite harsh conditions. If it was run on a proper LRMS machine, you have to consider what ion mode it was run in and take into account the mass of sodium ions, etc. Have you done a high-res mass spec on it? You should get a molecular formula from that. If you can't do that and, try doing a micro analysis on it (CHNO test) or see if you can get some x-ray crystallography done on it (if it's crystalline, of course). As for the spectra itself. There are a lot of peaks at the base line, which makes it hard to figure out if there is a molecular ion peak in there or if so, where it is. I would, as I suggest above, run a high res and see what you get out of that. How temperature sensitive is your compound, out of curiosity? Also, you assume that you absolutely will get a molecular ion peak out of MS. This is not always the case. Some compounds are temperature sensitive and will decompose under the conditions used to collect data. Other times, your compound will form dimers and you'll see a lot of 2M peaks. And in some cases, you might have a very minor impurity in your sample that ionises much more readily than your compound. The result of this can be a near complete masking of m/z peaks from your compound. Thank you so much for your answer! the fact that 2.06 is not acetone makes more sense ! I integrated the spectrum assuming that the acetone peak was 6 protons, which gave me the 2 proton value for the aromatic ring shifts, but I suppose all my integrations are actually divided by two; that would seem more logical... I did the integration on another spectrum which I didn't think to scan, sorry... So the acetone peak is not an acetone peak but possibly a CH3 peak!) I know that my 13C spectra is pretty bad, but you said that I should see quaternary carbons? I read somewhere that you can't see them on a 13C spectra... how can I tell if they're quaternary? And my solvent is CD3CN because my compound wouldn't dissolve in CDCl3 or D2O... Ah and a bit of background on my compound: all the 2nd year chemistry students in our university are given a few mg of an unknown compound at the end of the year and have to learn to use the different analysis machines to identify what it is, and we have to do a presentation about our compounds tomorrow... So I know my compound is pure. But I don't have the slightest clue as to where it's from or what it possibly could be. It's a white cristalline solid, adn it doesn't smell of anything. As for the HSQC, HMQC and COSY, I also thought that the missing peaks were strange. Yes I did do two measurements at different times. The first time I just did a proton nmr and a 13c nmr, and the second time I re-did the proton nmr (which came out a bit different to the first), 13c, and I did all the 2D spectra... Like you said, the peaks in the two H-NMR have different chemical shifts (I noticed that earlier in my second H-NMR) and there are peaks missing in the 2D spectra... But I'm pretty new to all this; I have no idea why the two measurements are different... And thanks for pointing out my mistake in the COSY spectra, I'll connect the peaks properly this time As for the mass spectra, yes it's from a GC-MS run, I don't think that the university has an LRMS machine (and if it did I don't think that the students would be allowed to use it haha). But I'll just forget about the mass spectra, because like you said, there are so many peaks at the base line and I'm not even sure my molecule has a molecular ion peak... And I don't know if it's heat sensitive, I didn't test its melting point or anything... Thank you so much for your help! I think I'll be able to figure out what my molecule is and actually have something to present tomorrow haha (I'd pretty much given up and resigned myself to failure...) edit: Been stuck for 4 hours now... I still can't find out what the molecule is Edited May 20, 2012 by evilmastermind
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