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Topic: Interpreting HNMR data to confirm the correct structure of a peptide aldehyde?  (Read 25323 times)

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Offline molecule_787

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Hello, I am looking for some help in interpreting the data from an HNMR report to confirm that it is the correct structure of the peptide Aldehyde "Proteasome Inhibitor I" (PSI).

Any help or details regarding the confirmation of the two is greatly appreciated.  Please feel free to PM me if preferred.

Thank you very much

Peptide Aldehyde/Chemical Structure (examples)



OR




HNMR Report



« Last Edit: August 16, 2011, 04:36:26 AM by molecule_787 »

Offline discodermolide

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Hello, I am looking for some help in interpreting the data from an HNMR report to confirm that it is the correct structure of the peptide Aldehyde "Proteasome Inhibitor I" (PSI).

Any help or details regarding the confirmation of the two is greatly appreciated.  Please feel free to PM me if preferred.

Thank you very much

Peptide Aldehyde/Chemical Structure (examples)



OR




HNMR Report





Don't see the aldehyde proton! Can't see which solvent was used is it DMSO?
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Offline Honclbrif

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I'm guessing you bought this and want to make sure its good? Your best bet with a peptide would be LC-MS-MS if you've got access to the instrument. If you don't, regular LC-MS would probably be OK. This proton spectrum looks pretty clean and free of crap, so as long as the mass works out I think its safe to assume they wouldn't spend all that time cleaning up a bad molecule.

The best way to do this by NMR would probably be to look up the spectrum and compare it to the one you've acquired. If you want to do this the hard way, you'll have to do a few more things:

1. Your spectrum cuts off before the region where aldehydes (which you're looking for), and carboxylic acids (which you don't want to see yet because yours is protected) show up
2. Get a 13C spectrum too. While not the largest molecule ever measured by NMR, you've still got 50 protons and 32 carbons in there and things get muddled. More information is better.
3. Consider some 2D experiments. Even the 90 MHz permanent magnet instruments can do those, and they tell you a lot.
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Offline molecule_787

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^ Thanks a lot for the information.

Yes you are correct, this is a peptide I have purchased and want to make sure that the compound is good/correct.

So basically, you are saying that by the NMR it looks clean and good but that a Mass Spec would help further due to its ability to determine the Molecular weight of 618.77 which if checks out then should solidify the identity of the peptide?

Or if I am off, please chime in.  How would I go about looking up the "spectrum" and comparing it exactly...

I also have an HPLC report I can post but I know that really only relates to its purity, if that helps any please let me know and I can post it as well.

Thanks again.

Offline molecule_787

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/szkd2u.png[/img]

Don't see the aldehyde proton! Can't see which solvent was used is it DMSO?

Hi, Yes the Solvent used was DMSO as indicated in the right hand column, I have highlighted it with a red arrow.



So you are saying that the Aldehyde proton is missing?  Obviously this is not good...?

Offline Honclbrif

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Since you've got the CAS#, I'd check scifinder or something similar for when it was first made. Someone had to have done an NMR spec on it, and you can compare. When it comes to the MS, make sure you know whether you're looking for the [m+H]+ or whatever you're set up to measure.

As for the proton spec you've posted. Do you have the spectrum file? You should be able to expand the view. Aldehydes tend to show up around 9 - 10 ppm and the field of view has been cut off right before this critical region.

Again, if you got it from a reputable supplier and the mass is right, there's really no reason to solve the structure for this thing. Unless, that is, you want practice solving structures but there's better molecules to start on.
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Offline molecule_787

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Since you've got the CAS#, I'd check scifinder or something similar for when it was first made. Someone had to have done an NMR spec on it, and you can compare. When it comes to the MS, make sure you know whether you're looking for the [m+H]+ or whatever you're set up to measure.

As for the proton spec you've posted. Do you have the spectrum file? You should be able to expand the view. Aldehydes tend to show up around 9 - 10 ppm and the field of view has been cut off right before this critical region.

Again, if you got it from a reputable supplier and the mass is right, there's really no reason to solve the structure for this thing. Unless, that is, you want practice solving structures but there's better molecules to start on.

Thanks, I will request an expanded file.  I had the same idea in terms of finding an NMR spec on it and comparing but could not locate/find one anywhere online.  I will try scifinder though.

Offline OC pro

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Number of protons seems to not fit with the structure (too less). Again, as mentioned already, aldehyde signal is missing.

Offline discodermolide

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Number of protons seems to not fit with the structure (too less). Again, as mentioned already, aldehyde signal is missing.
It is sad that a commercial company cannot provide proper data for their products.
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Offline OC pro

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Depends on the company  ;D. Our customers always get a specific QoA with spectra, HPLC etc. This is what I call quality.
I would not wonder if that peptide has been delivered from China (or India). I had this problem several times too. After the compound received from China, NMR and LC-MS was performed. When it is crap it goes right back without paying anything.

Offline molecule_787

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Depends on the company  ;D. Our customers always get a specific QoA with spectra, HPLC etc. This is what I call quality.
I would not wonder if that peptide has been delivered from China (or India). I had this problem several times too. After the compound received from China, NMR and LC-MS was performed. When it is crap it goes right back without paying anything.

So do you think this peptide is crap?  I did receive an HPLC report along with the NMR and they also have promised a Mass Spec.

Honclbrif said
Quote
"This proton spectrum looks pretty clean and free of crap, so as long as the mass works out I think its safe to assume they wouldn't spend all that time cleaning up a bad molecule."

So now I am a bit confused?

Btw, do you know of any other labs that can offer this peptide at a competitive price?  Feel free to PM me.  

They should get back to me regarding the expanded view and missing aldehyde issue along with the Mass Spec.  I will post their response for some further feedback.

Thanks again for the comments everyone.


Offline molecule_787

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Number of protons seems to not fit with the structure (too less). Again, as mentioned already, aldehyde signal is missing.

By the way are you just referring to the missing Aldehyde Proton as the reason it is not fitting with the structure? 

Offline molecule_787

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« Last Edit: August 16, 2011, 02:55:29 PM by molecule_787 »

Offline OC pro

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Not only the aldehyde signal. Structure and spectrum does not fit somehow.
I would do LC-MS additionally.
I see a Z group and Boc, but the rest is a bit strange.
There are some companies outside which sell crap. Especially when they offer a very cheap price.

The Merck price is realistic. 3k for 1g seems a bit too cheap since these companies will make it (synthesis after request). No one will store large amounts of a (sensitive) peptide. I know what I write, I work for such a CRO company.
They should provide a proper NMR and LC-MS at least. When it fits you can order it. I would only pay after analyzing this stuff soon after receiving it.
I´m sure half of the providers will not answer to your spectra-request. This will separate the boys from the men.

Where are these labs from you ordered situated? China?

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