Just want to say thank you for this intuitive video. I am a third year Biochemistry student revising a module including NMR and I found this a life saver as in 17 minutes with the real time video i got as much understanding as i would of got through hours of looking at a paper diagram. Many thanks
Well spotted. Yes, you are correct. Obviously on the real 2D spectrum the methyl would be in the right place (around 4 ppm) and the NOE would also be under the right alpha-H.
Thanks, I am currently doing HSQC and DEPT-edited-HSQC (which is much easier to interpret than HSQC). This should be available within a week. I also plan on doing DEPTQ (for observing quaternary carbons in a DEPT experiment), HMBC, ROESY and a series on artifacts. Let me know if there are any other experiments you'd like. I'm concentrating on the practical interpretation rather than the theory, but could explain the theory too if needed. NOE theory will be added though as this is useful.
Hi Phan Chin, this is a good question and not straight forward to answer believe it or not. The signal does indeed vary with distance but as the NOE can be distributed asymmetrically throughout a molecule then its intensity can vary. It is indeed possible for two nuclei in close proximity to NOT show a NOE signal. That would be bad luck and it can happen. Other artefacts can also make the spectrum look odd. I will do a video on artifacts and how to spot them if people want it. Let me know.
How do people interpret Noesy spectra of big proteins?, I mean, those spectra look so confusing I don't even imagine how can you differ from one residue to another.
The same principles will apply but as the molecule gets larger it will tumble more slowly and the NOE sign will change. Exchangeable protons show up as the same phase (sign, colour etc) as the diagonal for small molecules so are easy to spot in a NOESY. For larger molecules the NOE signals change sign so everything looks the same (i.e. only one colour for the cross peaks). Let me know a bit more info and maybe I could do a video to explain more.
Hi John, you must be careful interpreting the intensities of NOE cross peaks as they can be misleading. There are lots of variables that can construct and destruct the signal strength. I will do a video to explain in a week or two as this is a common question. If you are performing molecular modelling then it would be ok to set a constraint at 3-6 angstroms between two interacting protons. You can visit my website (above) to get downloads for calculating distances. Hope this helps.
A proton can not couple with itself. You 'will' see diagonal peaks in a real NOESY spectrum and for small molecules those peaks will have the opposite phase to the cross peaks. The diagonal peaks will be due to the resonances from the source protons and can be considered to be a one dimensional cross section of the 1H spectrum. Hope this helps.
This is already really complicated with a tripeptide. How do people read spectrums for entire proteins? I think it would be really hard to tell apart the amino acids. I don't see how this can be used on something that has 1000 amino acids.
Hi great video. I am interested in using 2D NOESY on a a relatively small molecule to assist in elucidating the 3D structure of the molecule. Please correct me if I am wrong but 2D NOESY is supposed to give quantitative numbers about H-H distances for protons that are nearby less than 6 Angstroms. The obtained distance are then used as constraints when running a geometry optimization calculation. However it is not clear to me how the distances are obtained from the spectrum. Thanks in advance.
I want to know, if I saw a peak in H-H NOESY spectrum does that mean these two protons must be near each other through space? If I saw a very high intensity peak in NOESY spectrum does that mean these two protons must be very near each other through space? Because sometime them not near but give a high intensity peak in NOESY. Also, sometime two protons were near but did not show NOESY spectrum, how can this happen?
but why don't we see the diagonal peaks for NOESY? You only drew the cross peaks. I mean shouldn't there be diagonal peaks as well (proton seeing itself)?
That's not quite true. You can get COSY type peaks which arise as a result of zero quantum transitions as they will be transformed into signals at the end of the pulse sequence. They are easy to spot as they have mixed or anti-phase just like a double quantum filtered COSY. If you get a NOE and COSY-type peak overlapping then they can interfere with each other. Most pulse programs will try and eliminate these artefacts by varying the mixing time, but as I mentioned they are easy to spot.
I really like your video but in parts of the video your voice level doesn't remain the same, it gets too low and then too loud. Would be helpful if you could speak at a constant loudness!
Just want to say thank you for this intuitive video. I am a third year Biochemistry student revising a module including NMR and I found this a life saver as in 17 minutes with the real time video i got as much understanding as i would of got through hours of looking at a paper diagram. Many thanks
What a great tutorial series on NMR! Thanks so much.
Well spotted. Yes, you are correct. Obviously on the real 2D spectrum the methyl would be in the right place (around 4 ppm) and the NOE would also be under the right alpha-H.
Thanks, I am currently doing HSQC and DEPT-edited-HSQC (which is much easier to interpret than HSQC). This should be available within a week. I also plan on doing DEPTQ (for observing quaternary carbons in a DEPT experiment), HMBC, ROESY and a series on artifacts. Let me know if there are any other experiments you'd like. I'm concentrating on the practical interpretation rather than the theory, but could explain the theory too if needed. NOE theory will be added though as this is useful.
Glad I could help. I plan on adding more NMR tutorials so let me know if there are any in particular that you would be interested in.
Many thanks :) I needed a quick reminder and you offered me more than I needed in quarter an hour! :)
Hi Phan Chin, this is a good question and not straight forward to answer believe it or not. The signal does indeed vary with distance but as the NOE can be distributed asymmetrically throughout a molecule then its intensity can vary. It is indeed possible for two nuclei in close proximity to NOT show a NOE signal. That would be bad luck and it can happen. Other artefacts can also make the spectrum look odd. I will do a video on artifacts and how to spot them if people want it. Let me know.
I'm lazy to log in.
But, your clip make me to log in.
I'm appreciated of your clip to help me understand about NMR spectrum. THank you very much
How do people interpret Noesy spectra of big proteins?, I mean, those spectra look so confusing I don't even imagine how can you differ from one residue to another.
The same principles will apply but as the molecule gets larger it will tumble more slowly and the NOE sign will change. Exchangeable protons show up as the same phase (sign, colour etc) as the diagonal for small molecules so are easy to spot in a NOESY. For larger molecules the NOE signals change sign so everything looks the same (i.e. only one colour for the cross peaks). Let me know a bit more info and maybe I could do a video to explain more.
Hi John, you must be careful interpreting the intensities of NOE cross peaks as they can be misleading. There are lots of variables that can construct and destruct the signal strength. I will do a video to explain in a week or two as this is a common question. If you are performing molecular modelling then it would be ok to set a constraint at 3-6 angstroms between two interacting protons. You can visit my website (above) to get downloads for calculating distances. Hope this helps.
A proton can not couple with itself. You 'will' see diagonal peaks in a real NOESY spectrum and for small molecules those peaks will have the opposite phase to the cross peaks. The diagonal peaks will be due to the resonances from the source protons and can be considered to be a one dimensional cross section of the 1H spectrum. Hope this helps.
This is already really complicated with a tripeptide. How do people read spectrums for entire proteins? I think it would be really hard to tell apart the amino acids. I don't see how this can be used on something that has 1000 amino acids.
This was very helpful. Thank you for posting!
thanks for this intuitive video. could you please help me to understand the assignment of NOE in DNA ( non-exchangeable and exchangeable proton).
Again, another awesome video!
Hi great video. I am interested in using 2D NOESY on a a relatively small molecule to assist in elucidating the 3D structure of the molecule. Please correct me if I am wrong but 2D NOESY is supposed to give quantitative numbers about H-H distances for protons that are nearby less than 6 Angstroms. The obtained distance are then used as constraints when running a geometry optimization calculation. However it is not clear to me how the distances are obtained from the spectrum. Thanks in advance.
Thanks so much quite easy to understand
I want to know, if I saw a peak in H-H NOESY spectrum does that mean these two protons must be near each other through space?
If I saw a very high intensity peak in NOESY spectrum does that mean these two protons must be very near each other through space? Because sometime them not near but give a high intensity peak in NOESY.
Also, sometime two protons were near but did not show NOESY spectrum, how can this happen?
you are a blessing sir
but why don't we see the diagonal peaks for NOESY? You only drew the cross peaks.
I mean shouldn't there be diagonal peaks as well (proton seeing itself)?
it is super helpful. thanks
Same here and i'm a first year Biochemistry student xD
That's not quite true. You can get COSY type peaks which arise as a result of zero quantum transitions as they will be transformed into signals at the end of the pulse sequence. They are easy to spot as they have mixed or anti-phase just like a double quantum filtered COSY. If you get a NOE and COSY-type peak overlapping then they can interfere with each other. Most pulse programs will try and eliminate these artefacts by varying the mixing time, but as I mentioned they are easy to spot.
thanks this bwas really helpful
Very useful. Thanks!!!
I really like your video but in parts of the video your voice level doesn't remain the same, it gets too low and then too loud. Would be helpful if you could speak at a constant loudness!
Helpful but your color coding makes it extremely confusing
Your video is good, but having difficulty to understand the accent. Expected more lucid voice. Thanks!
Spesak louder bro...lwshy ared u whispereing
confusing
god.
Weird accent !