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Chemistry Forums for Students => Organic Chemistry Forum => Organic Chemistry Forum for Graduate Students and Professionals => Topic started by: azmanam on October 27, 2015, 11:35:53 AM

Title: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: azmanam on October 27, 2015, 11:35:53 AM
I made a web app to turn NMRs into line lists. It will identify the signal (q vs dd), calculate the appropriate coupling constant(s), and format your line list for you.

For instance, I made this line list from this NMR in under 7 minutes. How long does it take you by hand?

(https://www.chemicalforums.com/proxy.php?request=http%3A%2F%2Fi.imgur.com%2FzdmM9OS.jpg&hash=00751c5f4e8efd66a4b7503d51201768)
(https://www.chemicalforums.com/proxy.php?request=http%3A%2F%2Fi.imgur.com%2FNVQEODX.jpg&hash=932be22563ada0305f579a8cb15f08be)

Enjoy :)

bit.ly/nmrformatter (http://bit.ly/nmrformatter)
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: ResStu on November 18, 2015, 02:43:25 AM
Well done....
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: azmanam on November 18, 2015, 08:57:39 AM
Thanks, friend.
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: BobfromNC on January 13, 2016, 11:04:58 AM
What input does the app take?    Does it use a PDF of the NMR, the raw data from a Varian or Brucker, or some other files?
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: azmanam on December 02, 2016, 04:03:56 PM
Sorry for the delay.

Right now, it takes manual input. You physically type in the ppm for each of the peaks within a signal, tell it the integration and coupling and it will format the output on your behalf.

One of the reasons for not taking raw data is that the formatter is only as good as the resolution of the spectrum and the sensitivity of the peak picker. How many times has your 'singlet' given two peaks by the peak picker due to a shoulder, real or imagined, or a blip in the side of the signal. Taking raw data could give false readings.
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: kriggy on December 31, 2016, 08:47:15 AM
Could you explain some of the advantages your app has compared to the common NMR software? For example, I use ACD labs or MestreNova and they both can generate those peak lists rather easily without the need to manualy imput anything
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: billnotgatez on December 31, 2016, 10:16:40 AM
@kriggy
Are ACD labs or MestreNova
Freeware
and
able to operate on any web device?

I have not used the OP WebAP
so I do not know how well it works on a smartphone etc
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: kriggy on January 01, 2017, 07:50:39 AM
I think MNova is not free, ACD academic edition was free but no longer is.

My point was that if you are using NMR in lab, then you need some kind of software to process the data and it should be able to make the report.

Im sorry if I sound harsh or somehing, OP did great job (did try few spectra to convert in the app and it worked great) but I fail to see the advantages of this app compared to standart NMR software. Or is it common for that only the NMR specialist has the software and process the data and you get only the spectra in PDF ? Because we process the spectra on our own unless there are some specific reasons to make the NMR specialist handle it for us
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: billnotgatez on January 01, 2017, 09:57:12 AM
@kriggy
... if you are using NMR in lab ...

I believe you are correct (with that caveat)
and also
You made my (alternative) point
mole snack for you
Thank You

@azmanam
Hope you do more
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: hypervalent_iodine on January 01, 2017, 10:35:54 AM
How does it handle overlapping splitting patterns in more complex signals? I don't have any of my data on hand as I'm on holiday, but I frequently have ddd or similar splitting, where the doublets often overlap one another. It can be quite tricky to tease apart.
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: azmanam on January 01, 2017, 02:16:03 PM
Thanks for the comments :)

@kriggy, It does nothing that the software you mention doesn't also do. However, in the event your university doesn't have a site license for those software suites, this is a cheap, short-term solution.

@hypervalent_iodine, it is all manual entry. So it will handle it as well as you can :) You'll enter the peaks manually, so as long as your spectrum is resolved well enough to get the individual peaks, it will handle them just fine.

Let me know if you have any more questions, friends!
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: hypervalent_iodine on January 31, 2017, 02:39:41 AM
Thanks for the comments :)

@kriggy, It does nothing that the software you mention doesn't also do. However, in the event your university doesn't have a site license for those software suites, this is a cheap, short-term solution.

@hypervalent_iodine, it is all manual entry. So it will handle it as well as you can :) You'll enter the peaks manually, so as long as your spectrum is resolved well enough to get the individual peaks, it will handle them just fine.

Let me know if you have any more questions, friends!

Okay, so since I have been back at work I decided to try it out with one of my more difficult peaks. This is one on an aromatic ring adjacent to two other protons, and exhibits different J coupling to each, as well as coupling to another proton one more carbon along the ring. I can see visually that this is a ddd, albeit a slightly tricky one due some overlapping peaks (though it is resolved perfectly well enough to see all of the ddd peaks), however, the program has assigned this simply as a multiplet. This is what I was asking about in my previous question. If I tell it that there are two neighbouring protons, it tells me it is a dq, which it most definitely is not. It seems that it is not so good where there is overlapping peaks of this nature, or perhaps it is struggling with the additional coupling I get from the more distant proton in the ring?
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: billnotgatez on January 31, 2017, 06:12:43 AM
@hypervalent_iodine
Did you also try using other
 common NMR software? For example,  ACD labs or MestreNova
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: hypervalent_iodine on January 31, 2017, 08:18:05 AM
@hypervalent_iodine
Did you also try using other
 common NMR software? For example,  ACD labs or MestreNova

I use MestreNova for processing, but I like to work out coupling constants by hand. No particular reason except that I enjoy the mental exercise.
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: billnotgatez on January 31, 2017, 11:47:16 AM
My point was -- did  MestreNova perform the task better than the WebAp for the substance you cited as a problem.
I assume you can do the problem very well by hand (actually brain).
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: azmanam on January 31, 2017, 12:15:45 PM

Okay, so since I have been back at work I decided to try it out with one of my more difficult peaks. This is one on an aromatic ring adjacent to two other protons, and exhibits different J coupling to each, as well as coupling to another proton one more carbon along the ring. I can see visually that this is a ddd, albeit a slightly tricky one due some overlapping peaks (though it is resolved perfectly well enough to see all of the ddd peaks), however, the program has assigned this simply as a multiplet. This is what I was asking about in my previous question. If I tell it that there are two neighbouring protons, it tells me it is a dq, which it most definitely is not. It seems that it is not so good where there is overlapping peaks of this nature, or perhaps it is struggling with the additional coupling I get from the more distant proton in the ring?

@hypervalent_iodine I'm sorry to hear about your struggles. It sounds like you're frustrated that your ddd peak is being misinterpreted by the formatter? Would you be willing to share a screen shot of the signal and it's peaks? I don't need the whole spectrum, just that signal so I can play around with it a bit. Also, you say you tell the interpreter you have 2 neighbors (which makes sense for an aromatic ring), yet a ddd has 3 j-values, and a dq has 4 neighbors (though only 2 j-values). Just clarifying how you're inputting the data into the form vs the result it's giving back to you.

Thanks for helping me field test the WebApp. I can't make it better if I don't know where it falters! :)
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: azmanam on January 31, 2017, 12:32:39 PM
Have you tried putting in '3' as # of neighbors? I know there's not really 3, but the question is more asking 'how many j-values.'

Also, have you tried leaving # neighbors as 'unknown,' and seeing what is responds with?
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: hypervalent_iodine on January 31, 2017, 07:00:49 PM
My point was -- did  MestreNova perform the task better than the WebAp for the substance you cited as a problem.
I assume you can do the problem very well by hand (actually brain).

Sorry, I must have missed the underlying question. Late night posting is never a good idea. I'll put it through ACD and / or MestreNova later and have a look.
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: billnotgatez on January 31, 2017, 10:20:54 PM
@hypervalent_iodine
I am sorry that I was not clear as I could be
I was trying to point out that the other software that is available might not be any better at figuring out your compound of interest.
It might be that you and @azmanam may make his WebApp better than others.

My point was -- did  MestreNova perform the task better than the WebAp for the substance you cited as a problem.
I assume you can do the problem very well by hand (actually brain).

Sorry, I must have missed the underlying question. Late night posting is never a good idea. I'll put it through ACD and / or MestreNova later and have a look.
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: hypervalent_iodine on January 31, 2017, 10:52:34 PM
@hypervalent_iodine
I am sorry that I was not clear as I could be
I was trying to point out that the other software that is available might not be any better at figuring out your compound of interest.
It might be that you and @azmanam may make his WebApp better than others.

My point was -- did  MestreNova perform the task better than the WebAp for the substance you cited as a problem.
I assume you can do the problem very well by hand (actually brain).

Sorry, I must have missed the underlying question. Late night posting is never a good idea. I'll put it through ACD and / or MestreNova later and have a look.

Yes, I see what you were getting at. I just had a look, and MestreNova determined the splitting and coupling constant of the peak just fine. Haven't looked at ACD.

Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: hypervalent_iodine on January 31, 2017, 11:17:18 PM
Have you tried putting in '3' as # of neighbors? I know there's not really 3, but the question is more asking 'how many j-values.'

Also, have you tried leaving # neighbors as 'unknown,' and seeing what is responds with?

I tried listing as unknown first, then tried two. Trying three does allow it to identify the peak as a ddd, however the coupling constants are not correct. The app gives this:

1H NMR (700 MHz, CD3COCD3): δ 7.53 (ddd, J = 1.2, 6.9, 8.5 Hz, 1H)

Whereas MestReNova gives this:

1H NMR (700 MHz, CD3COCD3): δ 7.53 (ddd, J = 8.1, 7.3, 1.6 Hz, 1H)

When I calculate by hand, I get the same numbers as MestReNova. I wonder if maybe it isn't identifying where the doublets actually are in the middle peak, since they overlap.

@hypervalent_iodine I'm sorry to hear about your struggles. It sounds like you're frustrated that your ddd peak is being misinterpreted by the formatter? Would you be willing to share a screen shot of the signal and it's peaks? I don't need the whole spectrum, just that signal so I can play around with it a bit. Also, you say you tell the interpreter you have 2 neighbors (which makes sense for an aromatic ring), yet a ddd has 3 j-values, and a dq has 4 neighbors (though only 2 j-values). Just clarifying how you're inputting the data into the form vs the result it's giving back to you.

Thanks for helping me field test the WebApp. I can't make it better if I don't know where it falters! :)

(https://www.chemicalforums.com/proxy.php?request=http%3A%2F%2Fimgur.com%2FsljZKA5.jpg&hash=d64d7b3110889635f1d4b6720ac336c0)

This is it.

I'm not especially frustrated by anything. As I say, I prefer to do these by hand anyway. As well, my university gives me a licence for MestReNova, which can process spectra and give me nice, formatted spectral data (inc. coupling constants) within about 30 seconds, not including anything I have to add or change manually. I specified two neighbours in one run through (but usually I just said unknown) because it only has two neighbours, but it experiences longer range coupling to another proton one more carbon along the ring.

Edit: Just so you know what I input into your app, these are the ppms given on Topspin:

7.5432, 7.5409, 7.5328, 7.5317, 7.5305, 7.5295, 7.5211, 7.5189
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: azmanam on February 01, 2017, 09:14:05 AM
FIXED!!!

(I love this stuff. It's so much fun to dig into the what's and why's and figure out what's going on!)

First, thanks for bringing this to my attention. I greatly appreciate it.

Second, a bit about how the code works. If you work through the 2002 Hoye paper (http://dx.doi.org/10.1021/jo001139v), it instructs you that peak {1 to 2} is j1, {1 to 3} is j2, then you add those together to eliminate the next peak out and so on until you identify all the j-values. But that's only half true. for even a simple dd, j1 is not only {1 to 2} but also {3 to 4}, and those should (in theory) have the same j-value. j2 is not only {1 to 3} but also {2 to 4}.

So my web app takes that into consideration, calculates both {1 to 2} and {3 to 4} for a dd, then averages them for the output for j1. Same for j2. That's fine for a dd where there is no amibguity. But for an 8-peak ddd, there is some ambiguity. There are two possible ways an 8-peak ddd could occur:

(https://www.chemicalforums.com/proxy.php?request=http%3A%2F%2Fi.imgur.com%2FK6SD3el.jpg&hash=0dcca502950f56024976f156cb014528)

Notice that this follows Hoye's guidelines. J1 is {a-b}, J2 is {a-c}, and J3 is either {a-d} or {a-e} depending on the overlap or non-overlap of the central peaks. My code erroneously neglected to account for the potential overlap of the central peaks :( So my code was averaging {a-b} {c-d} {e-f} AND {g-h} when really those middle two could be swapped, and it's not trivial to tell just by looking if the central peaks overlap or not. But even though some of the pairs are ambiguous, some are retained in both sets. I should be using these to calculate the j-values, not all possible pairs.

Calculating ALL the splitting out by hand shows that even though all j1s should be the same, they are not. Note the second example (original wrong WebApp version) where assuming no central peak overlap matches the old WebApp output of 1.2, 6.9, and 8.5:

(https://www.chemicalforums.com/proxy.php?request=http%3A%2F%2Fi.imgur.com%2Fe36p8gW.jpg&hash=384694e6be3fbb959c3cbdc504489d2e)

So now, the WebApp ignores the ambiguous pairs and only averages the pairs that are retained no matter the central peak overlap possibility. It also now matches the actual output of 1.6, 7.3, and 8.1.

Here's the WebApp after update showing the correct analysis of 1.6, 7.3, and 8.1:

(https://www.chemicalforums.com/proxy.php?request=http%3A%2F%2Fi.imgur.com%2FQMZa7Mg.jpg&hash=dd8d927e73f308e0281b70e068fcd04e)

Thanks again for all your assistance! :)
Title: Re: WebApp to turn your NMR into publication-ready line lists. Fast, simple, easy.
Post by: hypervalent_iodine on February 01, 2017, 04:18:24 PM
That's great. I had suspected that was what was happening. Glad I could *delete me*