Tuesday, October 20, 2009

NMR for Dummies

Here is where the real fun begins. I was not joking with my previous post. You can really do these things at home. The simple instructions are available on another site, and they are illustrated. After completing the tutorial (it takes 5 minutes in total) a working application will remain in your hard disc, and you will be free to apply the same treatment to your own spectra.
iNMR has always been available as a free download (since 2005). Access is unlimited and the program never expires. Other specialized simulation modules are included to cover most of the needs of an advanced spectroscopist (the few exceptions are motivated by the fact that other needs were already covered by existing freeware).
My blog is three years old. Half of the comments have been dedicated to a single post, which is clearly (and purposely) the least representative of the blog. When people find something useful (and this is certainly the case today) and free, they don't comment.
If you are not going to comment, I will comment by myself.
COMMENT: although it's a serious work, although it contains a lot of maths (and maybe just for this reason) it's funny too.


At 9:29 PM, Anonymous Jean-Marc NuzillardD said...

Dear Old Swan,

for sure, any serious NMR software should have such a tool that simulates a first order multiplet and that refines the user-proposed J-values.

BTW, how do you make the difference between a simple
doublet (J, antiphase) and
a doublet of doublet (J/2, in phase and J/2, antiphase)?



At 9:51 PM, Blogger old swan said...

The in-phase coupling is, mathematically speaking, a cosine modulation.
First I synthesize the FID of the singlet, then I multiply it by the function:
y(t) = cos( π J t ).
If it's a triplet I multiply it by the square of the cosine above.
The antiphase coupling is generated by a sin modulation:
y(t) = sin( π J t ).
The latter modulation actually adds a 90° phase shift, but the work-around is simple: just draw the imaginary spectrum instead of the real spectrum.
As far as I know there cannot be more than a single antiphase (active) coupling in a DQF-COSY cross peak.

At 10:59 AM, Blogger Carlos Cobas said...

Great work, Giuseppe
As you mentioned, anti-phase coupling comes from a sine modulation. Actually, this can be achieved by multiplying the FID by the complex term:
isin(pi * J * t);

Which is equivalent to what you wrote about the 90º phase shift and plotting of the imaginary part.
For a nice review on this subject, see this reference:

Concepts in Magnetic Resonance, Vol. 8(3) 175-189 (1996)


At 2:14 PM, Anonymous Jean-Marc Nuzillard said...

A J Hz antiphase doublet is described in the time domain by
y1(t) = sin(pi J t)

A J/2 Hz antiphase and J/2 in-phase doublet of doublet is described by
y2(t) = sin(pi J/2 t) cos(pi J/2 t)

Because y1(t) = 2 y2(t), an antiphase coupling pattern
is always ambiguous.



At 2:48 PM, Blogger old swan said...

Thanks, this is interesting. For my tutorial I have used an unknown spectrum, and it may be possible that my multplet contains 4 Js instead of 3, as you say.
In a real case, however, if I am going to use the values of the Js, it probably means that I have already assigned both the peaks and the couplings, then I would have enough information to tell if an apparent anti-phase doublet is an authentic doublet and not a triplet in disguise. Anyway, from now on I will try to remember your warning!
I invite the other readers to verify with my simulator what Jean-Marc (and trigonometry) say.
If you need a picture I will be glad to make another post.
Everybody knows that I create tools for spectroscopists, not magic boxes that give answers for the ignorant. Just because everybody knows it, I took the liberty of titling my post "NMR for dummies".
With my simulator, you are free to decide if to fit an anti-phase doublet as a doublet or as a triplet. You are responsible.

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