Monday, July 21, 2008

Second Love

Since the beginning of this series of "lessons", the stress has been on 1-D processing. I have shown that 1-D processing can be as tricky and important as 2-D processing. If you are working exclusively with large bio-molecules you may well live with the sensation that there's no NMR with less than 2 dimensions. The NMR field is divided in many rooms and there's not enough communication among them. I have attended several NMR conferences where there was indeed the possibility for the groups, working in distant field, to merge their knowledge for a week. My impression is that every one keeps speaking his own language and keeps doing the same things for decades. NMR is not a unifying technique. The main link between the researcher is not their society, but the factory that builds the instruments.
Today I want to write about a couple of processing operations that are specific to 2D. Symmetry is the first example that comes to my mind. In homo-nuclear correlation spectroscopy, we expect that the two halves of the map, divided by the main diagonal, are the mirror image of each other. They aren't for a couple of reasons:
  • The line-widths along the indirect dimension are generally larger.
  • The t₁ noise is specific to t₁, as the name says.

The software can force the two halves to be the same. Every couple of corresponding points is compared. The point with the lowest absolute value is the "correct" point; the point with the highest absolute value is replaced. In the case of J-resolved spectra, the axis of symmetry is different, but the principle the same.
After the substitution, the resulting shape of the peaks is that of a pilaster, instead of a column. I prefer the original shape, but in many cases the advantages are overwhelming. My rule is easily stated: I symmetrize all my COSY. Both the COSY experiment and symmetrization looks terribly old and out of fashion, but they are so simple and fast (I mean: the gradient enhanced variant), that I always acquire a COSY, if I must acquire another 2D of the same sample. The COSY comes almost for free. They say that symmetrization might create false cross-peaks. This is right, yet it's a rare event and not a dangerous one. If you have some experience you can usually recognize the false cross-peaks. If you haven't, you can compare the symmetrized and unsymmetrized versions of your COSY. It takes a few seconds.
I don't symmetrize my phase-sensitive spectra, unless the noise is exceptionally intense. In the phase-sensitive case I feel that the original shape of the peaks carries precious information (like a fingerprint), and that a baseplane correction is enough to clean the spectrum. You can combine baseplane correction and symmetrization, only in this order. Another trick, which Carlos taught me, can remove the "t₁ noise". Actually it's a modification of the baseplane correction and it's more an aesthetic trick than an operation to clean the spectrum. Tomorrow I'll describe my personal implementation of it.


At 10:27 PM, Blogger said...

Hi, was wondering if you'd like to exchange links with me?
If yes, please leave your blog url as a comment at:
I'll link to you first, then when you have time link back k?
Thanks, Michael
BTW--I'm michaelwong38 on digg. If ever you want something dugg, just send me a shout anytime.

At 10:36 PM, Blogger old swan said...

You could have written directly:

Big Money List

At 12:34 AM, Anonymous Ana Paula said...


I am having problems with my COSY giving the butterfly mirror image. Do you know how I can fix it?


At 8:46 AM, Blogger old swan said...

Dear Ana Paula,
I want to help you, but I need your email address and your COSY. Can you upload it somewhere?


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