Friday, November 03, 2006

2D phase correction with iNMR (for brukerists)

processing a 2D spectrum can sometime become a puzzle. It is necessary, therefore, to learn some theory.

DEFINITION
The dimension with the highest index is called "direct", all others being "indirect".

THEOREM
Half of what Bruker says is false.

COROLLARY
The other half is simply misleading.

DEMONSTRATION
Bruker calls "f2" the indirect dimension and "f1" the direct one. Being this in contrast with the definition, the theorem is demonstrated. Demonstration of the corollary is left to the reader as an exercise.

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Now the practice. First thing first: you should determine if yours is a problem of phase or a poor choice of FT parameters.

RULE 1
If your FT parameters are wrong, you get all the signals doubled, or they fall at the wrong chemical shift, or both things happen. If you get the correct number of peaks in the correct chemical shift order, your parameters are correct. Spend time on correcting the phase.

RULE 2
With the classic NOESY, TOCSY and ROESY experiments it is possible to bring in phase all signal simultaneously. When the pulse sequence become longer, and if you add a pre-saturation step, phasing all peaks may become impossible. In such case, ignore outlier peaks and phase the rest.

RULE 3
The option "Swap Sides" is normally ON. The only exception I remember is represented by Bruker spectra in "States-TPPI" mode, which require "swap sides" only along f2.

RULE 4
The option "Real FT" is normally OFF. The only exception I remember is represented by Bruker spectra in pure "TPPI" mode, which require "Real FT" only along f1.

HINT 1
If you have troubles with the phase correction, use a sine bell shifted by 90 degrees along f2 and a squared sine bell shifted by 90 degrees along f1, and do not use neither LP-filling nor zero-filling. When you have found the right phase parameters, you can add zero-filling or LP-filling.

HINT 2
If you know that a spectrum is phase-sensitive or "echo-antiecho", use the corresponding shuffling along the indirect dimension, but never along the direct one.

HINT 3
Learn the iNMR mechanism "Extract"-"Repeat" and use it to find the right FT parameters.

HINT 4
To become a wizard in phase correction, make practice with good-looking, good-behaving spectra. Each time you feel having reached the perfect correction, increase the amplitude factor (= press the plus key). Are all peaks still in phase?

the iNMR manual is on-line

8 Comments:

At 4:03 AM, Anonymous kirk_marat@umanitoba.ca said...

>>> Bruker calls "f2" the indirect dimension and "f1" the direct one. Being this in contrast with the definition, the theorem is demonstrated.

The Bruker Software and documantation that I have correctly refers to the direct dimension as f2 and the indirect one as f1.

For truly dreadful, awful 2D NMR phasing try VNMRJ

 
At 8:22 AM, Blogger old swan said...

The Bruker software that I know stores the f2 parameters into a file called acqus and the f1 parameters into a file called acqu2s. I agree that it used to be worse in the past.

 
At 10:50 PM, Anonymous kirk_marat@umanitoba.ca said...

Yes, the files are called acqus, for direct dimension and acqus2 for the first indirect dimension, etc. This is so you can add another dimension without changing the name of an existing file.

However, the parameter editors eda, edp, (which is what the user sees) correctly refer to the directs dimension as F2 (for 2D) for F3 (for 3D) and the documentation refers to it this way as well.

Cheers
-Kirk

 
At 11:18 PM, Blogger old swan said...

They improved a lot indeed. Now the files even report a meaningful value for the temperature!

 
At 11:18 PM, Blogger old swan said...

They improved a lot indeed. Now the files even report a meaningful value for the temperature!

 
At 10:56 PM, Anonymous kirk_marat@umanitoba.ca said...

The same sort if inconsistency exists with Varian parameters as well. For example sw is always the spectral width in the direct dimension. sw2 is not the width if F2 but is the width in the second indirect dimension.

It would have been a lot easier if they had numbered the dimensions the other way around! :-) With the acquisition period always being t1, the first indirect evolution time as t2 (2D NMR) the next indirect evolution time as t3 (3D NMR) etc.

Cheers
-Kirk

 
At 11:13 PM, Blogger old swan said...

Dear Kirk,
it looks like you prefer Bruker instruments! You know that the purpose of the blog is not to assess which spectrometer is better, but such a discussion would be accepted nonetheless. Whenever you want to write your own posts on this or other topics, I can give you the (shared) ownership of this blog. It's enough that you preserve the template. Cheers!

 
At 4:45 AM, Anonymous Kirk Marat said...

I actually have both Bruker and Varian systems, and I will say that I prefer the Bruker systems - for many reasons that I will not go into here.

However, that was not the reason for my post. I simply wanted to comment that the confusion between the way the dimensions are numbered and the files/parameters are named extends across brands - well I don't actually know about JEOL and Tecmag. I also wanted to postulate on how this confusion arose. Unfortunately, there is not much that we can do about it now. Alors..., if they had only called the acquisition time t1, the first indirect dimension t2....

Cheers from the frozen north
-Kirk

 

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