Category Archives: problems&solutions

When You Use a 3 mm NMR Tube…

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You need to use a 3mm NMR tube if you want to do diffusion NMR experiments on samples with low-viscosity solvents (CDCl3, acetone-d6, etc. In fact, I recommend that you use 3mm tubes even if you use D2O as I have observed that its results were slightly more reproducible than using 5mm tubes). Several things to keep in mind when you run NMR using 3mm tubes:

  1. You have less solvent due to the smaller sample volume, and the locking process needs the 2H signal from your solvent to work. So when you have less solvent in the tube, the locking process might sometimes become challenging. Topshim also uses the 2H signal to work, which also becomes more challenging when you have less solvent in your sample. You might see error message like “S/N is too low” during topshim. Note that this is not because your solute concentration is too low, as topshim only works with your solvent.
  2. Only use the simple topshim command; don’t use topshim convcomp. The latter needs more 2H signal to work with, which is a problem for 3mm tubes. Also, there will be almost no convection in 3mm tubes, so you don’t need the convcomp (convection compensation) trick.
  3. The best sample height is 3mm, for which you must carefully center your sample around that thin black line when you use the depth gauge.
  4. If topshim still doesn’t work after you have tried all the above, you could try manual shimming by following this blog entry. Manual shimming is what every NMR users had to do several decades ago.

Gaussian Line Broadening

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There are many choices of line broadening functions. The most popular one is exponential line broadening, in which each time-domain data point in the FID is given an exponentially decaying weight before Fourier Transformation. The drawback of exponential line broadening is that it suppresses the beginning part of FID too quickly, which results in long tails on the feet of tall peaks on the spectrum. If you want to cut those tails and reduce peak overlap yet still suppress a lot of noise, you could try Gaussian line broadening, in which you need to define two parameters: gb and lb. gb is between 0 and 1, while lb should be a negative number.

Gaussian line broadening is often used in the processing of solid-state NMR spectra, where peak overlapping issues are often severe. However, if you find peak overlapping is an issue in processing solution NMR spectrum (for example, if you want to resolve a small peak on the feet of a big peak), consider giving it a try. If you choose to do Gaussian instead of exponential line broadening, you will need to first define gb and lb, then type gfp instead of efp.

The Gaussian line broadening parameter pairs that I usually use are (from strongest to weakest):
gb / lb
0.01 / -10
0.015 / -8
0.02 / -5
0.03 / -3
0.05 / -2
0.1 / -1

The figure below shows the weighting function for a number of line broadening choices (for an acquisition time of 20 ms). You can see that the several Gaussian curves retain the beginning part of the FID better than exponential (blue curve).

C:\Users\hu\Documents\teaching\demo\gaussian-lb.opju/gaussian-lb/Folder1//Graph3

The figure below shows the different effect of the two types of line broadening. The blue spectrum was processed with exponential line broadening, with lb = 30 Hz. The red spectrum was processed with Gaussian line broadening, with gb = 0.03 and lb = -3. You can see that both ways suppress noise to a similar degree, while the latter way results in less peak overlap (deeper valleys between peaks).

What to do if you have insufficient solvent

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Normally, you should have 0.4-0.5ml of solvent, which is ca. 3-4cm tall in the NMR tube. If you have less than 3cm of sample, please follow these steps:

– instead of rsh shims.best, do rsh shims.short

– always lock after you do rsh

– You can try topshim, but watch if the lock line gets higher or lower after topshim. If it gets lower, topshim did not work, and you need to type rsh shims.short again to get back the better shim. Topshim does not always work for short samples.

– If topshim did not work, type bsmsdisp, and adjust z and z2 to get your lock level higher. z2 is the most important for short samples

– Shim is never perfect for short samples, so you need to be prepared to see low resolution on your spectrum. If every peak has the same tail, asymmetric lineshape, or fine splitting, it is mostly like a shimming problem.

“Sample Missing” and “lock” is not green?

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Bruker NMR’s detect the presence of sample by trying to spin it.  If the sample cannot spin, then the bsmsdisp panel will show “sample missing”.  After you lock the sample, the lock button will not be green even though it actually has been locked and the scanning line has risen to the upper part of the lockdisp window.  You can still run your experiment in this situation.

Spinning improves the resolution of your spectrum to some extent.  However, the resolution without  sample spinning is usable in most applications.

Related link:  When it helps to spin and when not.

Typing “dir” cannot find my files…

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Upon loading topspin, it will take a little time to load up the spectrum that you used last time. If you type dir when the screen is still blue, you will confuse topspin.

To solve the problem, go to File -> Open, and find the path that contains your data. It is usually /opt/topspin/data/[your login]/nmr. Open any data file. This will reset the default data file path to your own directory. If you type dir now, you will be able to see your directory.

If it seems to take quite long to load up the last data file once you start topspin, it is likely because you have too many data files. Delete some!