NMR Facility - Chemistry Department

After noticing that a few people have been encountering some difficulties running the common 2D HH and HC experiments in automation, I’ve updated the available experiments and would like to share a few tips.

“-opt” = “2D with optimized 1H spectral window”

All the 2D experiments whose names end in “-opt” use a script that analyzes the processed 1H spectrum, figures out where the significant peaks are, and shrinks the 1H spectral width of the 2D to improve resolution and eliminate large fields of empty space in the spectrum.

The “-opt” experiments currently include COSY-opt, HSQC-opt, HMBC-opt, HSQC-TOCSY-opt, TOCSY-opt, NOESY-opt, and ROESY-opt.

Keep it Simple

Success is easy if you keep things simple. If you want a COSY, simply choose “COSY-opt” and a PROTON8 experiment will automatically be added. If you add an HSQC-opt, the system will recognize that the PROTON8 experiment already in the queue will work fine, and neither you nor the automation need to add another. If you simply add the experiments you want, don’t delete anything, and click “Submit”, all should work fine.

NEW: “-manual” Alternatives

If you wish the set your 1H spectral width manually (a good idea if you have low-intensity peaks at the edges of your spectrum that the peak picking routines may skip over), there are now equivalent “-manual” 2D parameter available. You can find them at the bottom of the experiment lists on 400-1 and -2.


The setup script for the “-opt” experiments REQUIRES a preliminary PROTON8 experiment run under the same sample name.

  • DO NOT DELETE PROTON8 if it is automatically added. COSYs will fail to acquire and others will proceed with 16ppm widths.
  • DO NOT  SUBSTITUTE PROTON1. The script only reads PROTON8.
  • DO NOT use a DIFFERENT SAMPLE NAME. The script only looks for a spectrum in the same sample folder.
  • DO NOT change the SPECTRUM NUMBER of the PROTON8 experiment after the 2D has been set up.


There are a number of ways one can envision setting up the PROTON8 and 2D experiments on different occasions. I have not explored all the possibilities to see what succeeds and what fails, but I do have some advice:

  • It will always work if you create a new sample folder with a new name and queue up an “-opt” 2D and allow the system to add a PROTON8.
  • If you still see the initial PROTON8 experiment, choose that carousel position again and simply add the 2D. If it does not add a PROTON8 experiment, the 2D will probably run as expected.
  • If you no longer see the initial PROTON8 experiment, you should probably try naming your sample with the same name as before, select the 2D you want and let it figure out what number it should be and whether is needs to add a PROTON8 experiment. Alternatively, you could increase the spectrum number sufficient to avoid conflict (e.g., if all the previous spectra were #10-14, use #20), and let the system figure out whether a PROTON8 is needed. Do not delete anything.


If you tried running an “-opt” 2D and it failed (either the it didn’t run at all or it ran with the full 16ppm width), what do you do to move forward?

  • It will always work if you create a new sample folder with a new name and queue up an “-opt” 2D and allow the system to add a PROTON8.
  • If you already tried running a 2D and it failed, try adding a new “-opt” 2D and let it add a PROTON8. The system ought to be able to figure out how to number the spectra for success. Do not make changes (other than adding more spectra if desired).
  • DO NOT REUSE the 2D experiment that failed. I’m pretty sure that the identification of what spectrum to use for optimization is set when you first select the experiment, and after submitting it to acquisition the script wont run properly. Just abandon the failed experiment and set up something fresh. DO NOT try using the number of the failed spectrum.

Happy spectroscopy!