NMR Facility - Chemistry Department

How to Use Automation

Submitting Samples For Acquisition

  1. Approach the instrument with your samples (in a safe seconday container). Take a look at the carousel and look for open slots.
    1. It’s best to look for slots to the left of the vertical transport tube.
    2. Try to find a set of open slots that equals the number of samples you have. Note the slots numbers.
    3. If it’s hard to find a location, figure it out after you log in.
  2. Sit down at the computer and log in to the “Identify User” panel that lists all the users.
    1. Either type your username or click on it in the list.
    2. A new window will pop up asking for your password, which you need to provide.
  3. In the upper half of the interface, identify the slots you want to use.
    1. Recall the slot numbers from when you looked at the carousel OR find a slot or group of slots labeled “Available” and/or “Finished”
      1. If you want to use a slot that has a tube in it, and the interface says it is “Finished”, the remove the other person’s tube and place it in the rack on the TOP of the table next to the instrument
    2. Put your sample in a spinner and place it in that slot.
  4. For each sample you wish to submit
    1. Double click on the line corresponding to the slot number.
    2. Give your sample a name
      1. most people name it after their lab notebook page and any additional identifier, like “JPK-1-134A”
      2. Don’t use spaces in the name (this sometimes makes copying data difficult).
      3. Don’t use special characters like @, %, $, etc. Go ahead and use _ and –
    3. Give your first spectrum for that sample a number. The system automatically assigns it “10”, but you can change it here.
    4. Select your solvent from the pull-down menu.
    5. Select one experiment from the experiment list. They are described here: https://voices.uchicago.edu/chemnmr/experiments4automation/
    6. Optional
      1. Click the “=” box to edit parameters. (Editing P1 is strongly discouraged. Editing D1 and AQ is also discouraged. Editing NS to increase the number of scans.)
      2. Clicking the “Sun” box toggles your experiment to run at night; it become a “Moon” symbol.
      3. Click the button with a squiggly line if you wish to add extra text to annotate the spectrum (most people don’t, just to save time).
    7. To run more experiments on that sample, click “Add”.
      1. The sample name and solvent will stay the same, but the experiment number will go up by one (e.g., 11). Select an additional experiment.
      2. Continue adding experiments all you like.
        1. Note that the 2D experiments with “-Opt” in their names require a PROTON8 experiment to be run first. This is necesary to set the 1H SW value in the 2D.
    8. To submit the experiments to the queue, either click on the topmost row that specifies your slot number or click-shift-click to highlight all the desired experiments, then click the “Submit” button in the middle row of the screen.
      1. The status of your experiments should change to “Queued” or, if nothing is ahead in the queue, “Running”.
  5. For each additional sample, repeat Step 4.
  6. Click the “Change User” button at the right-hand edge of the middle of the screen.
  7. You are done with this stage. Go ahead and walk away.
  8. When your data are acquired, you can copy them to your computer using the steps spelled out here: https://chemnmrlab.uchicago.edu/data/

Post-Acquisition Sample Management

Shortly after your spectra have been acquired, you should retrieve your samples. They may be either in the carousel where you put them, or in the rack next to the instrument if someone else took them out. You do not need to do anything on the computer after your data are acquired.

Please review the details on our “two-rack” system for managing samples that have not been claimed quickly:


A Note on J. Young/Valved NMR Tubes

The autosamplers have a very strict limit on the total length of any NMR tube: 222 mm. Any tube longer than this will not fit in the carousel. Each carousel has a safety lever that mechanically detects tubes that are too long – if the tube is long enough to hit the lever, a safety circuit is enabled that stops the queue and lights up the red light on the carousel. The queue cannot be restarted until the sample is removed.

While most standard J. Young tubes will not fit, it is still possible to use them, either by modifying long ones or ordering new ones that meet the length requirement.

Commercial Valved Tubes (ambient pressure)

Bruker recommends the following tubes for use with their SampleCase autosampler (our model):

You can have a glassblower modify an existing J.Young tube. Specify that the straight part of the tube needs to be 137 mm long, and the total length of the tube must not exceed 222 mm.

Commercial Valved Tubes (increased pressure)

Other Options

Oftentimes one is interested in a controlled-atmosphere solution that does not need to last very long. One can often get by with simply applying parafilm or Teflon tape to a normal sample, but there are other solutions that are better, just as fast, and still cheap. Consider these:


  • If you or a glassblower is making the tubes, specify that they need to be no longer than 222 mm. Your existing long tubes can be modified to meet this requirement.
  • Flame-sealing tubes is always an option