NMR Facility - Chemistry Department


Transformative capabilities

It’s important to realize that the upgrade represents a transformation from how NMR data have been collected in GCIS in the past. The new instrument operates the same as 400-1 in Searle, which many of you have gotten to try. Key points:

  • The instrument is fully automated – do not try and use it manually.
  • No reservations are used. You just walk up any time, submit your sample, and the instrument will run it on a first-come-first-served basis (though some may be queued up for night-time acquisition later).
  • Anyone who is familiar with manual NMR operation can figure this out easily in a couple minutes. Step-by-step instructions are posted here, and they seem to be working for most people: https://chemnmrlab.uchicago.edu/using-automation/
    • In case you can’t recall the URL when you’re at the spectrometer, there’s a small sign with a QR code on it next to the instrument computer. Point your phone’s QR code reader (iPhones’ cameras do this natively) at it and open the link.
    • If you want me to walk you through the process, I can do so from a safe distance. It takes just a couple of minutes.
  • The new 400-2 is configured to acquire most routine NMR spectra, including a variety of standard 2D experiments and a preset for 1H spectra of paramagnetic samples. 1D heteronuclear spectra that can acquired just by selecting a menu choice include 13C, 19F, 31P, 11B, 7Li, 77Se, 119Sn. 75As and 2H will be coming soon. No more climbing under the magnet to tune the probe!
  • IMPORTANT: There is a mechanical limit to the total length of your sample: 222 mm. Many J-Young tubes are too long to fit into this system. See the P.S. here* for recommended commercial tubes that are compatible.
  • The GCIS room furniture and computers have been moved around to give us all some extra space. Whew!
  • Please ignore the crates and boxes that are still there.

Automation Workflow – Summary

  • Approach the instrument, noting empty slots on the carousel.
  • You’ll see the IconNMR automation interface on the screen. Don’t try to close it. Never log out of the Linux system.
  • You should see a panel listing all the users. You can either click your entry or type in your username. (If you requested a new username, the new one is the one to use.) Enter your password.
  • Find the line corresponding to the carousel slot where you’ll put your sample. Click it.
  • Type in the sample name, accept the default spectrum number, select your solvent, and select your experiment.
    • Click the “Add” button in the middle of the screen to add more experiments for that sample.
    • For each experiment, click the “=” button to edit parameters. But the parameters are really good, so it’s best to only edit NS if you want more scans.
  • Load your sample into a spinner like normal, then put it in to the correct carousel slot.
  • On the screen, highlight the experiments for your sample. Click the “Submit” button in the middle bar of buttons.
  • Continue submitting additional samples if you wish.
  • Click the “Change user” button at the right to make the system available for the next user.
  • You’re done! Walk away.
  • Do not process data at the instrument. Please transfer your data to your own computer and process your spectra there. See this page for instructions on downloading, installing, and lcicensing MNova: https://chemnmrlab.uchicago.edu/mnova/

Current Rules About Usage Time, Sample Limits

  • The automated instruments have a “night queue” for longer or less urgent experiments. Samples placed in the night queue during the day will be automatically run at night; they will be marked “Queued” and must not be removed from the carousel.
  • Night time runs from 22:00 to 09:00. Night experiments may run up to 4 hours per sample. Try the 3.5hr 13C 1D if the 10min daytime CARBON doesn’t give you enough S/N!
    • Try the daytime 10 min CARBON before you queue up a night time acquisition. You might be surprised at how much signal you get.
    • Try the “CHARACTERIZATION” experiment: one button sets up ~2 hours of night-time 1H 1D, 13C 1D, 13C DEPT, COSY, HSQC, and HMBC.
  • The system limits you to a total of 90 minutes of data acquisition per daytime period.
  • Please limit yourself to six samples at a time so the carousel does not fill up.
  • The system limits individual daytime experiments to no more than 20 minutes.
  • Our institutional rule is you are limited to 20 minutes of daytime use per sample.
    • Feel free to split up sets of experiments if you want to run, say, a quick 1H 1D asap and let longer experiments run at night.

Data Management

Part of this upgrade involved a (labor-intensive) transformation of user accounts and data placement. Key points:

  • Getting your data is now simpler:
    • Log in to the data transfer computer (nmr8 inside the room, or nmr60 from outside). Use your new password and, if you got one, new account name.
    • Type “get400-2”.
      • The first time you do this, you’ll get a big weird message discussing an RSA key. Just say “yes” and click return/enter, and all will be fine.
      • Provide your password when asked.
      • You should see a stream of file names appear when data gets transferred.
    • Log out. Your data are ready to be copied to your laptop with Filezilla or a similar program.
  • The new 400-2 saves its data in a new folder, /opt/nmrdata/(username).
    • The old way was needlessly long: /opt/topspin/data/(username)/nmr.
    • Your old scripts, if you used them, will probably not work. You’ll either need to modify them, or you can just use “get400-2”.
  • The old 400-2 computer is currently offline. All the old data are there, but managing them is not a high priority right now.

Sample Management

Though you can submit your samples and walk away, you still need to come back and get them. We have a “two-rack” system for handling them, described here: https://chemnmrlab.uchicago.edu/policies/#2racksystem

Briefly, if you need to use a carousel slot that has a sample in it AND the IconNMR interface says it is “Finished”, you may remove that sample and place it the top rack next to the instrument. People can come get their own (or their lab partner’s) samples any time. Every Monday, the top rack is moved to the bottom, where it will stay for a week, allowing people to get their samples. But the rack that has been on the bottom shelf for a week gets emptied and moved to the top; all those samples get moved to a “TAKE ME” beaker, and anyone who wants a free NMR tube and is willing to dispose of the contents properly can take it. PICK UP YOUR SAMPLES!

COVID-era Protocols

  • There can be only TWO PEOPLE in the GCIS NMR lab at one time. One person in the pink 400-2 zone, and one in the checkerboard Waiting zone.
  • If someone is using the instrument you must wait in the waiting area – do NOT go around the barriers and get your sample(s) while someone is already in the 400-2 zone.
  • The Waiting Zone is centered on data transfer computer.
  • In addition to the mask you must wear in the building, you must wear fresh gloves in the NMR room. They are available on the cart just inside the door.
    • Put on the new gloves as soon as you walk in. Do NOT just wear the same gloves you had on in lab.
    • Throw out your gloves as you exit the room



Automation-compatible valved tubes for air-sensitive samples

NMR samples longer than 222 mm will not fit in the sample changing apparatus. Longer tubes will trigger a safety catch that stops the queue, which will make everyone waiting for their samples to run mad at you.

If you have a glassblower make your valved tubes, inform them on the length requirement. They should be able to accommodate.

For commercial tubes, Bruker recommends the following


Data Transfer Script

** Every user account now has a unique alias in their .bashrc file. Typing “get400-2” executes an rsync command targeted at data in that user’s data folder. Every time it is used, it simply copies all new data from the spectrometer to the user’s location on the data transfer computer. This kinds took a lot of scripting to set up. This command will appear soon in Searle, where the corresponding commands will be “get400-1”, “get500-2”, etc. Each user’s .bashrc file now contains a line :

alias get400-2=’rsync -crv (username)@nmr400-2:/opt/nmrdata/(username)/* .’

Eventually, everyone will have a line like this for each spectrometer in each lab room.