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I am on Bruker 500

I am doing...

First things to do

Locking

Tuning

Shimming

Making a new experiment in the workspace

Proton 1D

Carbon 1D

Complex NMR experiments: 2D, selective, etc. (separate HTML page)

Using Temperature Control

Current  Temperature Calibrations

Data Processing

DOSY

Finishing my work

Solvent reference data

Troubleshooting

• Topspin frozen. Correct protocol for force-quitting Topspin

   YOU CAN DO THE ACTIONS LISTED BELOW ONLY IF YOU WERE DIRECTLY INSTRUCTED BY NMR CENTER STAFF !!!

• Restarting ELCB: Clearing KEY NOT VALID error

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• Restarting spectrometer

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• Restarting the sample changer

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First things to do

1. Log in

• Log into workstation
• start Topspin software
  
  

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2. Insert your sample

• Place the sample in the spinner
• Check for a correct depth of insertion with the depth gauge
• Place it in the carousel of the sample changer
• Issue:
  • lock off
  • ro off
  • sx N (N- your sample position)

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Locking

At this point, your sample is the probe.

1. Load the default shimset
   • Issue: rsh
   • Find bbfo-latest in the dialog window
   • Click Read button

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2. Issue: lock
3. Select your solvent in the dialog window

Wait for the lock system to finish locking (see the status messages)

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Tuning

Tuning system needs to know what nucleus you are going to work with. Follow these steps:

• Right-click on the appropriate dataset in the data browser of Topspin
  • If you only need to use proton, any proton-detected experiment is OK
  • if you will use both proton and carbon during you session - join a carbon 1D experiment because it uses both channels and they both will be tuned.
    
    
• Click "Display"

Automatic Tuning

• issue atma
• Watch the screen: you need to see how the tuning system successfully shifts the wobble curve minimum to the center line of the screen.
• Once it exits it is done.

Manual Tuning

Manual tuning mode allows you to see what channels are tuned, inspect the result of tuning and adjust if necessary

• issue atmm
• move the mouse cursor onto the Atma Control window and wait till the cursor stops rotating (during this time the computer talks to the motors in the probe - it is a slow communication)
• The lowest-gamma nucleus (13C) is automatically selected and a "wobble curve" - the probe response at different frequencies is shown.
• Select Optimize:Start to start automatic tuning
  
  
  
  
• The good tuning result should is when center of the wobble curve at the center line
  
  
  
  
• Click on 1H radio button to start tuning proton
  
  
  
  If the wobble curve is very much off (probe was tuned to a previous solvent that was very different) you have two choices
  1. Click Optimize:Start and let it optimize automatically
  2. (A little faster, applies to Stepan 400) Click 18 times on [>>>] button in Tuning section to bring a resonance closer to the center
     
     
     
     and then select Optimize:Start

  The result is the same:
  
  
  
  
  NOTE: The automatic tuning result is completely acceptable for most routine work. However, for best sensitivity you may want to adjust Tuning and Matching manually to make the resonance sharper.

• Finish tuning by choosing File:Exit and click Close button in a dialog.

Probe is now tuned and ready for experiments.

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Shimming

Shimming is required to achieve good resolution in NMR spectra.

• issue topshim in the experiment you intend to run
  
  
• Run a 1D 1H on you sample and look some multiplet (best - if it is a solvent multiplet like DMSO at 2.5ppm, etc.).
  
  
• Typically, you have multiplets with about 2 Hz splitting resolved to about 50% height.
  
  
• If reolution is not so good, you may try topshim optoff
  
  
• if resolution is still bad, your tube may be not of adequate quality - try shimming a different sample to check for that
  

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Proton 1D

• Spectral width, SW, FIrst you should seCenter of the spectrum, O1 is set to wherever

• Relevant parameters to adjust (click on Acqpars, "Square wave" symbol):
  • Relaxation delay, D1 is between 1 and 3 seconds
  • Acquisition time, AQ is from 2 to 4 seconds. If your signal dies off very fast, you may want to reduce AQ because after signal is gone receiver is only collecting noise, which reduces signal-to-noise ratio in the processed spectrum

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Carbon 1D

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Using Temperature Control

IMPORTANT NOTE: If you need to use temperature OUTSIDE of 20-40 Deg C range,
you must be trained on the "Variable Temperature" protocol: contact NMR center staff to schedule training.

For all Variable Temperature tutorials and instructions see Variable-temperature NMR operation

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Current  temperature calibrations on McCourtney 500

These calibrations were obtained in April of 2020 for McCourtney 500 with automatic BCU-II chiller and Z119470_0141 probe (main 500 BBFO) by EK.

Dataset for plotting (column 1, VTU setting; column 2, Real T): VTU_realT.Full_range_automatic_BCUII_500.txt

McCourtney 500: Overview

Black points: measurements

Red line: reference 1:1 line

McCourtney 500: High-temperature branch

McCourtney 500: Low-temperature branch

McCourtney 500: Moderate region

McCourtney 500: High-temperature no-trust region

McCourtney 500: (Suspected) low-temperature no-trust region

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Data Processing

Calibrating the chemical shift axis using a reference spectrum in 1D

• Open a spectrum that contains a peak of a reference compound
• Zoom around the reference peak
• issue .cal on Topspin command line
• Left-click in a center of the reference peak

• Enter reference chemical shift in ppm and hit OK
  NOTE: For tables of chemical shifts you may look at UW Chemistry or SpectraBase or some other reputable source.
  
  Now the chemical shift axis in this experiment is calibrated:
  
  
  
  
  
  
• You can transfer this calibration to a different experiment if it was acquired on the same spectrometer.
  
  Open Procpar tab of the calibrated experiment and copy SR value to a clipboard
  
  
  
  
• Next, you display the target experiment and enter this value in its Procpar, SR field.
  
  
• Hit Enter and check your Spectrum tab: it will show a properly calibrated 1D.
  

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DOSY Experiments

For detailed protocol see  DOSY on Bruker 400 and 500

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Finishing my work

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     Restarting ELCB: Clearing KEY NOT VALID error

YOU DO THIS ONLY IF YOU WERE DIRECTLY INSTRUCTED BY NMR CENTER STAFF !!!

Sometimes ELCB unit controlling the lock "locks up". When you try to lock in this situation you will receive the message that mentions Lock: Key not valid, or similar (below):

To clear this error follow the steps below:

1. Log out of your account (report the error!)
   
   
2. Click Restart on a login screen
   
   
3. Wait till the login screen comes back (3-5 min wait)
   
   
4. Open Firefox on a spectrometer workstation:
   
   
   
   
   
5. In a workstation Firefox browser:
   
   
   1. Navigate to this page
      
      
   2. Do a Right Click on the link below to open a service web interface in a separate tab or window: 

149.236.99.20/service.html?Button=Refresh

You will see the ELCB Service Web page:








6. Click Reset ELCB button
   You should see a message under this button Soft shutdown, Resetting ELCB
   
   
   
   
   
   
7. Wait 5 minutes    
   
   
   
   
8. start Topspin
   
   
9. Open any experiment
   
   
10. Issue ii restart on a Topspin command line
    1. the status line shows restart of ipsoserver
       
       
       
    2. after all is done it will display finished. In a few seconds this message will disappear. Proceed to the next step
       
       
11. exit Topspin
    
    
12. wait 10 seconds
    
    
13. start Topspin
    
    
14. Open your experiment
    
    
15. issue ii restart on a Topspin command line one more time
16. Wait till the status line displays finished
    
    
17. proceed to locking, tuning and shimming
    
    
18. If these steps did not help, a full spectrometer restart is necessary

     

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   Restarting spectrometer

YOU DO THIS ONLY IF YOU WERE DIRECTLY INSTRUCTED BY NMR CENTER STAFF !!!

To restart the Bruker 500 MHz system, follow these steps:

1. Restart the workstation:
1. Terminate Topspin
2. Log out
3. Choose "Restart" to reboot the computer

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2. Open the spectrometer cabinet (pull and turn the handle)
   
   
3. Locate all system switches according to this picture:
   
   
   

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4. Turn off power to the NMR system
1. AQS3 - push red button, flip power switch to OFF (see the image above)
2. Amplifiers: turn power OFF
3. BSMS: turn power OFF
4. turn Main Power Switch: OFF (push in red section)

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5. IMPORTANT: Take out all samples from the top of the sample changer.
   The sample changer will forget at which position it was and will place position 1 above the bore. If the bore has a sample and position 1 has a sample they will be jammed and broken in the bore!!!

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6. Wait till the computer workstation boots up and reaches the login screen

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7. Boot up the NMR system
1. Turn Main Power switch: ON (push in green section)
2. Turn AQS3 power: ON
3. wait for 1 minute to see the Post Code display increase the code from zero to around 94-98 (exact value does not matter)
4. Turn Amplifier power: ON
5. Turn BSMS power: ON
6. Turn Sample Express power: ON (push the button on the front of the sample changer)
7. wait for 1-2 minutes for all errors on amplifier and BSMS to clear and for the Sample Express to finish initialization and turn on a green light (sample will be ejected and re-inserted automatically).
8. close the spectrometer cabinet
9. place CDCl3 standard in a position 1

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8. Login to the workstation

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9. launch Topspin

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10. display any experiment (like Setup-1H)

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11. issue ii restart
    (ignore the "status line active" message)
    NOTE:   You may see a message "Error during BirdRack flush". If you see it, click Close and reissue ii restart

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12. Load a standard shimset (issue rsh bbfo-latest)

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13. Proceed with locking
• sx 1
• lock cdcl3

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14. join experiment with proton and carbon and issue atma
    NOTE: Startup of atm module takes long time (3-5 minutes) but it continually outputs messages in the status line indicating it is not just frozen.

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15. Shim the sample:
• issue topshim

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16. adjust gain:

• issue rga

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1. Run test 1D 1H on CDCl3 standard: you should see undeuterated trace CHCl3 in one scan.

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   At this point, spectrometer is ready for use.

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YOU DO THIS ONLY IF YOU WERE DIRECTLY INSTRUCTED BY NMR CENTER STAFF !!!

Restarting the sample changer

If sample changer lost track of a sample because it was lifted by too much VT gas, you need to restart it. There are two protocols, 'light' and 'full'. Try 'light' first.

Light restart

1. turn off the sample changer (push and hold the main button on the front)
2. take out all samples sitting on the carousel
3. turn on the sample changer and wait till it gives GREEN light 
4. put back samples to positions where the were. CDCl3 standard must be in position 1

If this did not help, try full restart:

Full restart

1. open ha and acknowledge any errors
2. turn off the sample changer (main button on the front)
3. take out all samples sitting on the carousel
4. take off the carousel
5. turn on the sample changer and wait till it give BLUE light (ha screen will say "cassette expected")
6. put on the empty carousel minding the orientation: see the grooves on the bottom and shapes on the rotor head
7. wait till it turns it and lights up green.
8. check sample eject/insert.
9. check insertion of the sample from far-away position (for example, 10). If cassete is installed in a wrong orientation it will lead to red light. Then start from item 1) above.

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