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I am on Bruker 400 in Stepan Chemistry Hall

 

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First things to do

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Tuning

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Locking

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Shimming

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Acquiring 1D data

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

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Using Temperature Control

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Current Temperature Calibrations

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Data Processing

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DOSY

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Finishing my work

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Known glitches of Bruker 400 in Stepan

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Solvent reference data

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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 spectrometer

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Restarting the sample changer

 

 

 

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First things to do

Before you operate NMR spectrometers you must view the following tutorials and print the corresponding Standard Operating Procedure:

• Notre Dame NMR Operation and Concepts

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• Notre Dame Basic NMR Operation Course

 

1. Log in

• Log into workstation
• start Topspin software
  
  

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2. Insert your sample

• Bruker 400 is equipped with an automatic sample changer Bruker SampleCase 24
  Before you use the changer you must read and view SampleCase Training

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• 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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Tuning

NOTE: If your solvent is toluene-d8 (Tol) and 'atma' fails with an error, follow these instructions: System will not tune when lock solvent is toluene-d8

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
  • qu ro off
  • qu atma
  • qu wobb
• When WOBB starts: you need to see the wobble curve minimum to the center line of the screen. Switch to the second nucleus - check it too. Click exit button.

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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Locking

Next step is to lock spectrometer on your solvent:

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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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 resolution 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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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

The instrument is equipped with manual BCU-1 refrigerated chiller and liquid N2 chiller.

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Current Temperature Calibrations on Stepan 400

• Black curve: calibration with ethylene glycol (KVT_Glycol_3ramps_July_15_2020)
  • Dataset for plotting (column 1, VTU setting; column 2, Real T): VTU_realT.KVT_Glycol_3ramps_July_15_2020.400.extended.txt
    
    
• Red curve: calibration with a commercial methanol standard (KVT_methanol_3ramps_July_16_2020)
  • Dataset for plotting (column 1, VTU setting; column 2, Real T): VTU_realT.KVT_methanol_3ramps_July_16_2020.400.extended.txt
    
    
• Green line: 1:1 line

Stepan 400: Overview (see zoomed regions next)

Stepan 400: Low-temperature branch (obtained with LN2 chiller)

Stepan 400: Same data for extrapolation

Stepan 400: Low-temperature kink on a curve (no-trust region)

Stepan 400: Mid-range region

Stepan 400: High-temperature kink on a curve (no-trust region)

Stepan 400: High-temperature branch

IMPORTANT: Make sure that your LN2 chiller is disconnected and BCU-1 is in "Flush" mode!

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Data Processing

For data processing in Topspin see NMR_data_processing_Topspin

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DOSY Experiments

For detailed protocol see  DOSY on Bruker 400 and 500

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Finishing my work

• Stop spinning and unlock spectrometer
  • ro off
  • lock off

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• Insert a standard sample
  • sx 1

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• Load standard shims and lock
  • rsh bbfo-latest
  • lock cdcl3

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• Once you see a message 'lockn: done', exit Topspin

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• Once Topspin window is gone, proceed to log out

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• Fill out the exit survey. If you had any problems, please, report in the last entry form "problems with spectrometer". We will promptly follow up with you to get things fixed.

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Known glitches of Bruker 400 in Stepan

Probe cannot tune. ATMA error "Channel cannot be wobbled with this probe (Probe [1H] cannot be selected on [1H] channel)

Sometimes ATMA will fail with a nonsensical message saying that "1H cannot be tuned on 1H channel". This is a glitch we are working with Bruker on resolving. It appears to happen at all times when the lock solvent is Tol, but may happen with other solvents too. Current workaround is this as follows. Any time you need to issue atma, you have to

• unlock first (issue 'lock off'),
• run atma, and
• lock back to your solvent after atma is done.

For example, the following is a basic sequence of commands for NMR acquisition with Tol (note how atma is flanked by lock commands):

1. rsh
   - select 'bbfo-latest'
2. lock Tol
3. lock off
4. atma
5. lock Tol
6. topshim
7. rga
8. zg

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

    Restarting spectrometer

To restart the Bruker 400 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:
   
   
      
   
   
4. Side view of the console with the red reset button and Post Code display:
   
   
   
   

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5. 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)
5. Ignore

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6. IMPORTANT: Eject current sample with 'sx ej'. If changer does not respond, you still proceed with next steps.

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

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8. 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

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9. Login to the workstation

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10. launch Topspin

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11. join a proton experiment

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12. issue "ii restart"
    (ignore the "status line active" message)

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13. Load a standard shimset: "rsh bbfo-latest"

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14. Insert standard sample (if not inserted yet)
• sx 1

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15. Tune the probe

1. join experiment with proton and carbon and issue
2. spooler
3. qu atma
4. qu wobb
   NOTE: Startup of atm module after a reboot takes long time (3-5 minutes)
5. When WOBB starts - make sure that you see a resonance dip at the middle line and click [Stop] button

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1. Proceed with locking
• lock cdcl3

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2. start spinning
• ro on

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3. Shim the sample:

• issue topshim

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1. adjust gain: issue 'rga'

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2. 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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   Restarting the sample changer

For instructions on resetting SampleCase, please, see SampleCase tutorial

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