How to Run an NMR Spectrum

Susan J. Kohler

June 24, 1997

Modified August 24, 2004

How to Reserve Time: There is a sign up calendar for the 300 Mhz spectrometer on the table next to the printer.  If you come in and the instrument is free, you may just use it. The schedule is to reserve time in advance.

The following is a very quick guide to running an NMR experiment manually. A separate sheet gives directions for the automated (ICONNMR) mode. All mouse control is with the left mouse button (LMB) unless indicated otherwise. All typed entries are followed by the Enter key.

  1. Log on
    • Sign the log book so we can keep track of how the instrument is being used. This is necessary for bookkeeping for the funding agencies. They like to know things like how many students use the spectrometer per month, etc.
    • Log on, and type "xwinnmr" in the blue unix window.

 

2) Set up windows - you will want these windows to stay open throughout your session.

    • From the Windows menu, open a Lock window.
    • From the Windows menu, open the BSMS Panel.

3) Set up the experiment.

    • Type "edc" in the pink command line, then fill in the experiment name and number. The software will make a directory with the root name you chose, and will make a series of subdirectories starting with the first number you provide (expno). There are also provisions for different processing directories (procno). You will want to keep procno set to 1. Only use letters and numbers and dashes or underscores in the name. Do NOT use ( * & $ % ? / . ) or other strange symbols! After you type in the appropriate information, click on the SAVE button in the lower left corner of the gray window.
    • Copy in the appropriate basic parameters by typing "rpar <name> all" where <name> is the name of the standard parameter set (i.e. proton5 or carbon5).
    • Type "ii" to initialize the instrument.

4) Insert sample

    • Remove the cap from the top of the magnet.
    • Click the Sample Button on the BSMS Display.
    • Click the LIFT ON-OFF button to turn on the eject air.
    • Remove the old sample and insert your sample into the spinner. Do not touch the sides of the spinner; just the top.
    • Set the spinner to the proper depth with the depth gauge and place the sample in the magnet.
    • Click LIFT ON-OFF to lower the sample.
    • Replace the cap.

5) Lock the spectrometer.

            Type "lock" in the pink command line at the bottom of the main window. Then choose the proper solvent from the list which appears. Alternatively, if you know how Bruker identifies your solvent, you may just type "lock <name>" where <name> is the solvent name. For example, "lock d2o".

 

6) Shim.

    • Click on the SHIM button on the BSMS Display to open the shimming window.
    • Make sure the spinner is on. You may determine this by looking at the SPIN ON/OFF button on the Shim Panel. When the sample is spinning, the button is yellow. If it is not yellow, click on it and wait for it to stop blinking.
    • Shim using the appropriate buttons. You will want to adjust the Z and Z2 shims. Click with the left mouse button on Z. It will turn yellow, indicating that it is the active shim. Then place the cursor along the slide bar under the buttons. If you click with the left mouse button and the cursor is to the right of the slide bar, the shim value will increase. If the arrow is to the left of the slide bar when you click, the shim value will decrease. If you wish to return to the original shim setting, click on the yellow button indicating the active shim (i.e. the Z button). The step size is controlled by the button to the right of the slide bar. If you click on it with the left mouse button, the step size will increase. If you click on it with the middle mouse button, the step size will decrease. Keep adjusting the shim value to maximize the signal displayed in the lock window. If the lock signal rises above the top of the window, you can get it back on scale by clicking on the LOCK GAIN button on the shim panel, then clicking with the cursor to the left of the slide bar to lower the value just as you did with the shim control. After the Z shim is maximized, adjust the Z2 shim. Then click on the SPIN button to turn off the spinner, and observe how much the lock signal falls. If it decreases a lot, you can try adjusting the X and Y shim values to bring the level back up close to the value it has when the sample is spinning. Then turn the spinner back on, and check the Z and Z2 shims once more.
    • When you are done with the shimming, you can click with the LMB on the top bar of the main window to bring it to the front.

 

7) Collect the data.

    • Type "rga" to automatically set the receiver gain. Then wait until it says

rga: finished in the gray area under the command line.

    • Type "zg" to start the acquisition. You may look at the FID by moving to the acquisition window (type "acqu").
    • If necessary, you may stop the acquisition by typing "halt". This will save the data which has already been acquired. If you type "stop", everything stops immediately, and all data are lost. The acquisition will normally run to the end. When it is complete, a message "checklockshift: Finished" appears below the pink command line.

8) Process the data.

    • Typical processing includes exponential multiplication (Type "em"), Fourier transformation (type "ft"). Combining these two steps may be done by typing "ef"
    • After the Fourier transform, your spectrum will need to be phased to get all of the peaks pointing up. First move the spectrum up with the up arrow on the left panel of buttons so that the baseline is in the middle of the window. Then expand the vertical scale with the 2* or 8* button so that you can clearly see the baseline deviations. Then click on the Phase button to start the phasing session. Click on Biggest to fix the reference, then place the cursor over the PH0 button. Hold down the LMB and move the mouse up and down to adjust the baseline. You will see a vertical dotted line through the reference peak; adjust the baseline for this peak so that it is symmetric. If other peaks are not in phase after the reference peak has been properly phased, place the cursor over the PH1 button, hold down the LMB, and move the mouse to adjust the baseline. This correction does not change the phase of the reference peak, and applies increasing amounts of correction to peaks farther away. When you are done, click on the Return button, then on Save and Return.

9) Shutdown and Log out.

    • When you are finished with your experiments, please put a sample back in the magnet.
    • Log out by pressing the Right Mouse Button to get a menu, and choosing the Logout option. You will be asked to confirm your choice.

Some Useful Commands:

            rpar     read a set of parameters

            edc      edit configuration (make new data set name)

            edc2    edit configuration for dataset #2 (used with the dual display option)

            eda      edit acquisition parameters (all of them, even if not used)

            ased    edit acquisition parameters specific to the chosen pulse program

            edp      edit processing parameters

            edg      edit parameters for graphing (plotting)

            setti     set title for plot

            rsh       read a shim file

            wobb    start wobble (to tune & match probe)

            acqu    switch to the acquisition window

            re <number>    recall experiment number <number>

            iexpno increment experiment number

            expt     show time estimate for experiment

            zg         zero memory & go (collect data)

            em       exponentially multiply

            ft          Fourier transform

            ef         em + ft

            efp       em + ft + phase to last performed phase correction

            ns        number of scans

            lb         line broadening

            sw        sweep width (in ppm)

            o1p      center frequency (in ppm)