Mercury-300 NMR Operation

  1. Login using your username and password.
  2. Double click  the “vnmrj” icon on the desktop (or open a terminal window, using Right Mouse Button-RMB-, and in the terminal window type “vnmrj” and Enter)
  3. Type “start” in the command line.
  4. Select the type of experiment you would like to perform: click on the gray protocol buttons on the upper left (e.g. Proton, Carbon, Phosphorous…).
  5. Start Tab:
    • “Standard”Submenu:
      • Click on the “Eject” button to eject the standard sample from the magnet. Change samples and adjust the sample height in the spinner using the depth gauge.
      • Insert the sample into the sample bore, carefully letting it go while making sure that it floats at the top of the sample bore.
      • Click on “Insert” button to insert sample.
      • Choose the solvent (e.g. CDCl3).
      • Type sample name and  any comments about the sample.
    • “Lock” Submenu:


      • You may auto-lock your sample by clicking on the “Find z0” button. This method is recommended for solvents with multiple deuterium signals (toluene, pyridine, and THF) to ensure that the proper signal is selected for solvent referencing. Verify that the correct solvent has been selected in the Standard Submenu before clicking the “Find z0” button.
      • After the process completes, wait a few moments for the lock level to stabilize and then adjust “Gain” as necessary to bring the lock level between 30 and 50. The “Gain” slider should remain above the “Power” slider, so you may adjust “Power” if necessary. You may then skip to the Shim Submenu instructions, or continue with the following to verify the lock condition.

      • Manual Lock:

      • Click the Lock “Off” button.
      • Click the “Lock Scan” button.
      • Click the “Spin On” button and wait for the spin to regulate.
      • Adjust “Z0” to obtain zero beat frequency (on resonance, single horizontal line).
      • If necessary, adjust “Gain” to keep the lock level between 30 and 50 while adjusting “Z0”. The “Gain” slider should always remain above the “Power” slider. Do not continue adjusting “Z0” if the line reaches the top of the screen (Lock Level > 80). Reduce the “Power” or “Gain” first, and then continue. If “Gain” reaches the maximum, you can increase “Power”, but it should not be increased past 40 except for low sample sizes or low deuterium-concentrated solvents.
      • Reduce “Power” if the signal oscillates (goes down and then back up) and it is difficult to establish lock. The deuterium nuclei become “saturated” if the lock power is too high. Acetone is more easily saturated than most solvents.
      • Click the Lock “On” button.
    • Shim Submenu:
      • Adjust the “Lk Power” and “Lk Gain” if necessary so the lock level is around 30-50.
      • Adjust “Lk Phase” to maximize the lock level. If the lock level rises above 80, decrease the “Lk Power” and/or “Lk Gain” to return the lock level to around 50.
      • On the 300: Adjust “Z1C” to maximize the lock level and then adjust “Z2C”. Any time you adjust “Z2C” you should then readjust “Z1C”. Repeat adjustments until a maximum is reached.
      • On the 300 and 400: Adjust “Z1” and “Z2” in the same manner as above to make fine adjustments to the lock level.
      • Adjust “Lk Power” and “Lk Gain” to set the Lock Level between 30 and 70. Verify that the “Gain” slider in the Lock submenu is above the “Power” slider and make adjustments as needed.
  • Acquire Tab:

  • The default instrument parameters are set to obtain survey spectra with the optimum signal-to-noise in the shortest time for average MW. They usually work for proton counting (i.e. distinction between CH, CH2 and CH3 proton resonances), but are NOT suitable for quantitative analysis. The user can modify the parameters to get desired results according to their project needs.

    For accurate quantitative analysis parameters must be altered (e.g. for quantitative 1H spectra pw(90) and d1=5xT1; for quantitative 13C spectra pw(90), d1=5xT1  and dm=’nny’). You can guess T1 based on prior knowledge from your group’s work with similar samples. However, ideally you should perform a T1 measurement experiment and use identical sample preparation conditions (solvent, analyte, concentration, experimental temperature) for future samples if you wish to use that measured T1 as a basis for quantitative analysis of future samples.

    If you work with atypical structures (e.g. paramagnetic materials, anions or cations) the default spectral window might not be suitable.

    Other parameters can be adjusted to satisfy the needs based on other unusual sample characteristics.

    Data processing can dramatically influence the reliability of quantitative analysis. For best results, contact the lab staff for instructions on data processing.

    •  Default [Nuclei] Submenu:
      • Set “Transform Size” to 4 x np (e.g. 64K for 1H and 128K for 13C)
      • The default “Line Broadening” is 0.5 Hz for 1H and 1 Hz for 13C; these values can be changed to match the natural signal width in order to improve signal-to-noise.
    • Acquisition Submenu:
      • Set the number of “scans” to 16 by default for 1H spectra and a higher number for 13C.
      • S:N can be improved using larger nt. Always use nt equal to a multiple of 4 to avoid artifacts in the spectra.
      • Make sure that the Auto box is checked under receiver gain.
      • Click on “Showtime” to know the length of experimental time
    1.  Acquiring Spectra
      •  Type “ga” in the command line to start the acquisition. Wait until data acquisition is done.
      • Switch off integral line when the spectrum is displayed (use the interactive panel on the Right side of the screen): click the “Show Full Integral” icon twice.
      • Type “aph0 dc” to automatically phase and correct baseline tilt/offset problems.
    2. Referencing
      • Zoom in on the solvent peak region by defining the zoom region; left click on the left side of the desired region and then right click on the right side; click the + magnifying glass (i.e. zoom in) button.
      • Place the cursor near the peak of the solvent line and left click, then type “nl”.
      • Type “rl(x.xxp)” where  x.xx is the chemical shift of the residual solvent resonance (e.g. 7.26 ppm for CHCl3). Refer to the chart on the desk with the chemical shift reference information for different solvents
    3. Integration
      • Click the “Show Full Integral” icon once to display the green integration line.
      • Select the “Define Integral Region” icon (the scissors) and left click first on the left side and then on the right of each resolved set of resonances.
      • If you make a mistake you can undue a left click with a right click, or totally erase your integration by typing “cz”.
      • Make sure to that the integral regions you define for integration are completely resolved, i.e. the signal completely to the baseline. Otherwise your integrations will not be accurate.
      • See above note about the importance of T1 determination in quantitative analysis using NMR spectroscopy.
      • Type “dpirn” to display the normalize integrations.
    4. Peak Picking
      • Click on the “Set Threshold” icon (horizontal yellow line) and move the yellow line that appears to a height that transects your resonances of interest, but not the noise.
      • type “dpf” to display the peak frequencys
    5. Printint
      • For printing start a command line with pl and finish the line with page as in this example: pl pscale pltext pirn page and enter.
      • pscale: prints scale; pltext: prints comments typed in the start tab; pirn: prints the values of integrals under the peak regions; ppf: prints frequency values above peaks; pap: prints all parameters.
    6. Saving data: Click on File (drop down menu) and select Save as.
      • Select the folder in which the file is going to be saved or create new folder and select it
      • Type the filename.
    7. Eject your sample and put the standard sample back in the magnet.
    8. Exiting: Type done in the gray command line to exit the vnmrj program.
      • In the desktop upper left, click on System (drop down menu) and select Logout to log out completely from the computer. Be sure to wait as the system might ask if you are sure you want to log out. Confirm that you wish to logout and wait for the logout procedure to complete. If you do not complete the logout procedure properly,



    The screen will be locked by your account, AND this will prevent others from using their instrument time. You will be charged based on the amount of time you are logged onto the instrument.



      • If the sample is too concentrated (i.e. if you see ADC overflow when you start the acquisition), Click STOP Button (RED button on the upper left panel) to stop your experiment, set Observe Pulse to 10 degrees, and restart your experiment.




    Display integral regions normalized


    Display frequencies


    Exit processing submenu and return to spectrum with cursor displayed

    ds cz

    Erase previous integrals

    f ds

    Display full spectrum



    ** Users are NOT ALLOWED to create any new Experiments.

    *** In case the instrument is INACTIVE or for any other PROBLEMS with the system, CONTACT the NMR Staff Immediately OR in off hours e-mail to: