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Varian NMR Training

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Varian Advanced Training Guide:  Varian_Advanced-training.pdf

NMR Training PowerPoint: NMR_Training_Powerpoint.pdf (1.3 MB PDF)

How to:

Login into NMR facility computers

If your NMR account has been created, use your university afs ID and password to login into any NMR facility computer; otherwise, contact NMR facility personnel.

Measurement of 1D 1H spectra

  1. Type the command setexp_H1_solvent were solvent is the name of deuterated solvent of your sample, for example, setexp_H1_cdcl3, setexp_H1_d2o, setexp_H1_cd3od, setexp_H1_dmso, setexp_H1_acetonitrile, setexp_H1_acetone, etc, and press the return button on the keyboard. All shim and lock parameter values will be updated accordingly to the used solvent and necessary acquisition, processing and plotting parameters will be loaded. The parameter window can be displayed by using command dg. 
The return button on the keyboard must be always pressed after typing a command, a set of commands separated by spaces, or parameter with its new value to execute the command(s) or change parameter value.
  2. Open the acquisition window by putting arrow cursor on the Acqi button (the last button in the first row) and click the left mouse button. Put arrow cursor on the LOCK button and click the left mouse button. Turn off spinning and lock by subsequently putting arrow cursor on the corresponding Off buttons and clicking the left mouse button.
  3. Eject the standard sample by putting arrow cursor on the eject button and click the left mouse button. Remove the standard sample from the spinner and replace it with your sample. Adjust sample height in the spinner using the gauge attached to the console door.
  4. Place spinner with your sample on the top of the magnet. Before you do so make sure the air is flowing from the bottom of the magnet to its top. Never attempt to place spinner with the sample on the top of the magnet if the air is not flowing. Put arrow cursor on the insert button and click the left mouse button. Wait until the sample reaches its correct position inside the magnet. Turn on spinning and lock by subsequently putting arrow cursor on the corresponding On buttons and clicking the left mouse button.
  5. Put arrow cursor on the SHIM button and click the left mouse button. Adjust Z1C, Z2C, Z1, Z2, and if necessary Z3 shims by maximizing the lock signal level. Current shim values shown in the square brackets next to the shim labels can be changed in steps of 1, 4, 16, and 64. Place arrow cursor on the corresponding step button and by clicking the left mouse button the current shim value will be accordingly decreased. Clicking the right mouse button will increase the current shim value. See the section Shimming on the Lock Signal for a detailed description of the shimming procedure. Close the acquisition window when shim adjustment is finished, by putting arrow cursor on the CLOSE button and click the left mouse button.
  6. Set number of transients (parameter nt) according to the concentration of your sample, for example, nt=16 and press the return button on the keyboard. If the parameter window is not displayed, type command dg and press the return button on the keyboard first. 
To start the data acquisition, type the command au and press the return button on the keyboard. Alternatively, one can start the experiment as follows. Put arrow cursor on the Main Menu button and click the left mouse button. Place arrow cursor on the Acquire button and click the left mouse button. Put arrow cursor on the Automatic button and click the left mouse button. Data acquisition, processing including referencing, integration and plotting of the spectrum will be performed automatically.
  7. The acquired data can be stored in user afs space. See the section Archiving and Retrieving NMR Data how to perform these tasks.
  8. The data acquisition can also be started using the commands go or ga. Alternatively, the experiment can be started by subsequently clicking the following buttons Main Menu, Acquire and Go or Go, Wft. In both cases the spectrum must be phased, referenced, integrated and plotted manually. See the section 1D NMR Data Manipulation how to perform these tasks.

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Homo Decoupling

  1. Check whether the first button in the second row has label either Box or Cursor. If yes, then go to 2, otherwise set the arrow cursor on the Main Menu button and click the left mouse button. Set the arrow cursor on the Display button in the second row and click the left mouse button. Set the arrow cursor on the button Interactive in the second row and click the left mouse button.
  2. Set the arrow cursor on the Box button and click the left mouse button. If the label of the first button in the second row is Cursor, set the arrow cursor on this button and double click the left mouse button. Two vertical red cursors will appear on the screen.
  3. Set the arrow cursor on the left side of the region containing multiplet you want to irradiate and click the left mouse button. Set the arrow cursor on the right side of the region containing multiplet you want to irradiate and click the right mouse button.
  4. To expand the region enclosed by the red cursors, set the arrow cursor on the Expand button in the second row and click left mouse button. You can also expand a desired region using commandexp1d(right, left), where right and left are corresponding right and left margins in ppm of the selected region, for example, exp1d(2.2,3.5) will expand the spectral region from 2.2 ppm to 3.5 ppm.
  5. Set the arrow cursor on the Cursor button and click the left mouse button. If the label of the first button in the second row is Box set the arrow cursor on this button and double click the left mouse button. A vertical red cursor will appear on the screen.
  6. Set the arrow cursor in the middle of the multiplet you want to irradiate and click the left mouse button. The vertical red cursor will move in the position of the arrow cursor. Type the command sd and press the return button on the keyboard. The value of the parameter dof will change and correspond to the position of the red cursor.
  7. Type dm='yyy' homo='y' dpwr=20 and press the return button on the keyboard.
  8. Type the command au and press the return button on the keyboard. Alternatively, one can start the experiment by subsequently clicking the following buttons Main Menu, Acquire and Automatic. Data acquisition, processing and plotting will be performed automatically. It is recommended to start homo decoupling experiment with the command go or ga and process spectra manually. See the section NMR Data Manipulation how to perform these tasks.
    Alternatively, homo decoupling experiment can be started by subsequently clicking the following buttons Main Menu, Acquire and Go or Go, Wft​.

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Measurem​ent of both homodecoupled and nondecoupled 1H spectra in one experiment

  1. Set the values of parameters dof, homo, and dpwr as described in the preceding section Homo Decoupling.
  2. Type dm=’nnn’,’yyy’ gain=’y’ and press the return button on the keyboard.
  3. Set number of transients (parameter nt) according to the concentration of your sample, for example, nt=16 and press the return button on the keyboard.
  4. Start the data acquisition using commands go ai or ga ai. Alternatively, the experiment can be started by subsequently clicking the following buttons Main Menu, Acquire and Go or Go, Wft. Two spectra will be acquired, one without decoupling corresponding to dm=’nnn’ and the other with decoupling corresponding to dm=’yyy’. If the acquisition was started by clicking buttons, the spectra must be reprocessed using the commands ai ft, after the acquisition is finished. Regardless how the acquisition was launched, the spectra must be phased and referenced manually. See the section NMR Data Manipulation how to perform these tasks.

Measurement of 1D 13C{1H} spectra

A. The following set up procedure assumes that you intent to measure 13C{1H} spectrum right after 1H spectrum was measured otherwise proceed to B. There is no need to change lock and shim values, because locking and shimming was done before as a part of the measurement of 1H spectrum.

  1. Set the arrow cursor on the Main Menu button and press the left mouse button. Set the arrow cursor on the Setup button in the second row and press the left mouse button.
  2. Set the arrow cursor on the Nuc,Solv button in the second row and press the left mouse button. Set the arrow cursor on the C13 button in the second row and press the left mouse button. Set the arrow cursor on the corresponding solvent button in the second row and press the left mouse button. The necessary acquisition, processing and plotting parameters will be loaded.
  3. Set the number of transients (parameter nt) according to the concentration of your sample, for example, nt=128 and press the return button on the keyboard. Type command au and press the return button on the keyboard. Alternatively, one can start the experiment as follows. Put arrow cursor on the Main Menu button and click the left mouse button. Place arrow cursor on the Acquire button and click the left mouse button. Put arrow cursor on the Automatic button and click the left mouse button. Data acquisition, processing including referencing, peak picking and plotting of the spectrum will be performed automatically.
  4. The acquired data can be stored in user afs space. See the section Archiving and Retrieving NMR Data how to perform these tasks.
  5. The data acquisition can also be started using commands go or ga. Alternatively, the experiment can be started by subsequently clicking the following buttons Main Menu, Acquire and Go or Go, Wft. In both cases the spectrum must be phased, referenced, and plotted manually. Also the threshold for peak picking must be set manually. See the section NMR Data Manipulation how to perform these tasks.

B. The following set up procedure assumes that 1H spectrum was not measured right before measurement of 13C{1H} spectrum.

  1. Type command setexp_C13_solvent were solvent is the name of deuterated solvent of your sample, for example, setexp_C13_cdcl3, setexp_C13_d2o, setexp_C13_cd3od, setexp_C13_dmso, setexp_C13_cd3cn, setexp_C13_acetone, etc, and hit the return button on the keyboard. All shim and lock parameter values will be updated accordingly to the used solvent and necessary acquisition, processing and plotting parameters will be loaded.
  2. Follow the steps 2-8 in “Measurement of 1D 1H spectra.”

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Measurement of APT spectra

  1. Set parameters to measure 13C{1H} spectrum as described in the preceding paragraph “Measurement of 1D 13C{1H} spectra”. If 1H spectrum was measured right before setting up APT experiment, follow the steps 1-2 in the section A. If 1H spectrum was not measured right before setting up APT experiment, follow the steps 1-2 in the section B and the steps 2-5 in “Measurement of 1D 1H spectra”.
  2. Set the arrow cursor on the Main Menu button and press the left mouse button. Set the arrow cursor on the Setup button in the second row and press the left mouse button. Set the arrow cursor on the Sequence button in the second row and press the left mouse button. Set the arrow cursor on the APT button in the second row and press the left mouse button. Alternatively, type command apt and press the return button on the keyboard to set up apt experiment.
  3. Set the number of transients (parameter nt) according to the concentration of your sample, for example, nt=128 and press the return button on the keyboard. 

  4. To start the experiment, type command au and press the return button on the keyboard. Alternatively, one can start the experiment as follows. Put arrow cursor on the Main Menu button and click the left mouse button. Place arrow cursor on the Acquire button and click the left mouse button. Put arrow cursor on the Automatic button and click the left mouse button. Data acquisition, processing including referencing, peak picking and plotting of the spectrum will be performed automatically.
  5. The acquired data can be stored in user afs space. See the section Archiving and Retrieving NMR Data how to perform these tasks.
  6. The data acquisition can also be started using commands go or ga. Alternatively, the experiment can be started by subsequently clicking the following buttons; Main Menu, Acquire and Go or Go, Wft. In both cases the spectrum must be phased, referenced, and plotted manually. Also the threshold for peak picking must be set manually. See the section NMR Data Manipulation how to perform these tasks.

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Measureme​nt of DEPT spectra

The measurement of DEPT spectrum requires you acquire a regular 13C{1H} spectrum first. It is adequate to measure this spectrum with only one transient (nt=1). You do not need to see any carbon signals corresponding to the solute molecules. Detecting just the solvent signal is satisfactory. After you measured a regular 13C{1H} spectrum do the following.

  1. Set the arrow cursor on the Main Menu button and press the left mouse button. Set the arrow cursor on the Setup button in the second row and press the left mouse button. Set the arrow cursor on the Sequence button in the second row and press the left mouse button. Set the arrow cursor on the DEPT button in the second row and press the left mouse button.
  2. Adjust number of transients (parameter nt) corresponding to the concentration of your sample. The number of transients must be multiple of 8, e.g., nt=8, 16, 24, etc.
  3. Set the arrow cursor on the Acquire button in the second row and press the left mouse button. Set the arrow cursor on the Automatic button in the second row and press the left mouse button. The experiment will proceed automatically to the end when the final results will be plotted, 4 vertically stacked spectra.

Shimming on the Lock Signal

  1. In the SHIM display window, try a change of +4 or -4 in the setting for Z1C. If the lock level goes up with one of these, continue in that direction until the level is maximized (It no longer increases, but instead begins to fall.). If the lock level drops when using +4 or -4 step try a change of +1 or -1.
  2. Change the setting for Z2C by +4 or -4 and continue in that direction until the level is maximized. Try a change of +1 or -1, if the step ±4 seems to be excessive.
  3. Readjust Z1C for maximized lock level. Change the Z1C in steps of 1.
  4. Readjust Z2C for maximized lock level. Change the Z2C in steps of 1.
  5. Repeat steps 3 and 4 until the lock level goes no higher.
  6. Adjust Z1 and Z2 shims (the fine Z shim controls) in the same way as Z1C and Z2C until the lock level is maximized. Use the step +4 or -4. You also may try a change +16 or -16.
  7. After Z1 and Z2 have been adjusted for maximum lock signal, write down the lock level, adjust Z3 in one direction, say by +4, and then iteratively reoptimize Z1 and Z2 until lock signal is at its maximum. Note this level of the lock signal. If the lock signal is higher than it was before (when you first wrote it down), continue changing Z3 in the same direction. If the lock signal is lower than it was before, Z3 must be changed in the opposite direction. Every change in Z3 must be followed by optimization of Z1 and Z2 until the lock level is at a maximum.
  8. If the lock level increases to 100, stop shimming, select z0/pwr/gn/ph from the SHIM menu (Put arrow cursor on the axial z button and press the right mouse button.) and decrease lock power. The reduced lock level should be ~60. Return to shimming by selecting axial z from the same SHIM window.

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Archiving and Retrieving NMR Data 
 


  1. To store the acquired data in user afs space type command connect_afs and press the return button on the keyboard.
  2. Type command svf('xyz') and press the return button on the keyboard. xyz is the name of the file in which the data is stored.
  3. To reload NMR data stored in user afs space into any NMR facility Sun computer type command connect_afs and press the return button on the keyboard. Place arrow cursor on the Main Menu button and click the left mouse button. Put arrow cursor on the File button in the second row and click the left mouse button. The names of archived data files will show up on the screen. Put arrow cursor on data file name you want to load and click the left mouse button. Put arrow cursor on the Load button in the second row and click the left mouse button. The chosen data will be loaded into the computer and ready for processing.

1D NMR Data Manipulation

Processing

  1. Data acquired with the command go (FID signal) must be processed using the command ft or wft to obtain a spectrum. To convert (Fourier transform) the FID signal into a spectrum, type the command ftor wft and press the Return button on the keyboard. Alternatively, you can consecutively click the buttons Main Menu, Process, Transform or Weight, Transform using the left mouse button.
 If the command wft is used, the FID signal is multiplied by a weighting function, which corresponding processing parameter has non zero value, prior Fourier transformation. The command ft performs only the Fourier transformation and skips the application of weighting function. o enhance signal to noise (S/N) ratio in 1D proton spectra, set the value of parameter lb in the range of 0.1 to 0.5, by typing lb=x, where 0.1£x£0.5, and pressing the Return button on the keyboard. For resolution enhancement of 1D proton spectra, set the lb value in the range of -0.5 to -0.1, by typing lb=x, where -0.5£x£-0.1, and pressing the Return button on the keyboard. To enhance S/N ratio in 1D carbon or other heteronuclei spectra, type lb=1 and press the Return button on the keyboard.
 To remove a particular weighting function from use, the value of its corresponding parameter should be set to 'n', for example type lb='n' and press the Return button on the keyboard.
  2. If the command ga is used for data acquisition, the FID signal is converted into a spectrum by performing Fourier transformation automatically, immediately after the acquisition is completed. Provided some processing parameters have non zero values, the FID signal is also automatically multiplied by corresponding weighting functions prior Fourier transformation.

Phasing spectra

  1. Automatic phasing: 
Type the command aph0 and press the Return button on the keyboard. Alternatively, you can consecutively click the buttons Main Menu, Display, Massage and Autophase using the left mouse button.
  2. Manual phasing: 
Consecutively click the buttons Main Menu, Display, Interactive and Phase using the left mouse button.
Put the arrow cursor above the far right peak of displayed spectra approximately to the middle of the display window in vertical direction. Press and hold down the left mouse button and slide the mouse on the mouse pad until the right part of spectra is phased correctly. Release the left mouse button and move the arrow cursor above the far left peak of displayed spectra approximately to the middle of display window in vertical direction. Press and hold down the left mouse button and slide the mouse on the mouse pad until the left part of spectra is phased correctly. Release the left mouse button and click the Phase button using the left mouse button to exit the phasing procedure.

Referencing spectra

  1. Consecutively click the buttons Main Menu, Display, Interactive and Cursor (the first button in the second row) using the left mouse button. A red vertical cursor will appear in the display window. If the first button in the second row has the label Box, double click on this button.
  2. Put the arrow cursor on the top of the peak you want to use for referencing, usually TMS or solvent signal, and click the left mouse button. The red vertical cursor will move to the position of the arrow cursor. Type the command nl and press the Return button on the keyboard.
  3. Click the button Ref, type the correct chemical shift value for the chosen signal and press the Return button on the keyboard.
  4. To display a scale below the spectrum, type the command dscale. Alternatively, you can consecutively click the buttons Main Menu, Display, Interactive and Dscale using the left mouse button. To set units of the scale to Hz, type axis='h' and press the Return button on the keyboard. To set scale units to ppm, type axis='p' and press the Return button on the keyboard.
  5. To expand a spectral region which spans form the chemical shift value of x ppm (right margin) to the chemical shift value of y ppm (left margin), set sp=xp and wp=Dp, where D=y-x, and press the Return button on the keyboard. For example to expand the region which extends from d=2.8 ppm to d=3.4 ppm, type sp=2.8p wp=0.6p and press the Return button on the keyboard. 
Alternatively, you can perform spectral expansion using one of two procedures outlined in the Homo Decoupling section, paragraph 4.

Adjusting vertical scales of the spectra

  1. To adjust the heights of the peaks in 1D spectra, type the command vsadj(x), where 0<x£170 is a desired height of the tallest peak in the spectrum in mm, and press the Return button on the keyboard.
  2. Alternatively, the peak heights in 1D spectra can be adjusted by consecutively clicking the buttons Main Menu, Display, Massage and Adj VS using the left mouse button.
  3. The peak heights in 1D spectra can also be adjusted putting the arrow cursor above a selected peak and sliding the mouse on the mouse pad with the middle mouse button continually pressed.
  4. To set a threshold for display and printout peak frequencies, click consecutively the buttons Main Menu, Display, Interactive and Th using the left mouse button. A yellow horizontal cursor will be displayed. To adjust its vertical position, put the arrow cursor on the yellow horizontal line, press and hold down the left mouse button and slide the mouse on the pad. By typing the command dpf or ppf the peak frequencies will be displayed or printed, respectively, on top of the peaks, which are above the threshold line. Peak frequency units are defined by the parameter axis.

Integration spectra

  1. Consecutively click the buttons Main Menu, Display, Interactive and Part Integral (the second button in the second row) using the left mouse button. If the second button has the label Full Integral, click three times on this button. If the second button has the label No Integral, double click on this button. Previously defined integral regions will be displayed.
  2. Type the command cz to clear the previously defined integral regions. An integral curve over whole spectrum will appear.
  3. If the integral curve is tilted, click the button Lvl/Tlt using the left mouse button. Put the arrow cursor on the right side of the integral curve about halfway vertically up the screen, press and hold down the left mouse button and slide the mouse on the mouse pad until the integral curve over the regions without peaks is parallel to the baseline. Release the left mouse button and click the Lvl/Tlt button using the left mouse button to exit the tilt adjusting procedure.
  4. To integrate spectral regions containing peaks, click the button Reset using the left mouse button. Start with the far-left region. Put the arrow cursor on its left side right behind the last peak and click the left mouse button. Place the arrow cursor on the right side of this region right in front of the first peak and click the left mouse button. In the same way integrate all other spectral regions going successively from left to right.
  5. Alternatively, the spectral regions containing peaks can be integrated by consecutively clicking the buttons Main Menu, Display, Massage and Adj IS using the left mouse button.
  6. To assign the integral value to a chosen integral region, place the red vertical cursor over this region and click the button Set Int using the left mouse button. In the command window enter the desired value and press the Return button on the keyboard. See Referencing spectra paragraph 1 how to display the red vertical cursor.
  7. The position of the integrals with respect to the spectrum is governed by the parameter io. Its values must be entered in units of millimeters. For example, typing io=30 and pressing the Return button on the keyboard will move the integrals 30 mm above the spectral baseline.
  8. The height of the displayed integrals can be adjusted by using the parameter is. Its values can be set in the range of 1 to 109. For example, type is=600 and press the Return button on the keyboard.

Plotting spectra

  1. Plotting spectra by using commands: 
Type the commands pl pscale pap pir ppf page and press the Return button on the keyboard. 
pl - plots spectrum, pscale - plots scale under the spectrum, pap - prints all parameters, pir - prints integral values under the scale, ppf - prints peak frequencies, page - submits the current plotter file, which has been created by all previous plotter commands, and changes the paper after the plot has been completed.
  2. Plotting spectra by clicking buttons: 
Click consecutively the buttons Main Menu, Display, Plot, Plot, Scale, All Params, Peaks, Page using the left mouse button. You must type the command pir if you also want to print the integral values.
  3. The parameter vp positions the whole spectrum vertically on the screen and consequently on the paper when plotted. Its values must be entered in units of millimeters. For example, typing vp=50 and pressing the Return button on the keyboard will move the spectrum up by 50 mm. 
To plot the scale at the bottom of the paper when the spectrum is moved up by xy millimeters (vp=xy) the command pscale(vp-xy) must be used.

Plotting two spectra stacked vertically

  1. Display the first spectrum by typing the command ds(1) and press the Return button on the keyboard.
  2. Set a spectral region you want to plot as described in the section Referencing spectra paragraph 5.
  3. Adjust vertical scale and position of the first spectrum by typing the command vsadj(85) and vp=0. Press the Return button on the keyboard.
  4. Type the commands pl pscale pap and press the Return button on the keyboard or alternatively click consecutively the buttons Main Menu, Display, Plot, Plot, Scale, All Params using the left mouse button.
  5. Display the second spectrum by typing the command ds(2) and press the Return button on the keyboard.
  6. Type vp=85 and press the Return button on the keyboard.
  7. Type the commands pl page and press the Return button on the keyboard or alternatively click consecutively the buttons Main Menu, Display, Plot, Plot, Page using the left mouse button.

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