University of California, Riverside

NMR Facility



Varian Inova 300 Help Sheets



1D Basics || Console Reboot || Comands


Basic Operation Guide: Varain Inova 300 NMR Spectrometer

Conventions used in this guide are as follows:

LMB indicates the Left mouse button.
MMB indicates the Middle mouse button.
RMB indicates the Right mouse button.

Unless otherwise noted, "Click" means clicking with the left mouse button and all commands typed on the command line are followed by a <return> keystroke.  

Currently the INOVA300 and INOVA400 NMR spectrometers are equipped with the NALORAC 5mm Four Nucleus Gradient Probes (4Nuc) with the capability to observe or decouple 1H, 19F, 13C and 31P without re-tuning the probe. 

I  Logging in to VnmrJ         

  1. Sign the logbook with your name, adviser’s name, date, time in, nucleus and solvent.
  2. If the screen is black, move the mouse.
  3. Type in your user name <return>, type in your password <return>.
  4. Click the VnmrJ icon in the top bar to open the VnmrJ interface. (Do not double click!!)

 vnmrj main window

II  Ejecting and inserting sample

  1. Click the start tab and select Standare page, click the Eject button to eject the reference sample.
  2. Remove the reference sample from the spinner and position your sample properly in the spinner using the depth gauge.  With the eject air still on, place the sample and the spinner into the top of the magnet. Click the Insert button to insert the sample.  (Caution! Never place a sample in the magnet bore without eject air flowing).
  3. Wilmad 506PP or equivalent NMR tubes are required for this instrument.  The normal sample height should be 4.5 cm or more (approx. 0.7 ml). For normal height samples the bottom of the NMR tube will go to the bottom of the depth gauge, and for shorter samples the sample must be centered on the middle line of the depth gauge.  This will make shimming on short samples easier.

III  Lock and shim

In the Lock and Shim pages, the buttons (Z0, Lk Power, Lk Gain, Lk Phase, and Z, X, and Y shims) provide on-the-fly configuration.  The slider values can be moved with the mouse or entered directly.

Lock buttons and controls:

vnmrj lock controls

Shim button and controls:

vnmrj shim controls 

Mouse control of buttons and sliders:       

vnmrj mouse function

1. Optimizing lock

a) Select the Standard page under the Start tab, click the Solvent drop-down menu and select the solvent you are using.  Click the Find z0 button. [Do Not Click the Gradient Shim button!!!]  Select the Lock page in the Start tab.  If lock is On (status shown is either NotReg or Regulated), click on Lock Off, then click Lock Scan to open the lock display.  The line that crosses the spectral window represents how close the deuterium resonance field is to the lock frequency.  When the two are matched, the line should be flat.  The poorer the match, the greater the number of sine waves in the line.

b) Adjust the lock Gain to the maximum setting (=48) and the lock Power to a proper value in accordance with the solvent by mouse clicking the button or dragging the slider bars.  Adjust Z0 by mouse clicking the button or dragging the slider bar until the lock signal changes from a sine wave to an essentially flat line (looks like a step function or a square wave).  Click the Lock On button.  Adjust the lock Phase to achieve the maximum Lock Level.  Once the Z0 field is optimized adjust the lock Gain such that the Lock Level is at about 50%.

vnmrj lock resonance

If you have difficulty matching the ON RESONANCE condition, you may need to recall the default shimming file and start over.

To recall the default shimming file, click the Locator Statement button vnmrj magnifying glass(magnifying glass icon).  Go to Sort Shimsets and select by probe & shims.  Select the 4Nuc shim set and drag-and-drop it onto the graphics canvas.  Select the Lock page in the Start tab and click the Load Shims into Hardware button.

2. Shimming on the lock signal

Start by selecting the Shim page in the Start TabAdjust Z1 by mouse clicking the button or dragging the slider bar until the lock level is maximized.  Next, adjust Z2 to maximize the lock level.  As these two shims are coupled, iterate back and forth between Z1 and Z2 until you can no longer increase the lock level.  If the lock level goes off the top of the lock display window, decrease the lock gain until the lock level is ~70%, start shimming again. 

IV  Setting up and running NMR experiment

1. Selecting an experiment

VnmrJ provides you with several ways to choose and load an experiment.  This section describes two, from the Locator (a) or from a saved data file in your folder (b).

a)   Click the Locator Statement button vnmrj magnifying glass , go to Sort Protocols and select for liquids experiments.  Click on an experiment in the Locator and drag it into the graphics canvas (or double-click on the experiment). 

b)   Go to File on the menu bar and select Open.  Click on a data file and drag it into the graphics canvas (or double-click on the experiment).                

2. Selecting the solvent

Select the Standard page under the Start tab.  Click the Solvent drop-down menu and select the solvent you are using.  Enter text in the Comment box if you want.

3. Setting up the acquisition parameters and starting the acquisition

a) Click the Acquire tab and select the Default page, by clicking on the drop-down menu, set up the spectral width, relaxation delay (3 sec.), and number of scans (n=8*).  Select the Acquisition page, select Auto for Receiver Gain.  Click the green Acquire button to start acquisition.  To abort acquisition, click the red Stop button.

4. Saving the data

Go to File on the menu bar and select Save as …  Navigate to your Directory (/data/user name), type the file name in and click Save.

If you want to view the spectrum before the acquisition has finished, type wft aph.

V  Processing data and plotting a 1D spectrum

1. Fourier transform

Click the Process tab and select the Default page. Select exponential under Weighting and click on the Auto Process button to display the spectrum.  Click the Display scale button vnmrj scale to display the scale.

2. Graphics control buttons

 vnmrj graphics controls

To the left of the display is the spectral display graphics control buttons.  Use the buttons in combination with the mouse buttons for complete interactive control of the displayed spectrum.

3.   Zooming – In/Out using the mouse

To expand a region, click the Cursor button vnmrj single cursor , place the cursor at the left side of the region of interest, then place the right cursor by clicking the RMB. Select the Expand button vnmrj expand .  You should now see the expanded region on the screen.  Click the same button again to go back to a full spectrum. To automatically adjust the vertical scale, type vsadj.  By clicking the MMB you can manually adjust the vertical scale.  To increase the height of the spectrum, click the MMB above the peaks of interest.  To decrease the scaling, click below the peaks.

4.   Phasing

By clicking the Auto Process button, the Fourier transform and auto-phasing of the spectrum has been done.  If auto-phasing does not work properly, manual phasing must be performed.

a) To start phasing, click the Phase button vnmrj phase .  Click above a peak near the right edge of the spectrum.  Adjust the phase of the peaks between the cursors by clicking and dragging up or down with the LMB (coarse) or the RMB (fine) until the peaks are properly phased (pure absorption line shape). 

b) Once the peaks on the right side of the spectrum are properly phased, click above a peak near the left edge of the spectrum, and drag up or down to phase these peaks properly. 

c) When the spectrum is phased, click the Cursor vnmrj single cursor or the Box  button vnmrj box .

5.   Calibrating the chemical shift

Click the Process tab and select the Default page.  Zoom-in on the reference peak, click the reference peak to move the cursor to that peak and click the Find nearest line button under Display.  Under Reference cursor to, select ppm and enter the reference value followed by <return>, the spectrum will be calibrated and re-displayed.  To reset zooming to the full spectrum, click the full display button vnmrj full display .

6. Integration

a)   Click the Set integrals button vnmrj integral display to display the partial integrals picked up by VnmrJ. If you are satisfied with the partial integrals and want to print the spectrum with the integral values under the axis, proceed to section (d).

b)  To print the spectrum with the full integral, type cz and adjust the integral height by clicking the MMB above or below the integral curve (or type isadj ).  Select Plot page, click the Automatic Plot Page button. 

c)   To manually do partial integration, type cz and expand a region of interest.  Click Integral resets button vnmrj set integrals . Click the LMB on the left then the right for every peak you want integrated.  Click the Full integral button vnmrj full integrals three times to display the partial integrals.          

d)   To calibrate a given integral, select the Integration page and place the cursor over the desired region.  Select Single Peak under Set Integral Area and type in the value in Integral Area, click the Set Integral Value button to show the integral list.  Click the Show Integral Value button to display the integral values under the spectrum.

e)   To print the spectrum with the integral values under the axis, select Plot page, click   the Plot Spectrum and the Plot Spectrum Scale buttonsUnder Integral Values, select Plot Scaled and click the Plot Page button.

7. Peak picking

a)   Click the Process tab and select the Display page.  

b)   Click the Peak Threshold button vnmrj threshold .  This will display a yellow horizontal line that can be dragged up and down using the LMB to set the appropriate level for peak picking.

c)   Once you have set the threshold, click the Find Peaks button to pick all peaks above the threshold line and display those frequencies.

d)      To print the spectrum with peak picking, go to the Plot page and click the Plot Spectrum and the Plot Spectrum Scale buttons.  Under Plot Peak Frequencies, select On Peaks or As a List and click the Plot Page button.

VI  Logging out

  1. Click the Start tab and select the Standard page, click the Eject button to eject your sample. Remove your sample from the spinner and position the reference sample properly in the spinner using the depth gauge.  With the eject air still on, place the sample and the spinner into the top of the magnet.  Click the Insert button to insert the reference sample.
  2. Go to File on the menu bar and select Exit VnmrJ to close the window.
  3. Click Actions in the top bar and select Log Out, then click the OK button.
  4. Sign the logbook with time out.

Inova 300 Console Reboot

Reboot the console if:

  • The spectrometer ignores your command to start an acquisition or to eject the sample.
  • The spectrometer queues your acquisition even though no acquisition is currently running.
  • The lock signal is a strange-looking series of vertical lines.

 

  1. Exit vnmrj. With the right mouse button pressed, select "Open Terminal".
  2. Within the terminal window type su acqproc<return>. The system will respond with "Stopping Acquisition Communication". Wait until the system displays a new prompt before proceeding.
  3. Open the left door of the console. Locate the "Magnet/Sample Regulatio" module (8 slots to the right of the left edge), depress the RESET button. Then press the RESET button on the CPU module (the left most board). You will see the LED on the "Magnet/Sample Regulation" module turn red. Wait until it turns green and you see the LEDs on the remote status module (The unit sitting to the left of the computer monitor) cycle.
  4. Return to th eterminal window and type su acqproc<return>. The system responds with "Acquisition Console at x00 MHz Ready". Press <return> to get the prompt, type exit to exit the Unix terminal shell. Type load='y' su<return> on the vnmrj command line. The system should display a message "setup complete". If is doesn't try exiting vnmrj and repeating the above proceedure. It it still doesn't work contact one of the NMR Facility Staff.

 



Common Commands and Parameters

Sample

e   eject sample

i   insert sample

Acquisition

nt   number of transients to collect                                          

np   number of data points                      

sw   spectral with in Hz                                                

pw   pulse width in micro seconds                      

at    acquisition time in seconds

d1   first delay that allows the magnetization to equilibrate prior to initiating another pulse sequence

tn   transmitter nucleus         

dn   decoupler nucleus         

tof  transmitter offset (center of the spectrum)

dof  decoupler offset

ga   acquire and process data when nt scans are complete

go   acquire data and do nothing when nt scans are complete             

aa   abort acquisition immediately

sa   stop acquisition after end of phase cycle

ra    resume acquisition (stopped by sa)

bs   block size

Processing

ft   fourier transform the data and display the spectrum

wft   do a weighted fourior transform of the data and display the spectrum                                                         

lb   exponential line broadening applied when using wft. For C13 lb=3, for H1 lb=0.1-0.3

aph   automatic phase adjustment 

Display                                               

dg   display parameter group in screen

ds   display spectrum on the screen

dscale  draw a scale under the spectrum

vsadj  adjust vertical scale

cz   clear integral resets

Plotting

pl   plot spectral display

pscale  plot scale

pap  plot all parameters

ppf  plot peak frequencies

pll  plot peak list

pir  plot digital integral values below the scale

pltext  plot text associated with file

page  send plot buffer to plotter (e.g. pl pscale ppf pap page)

Misc.

jexp#  join experiment, you can have multiple acquisition blocks each containing different parameters

movesw  move spectral window according to the right and left curser positions

movetof  move thr transmitter offset to the curser position which now becomes the center of the spectrum

 

More Information

General Campus Information

University of California, Riverside
900 University Ave.
Riverside, CA 92521
Tel: (951) 827-1012

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Facility Information

Nuclear Magnetic Resonance Facility
Chemical Sciences Bldg.

Tel: (951) 827-3628
Fax: (951) 827-4713
E-mail: danb@ucr.edu

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