NMR Spectroscopy with VnmrJ
University of Toronto, Department of Chemistry
Walk-up interface
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Logging in
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Starting VnmrJ
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Inserting sample into the magnet or sample changer
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Enter sample information
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Experimental Protocol Tabs
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Select Experiments from the Experimental Protocol Tabs
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Changing acquisition parameters
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Submit Study Queue
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Submit another sample
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Follow progress of spectra
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Data saved automatically
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Processing 1D data
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Load FID
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Spectra Display tools (from Varian)
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Command line
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Using the mouse
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Expansions
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Display
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Manually phasing the spectrum
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Referencing a peak
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Baseline correction
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Integrating
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Threshold
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Plotting spectra
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Log out
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Online help
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Advanced topics
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Manual locking
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Gradient shimming
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Shimming
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August 21, 2006 5:31 PM
Walk-up interface
Logging in
Log into Solaris. You will have your own username and password. Do not use another person’s username and password and do not share your username and password. Shared accounts will be deleted.
Starting VnmrJ
In Solaris, click on the VnmrJ icon in the CDE bar:
Inserting sample into the magnet or sample changer
• Use clean NMR tubes
• The optimal solvent height is 4 cm; use about 750 µL of solvent in a 5-mm tube
• For best shimming, the sample should be free of undissolved particulate material
• Filter the sample, if necessary, through glass wool or celite
• Put the sample part-way into the spinner then position in the depth gauge
• Take care not to break the tube when putting into the spinner
• If the solvent height is shorter than recommended, pull the tube up to centre the sample on the middle line
• Turn the eject air on by pressing the Eject button (Start tab, Study page)
• The air should be on: Do not proceed if the eject air does not turn on!
• Put the sample into the magnet upper barrel. It should float at the top now
• On the Varian 400, do not touch or rotate the carousel sample changer
• Click Insert: The sample drops in a controlled manner into the magnet
Enter sample information
Put the sample information into the study. Go to the Start tab, Study page:
• Enter sample identification in the sample field; this will be used in the name of the saved FID
• Do not use characters other than a-z, A-Z, 0-9, hyphen, underscore and space
• Enter Notebook and Page, if desired
• Select the solvent from the popup menu
• Check Find z0 and Gradient Shim for automatic lock and shim
• For manually locking and shimming, go to the section Advanced Topics
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Experimental Protocol Tabs
Select experiments from the Experimental Protocol tabs:
• Std1D: One dimensional experiments
• Proton, Carbon
Homo
2D: Two dimensional homonuclear experiments
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• COSY, ROESY
Hetero
2D: Two dimensional heteronuclear experiments
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• Ghsqc,
Sel1D:
One dimensional selective excitation experiments
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• Roesy1d
Dosy
2D: Two dimensional diffusion experiments
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Experimental Protocols
Select Experiments from the Experimental Protocol Tabs
• Select each experiment by single clicking on the Experiment protocol button
• Multiple experiments can be run on the same sample by clicking on the desired
experiments
• Queued experiments are shown in the Study Queue underneath the Experiment protocol buttons
• Experiments are run in the order queued
• The order may be changed by dragging to re-arrange
• Experiments can be deleted by dragging to the Trash icon
Study Queue
Changing acquisition parameters
• Double-click on the time field in the Study Queue of the experiment you want to customize
• All changes must be made before the sample is submitted
• Click on the Acquire tab and select the Default page:
• Change the number of scans depending upon the concentration of the sample and how long you want the experiment to run
• The Show Time button shows the amount of time the experiment will take to run
• Change the spectral width to include the peaks expected
• On the Varian 400, peaks outside this range do not appear at all!
• On the Unity, Mercury and Gemini spectrometers, peaks outside this range will appear out of phase and folded
into the opposite side of the spectrum
• Change the relaxation delay if accurate integration is required
• Double the delay and compare relative integration–there should be no change if the delay is sufficient
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Submit Study Queue
• Click the Submit button to start the experiment
• The experiments run in the background and shown only when finished
• The red Stop button in the “Acquire” tab stops the experiment in progress
• After the experiment is finished, dragging the Study Queue to Trash deletes the data!
Submit another sample
• Another sample can be submitted after the first one is done
• If there is no sample changer, the samples have to be ejected and inserted manually before submitting
Follow progress of spectra
• Double click on the time field of the experiment while the experiment is running
• Click on “Transform all” in the Default page of the Process tab
Data saved automatically
• The data is saved automatically, using the format “Date-samplename-experiment-number”
• For example, 20060224-mysample-Proton-001
• For automatic 2D processing and plotting do not change the FID names
Processing 1D data
Load FID
• To load a FID, drag the file from the File Locator to the Graphics canvas:
• Completed experiments from the Study Queue can also be dragged to the Graphics canvas
• Processing is done automatically
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Spectra Display tools (from Varian)
• Cursor or Box
• Box
• Changes to the box mode with two cursors.
• Cursor
• Changes to the cursor mode with one cursor
• Expand or full display
• Expand
• Expands the area between the cursors
• Full
• Displays the full area
• Set integrals
• The first click displays the integral function buttons and selects partial integral display
• The second click displays the No Integral and Clear Resets buttons
• Full integral
• Displays all integral regions
• Integral resets
• Opens interactive integral reset mode
• The left mouse button defines an integral reset at the current mouse position
• The right mouse button removes an integral reset closest to the current mouse position
• The middle mouse button adjusts the vertical scale
• No Integral
• Turns off display of the integral
• Integral Lvl/Tlt
• Opens interactive zero- and first-order baseline correction mode
• Display Scale
• Displays a frequency scale under the spectrum in units specified on the Display page, usually ppm
• Grab and Move
• Opens the interactive spectral windowing mode
• Use the left mouse button to adjust the start of the display and move the display left or right
• Use the right mouse button to adjust the width of the display
• Threshold
• Toggles the display of a horizontal cursor
• The left mouse button positions this cursor at the mouse arrow position
• The middle mouse button adjusts the vertical scale
• Phase
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• Opens the interactive phasing mode
• Use the left mouse button for coarse adjustment
• Use the right button for fine adjustments
• See Phasing the spectrum, below
Refresh
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• Redraws the Graphics canvas.
Return
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• Returns to the last menu
Command line
To type commands, pull down the command line:
Using the mouse
• The three mouse buttons control the cursors and the vertical height of either the spectrum or the integrals
• The left mouse button controls the left cursor and moves the right cursor if in box mode
• The right mouse button controls the right cursor (the delta)
• The middle mouse button controls the vertical scale of the spectrum (if “No Integral” is selected)
• If an integral is displayed (the middle value says is), the middle mouse button scales the integral
Expansions
• When both vertical cursors are shown clicking the expand button
expands the horizontal scale between the cursors
• When one cursor is shown the expand button becomes the full button
and shows the entire spectrum in the horizontal dimension
Display
• Click the Autoscale button to scale the tallest peak into the screen
• Click Full Spectrum to see the full spectrum horizontally
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Manually phasing the spectrum
• Click on the Phase icon
• Click on the right-most peak with the left button and keep the mouse button pressed
• Phase that peak by dragging the mouse up and down, with the button pressed
• The left button is coarse and the right button fine adjust
• Phase only the right hand peak
Click
on the left-most peak and phase as you did for the right hand side
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• Phase the left hand peak
Referencing a peak
• Select a peak by centering the cursor on peak
• In the Default page of the Process tab, choose one of
• “Reference By Solvent” or
• “By TMS” or
• Click “Find nearest line” then put value in “Reference cursor to”
• Select ppm first if your are referencing to a value in ppm (like 7.26 ppm)
Baseline correction
• For linear baseline correct click the DC Correct button.The edges of the spectrum as displayed must be flat.
• For non-linear baseline correct (when the baseline is curved), integrate all peaks (Find Integral button does this
automatically) then click BC Correct.
Integrating
, then Integral Resets
• Click on the Set Integrals tool
• Integrate spectrum by:
• Left click cuts the integral
• Right click removes the cut nearest the click
Select
the Integration page in the Processing tab
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• Put cursor over integral trace
• Click Set Integral Value
• Click Display Normalized Integrals
Threshold
• Click on the Threshold button
• Left click to adjust the threshold to intersect with the peaks to be picked
Plotting spectra
• Select the Plot page of the Process tab
• Click Automatic plot page
• OR click as desired:
• Plot Spectrum
• Plot Spectrum Scale
• Plot Text
• Select one of Plot Peak Frequencies:
• On Peaks
• As a List
• None
Plot
Integrals
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• Plot Normalized (integral values”)
• Plot Page
• Note: Plot Page prints those options previously clicked
Log out
• Exit from VnmrJ (Utilities menu>Exit)
• In Redhat Linux:
• Select the Actions>Log Out in the top menu
• In Solaris:
• Click Exit in the CDE bar
• Do NOT use Switch Operators if you logged into Solaris or Redhat
• Use Switch operators on the Sample Changer computer
Online help
• Online help is available from the Help… menu in VnmrJ
• Firefox is launched and a searchable help is shown in the browser
• Select Liquids in the menu:
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Advanced topics
Manual locking
Find the resonance of the deuterated solvent by scanning z0:
• Click the Find z0 button to rapidly find the resonance (not available on Gemini or Unity)
• The Message window shows the new value of Z0:
• Select the Lock page in the Start tab
• Click Lock Scan button to turn on the lock display
• Set Lock Phase, Lock Gain and Lock Power appropriately (refer to values by the spectrometer)
• Keep the lock power low: a change of 6 in the lock power should result in a change of factor of 2 in the lock
level. Decrease the lock power by 6. If the lock level is not ½ of the starting value, the lock power is too high.
• Turn the lock off
• Scan z0 to find the resonance exactly
• If you did not use find z0, the sine wave indicates the distance from resonance
• The yellow line should be maximum and the blue line minimum
• Drag the z0 slider or use ±10 or ±100 button
• Using the mouse:
• Right click increases by the value shown on the button
• Left click decreases by the value shown on the button
• Middle click changes the value shown on the button between 1, 10 and 100
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• Turn the Lock on, adjust the Lock Gain and Lock Power so the lock level is between 50 and 90.
• Click Lock Scan button to turn off the lock display
Before Locking
After Locking
Gradient shimming
Use gradient shimming when possible. Click on the Gradient Shim button. When the shimming has finished, the
Message window (bottom right) will show a message:
Shimming
Select the Shim page under the Start tab:
• On the Varian NMR System 400, there are 24 shims. On the Varian Mercury and Gemini spectrometers, there are 14
shims.
• The Varian Unity, Mercury and Gemini spectrometers have Z1C and Z1 and Z2C and Z2
• The Varian NMR System 400 does not have Z1C and Z2C
• Z1C is 50×Z1, Z2C is 50×Z2
• On the Varian Mercury and Gemini spectrometers, use Z1C and Z2C
• Spin the sample when shimming Z1 to Z6 (usually Z1C and Z2C or Z1 and Z2 are used)
• Do not spin the sample when shimming any shim that has X or Y components (not routinely used)
• The lock level is represented by a clock
• The hour hand (shorter hand) represents the lock level, from 0 to 100
• The minute hand (longer hand) is used to see the lock change as the shims are changed
• The lock level is shown the middle of the clock
• Clicking the blue dot shows the highest level of the lock level
• The lock should not be saturated (with too much power)
• Decreasing the lock level by 6 should change the lock level by a factor of 2
• Using the mouse buttons:
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• Right click increases by the value shown on the button
• Left click decreases by the value shown on the button
• Middle click changes the value shown on the button between 1, 10 and 100
• Iteratively shim:
• Change Z1 by +10 or -10. If the lock level increases, continue in that direction
• If the lock level decreases, go the opposite direction
Continue
changing Z1 until the lock level is maximized
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• Some solvents (methanol, acetone) have a very slow response, so change the shims slowly–wait until the lock
level stops changing before clicking the shim button
• Change Z2 by +10 or -10 and continue in the direction that increases the lock level until the lock is maximized
• If the lock level reaches 100, decrease the lock gain and continue
• Return to Z1 and maximize the lock level, then use Z2 to maximize the lock level
• Iterate between Z1 and Z2 until the lock level is maximum, use ±1 as necessary
• If the lock level reaches 100, turn down the lock gain and continue
Adjust
the lock phase if a large change is made to either Z1 and Z2, the lockphase may be needed to be
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changed several times during shimming
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