Basic NMR Operation
The purpose of this guide is to provide instruction on the basics of obtaining and plotting an
nmr spectrum. For more advanced operations, refer to the Varian manuals, or consult someone
with the relevant experience.
The basic steps to obtain a spectrum are:
1. Log in.
2. Launch VNMR.
3. Setup the basic parameters.
4. Acquire the data.
5. Process the data.
6. Process the spectrum.
7. Plot the spectrum.
8. Log-out.
1.
Log In
The monitor should be on, but will likely be in powered down. Jiggle the mouse to get the
log-in screen. If you see a message requesting a particular user's password, someone else is
already logged in.
To log on, type your account name, and when prompted your password. When you are
logged in, the VNMR software will be automatically loaded.
2.
Launch VNMR
At the bottom center of your screen is the CDE (common desktop environment) toolbar. Just
to the left of center is an icon that resembles a spectrum of methyl propionate. Clicking that icon
will launch VNMR
3.
Experiment Setup.
Place your sample in the spinner and adjust it to the proper depth using the gauge on the leg
of the magnet. Setup the standard parameters by clicking the [Setup] button. If your solvent is
CDCl3, then click the [H1, CDCl3] (or [C13, CDCl3]) button. If you are using another solvent,
click the [Nucleus, Solvent] button. Click the [H1] (or [C13]) button and then the button for
your solvent. The standard parameters for you experiment will then be automatically setup, and
the parameter window will be brought to the foreground.
By default, the number of transients (scans) is set to eight (8). If your sample is dilute, you
may wish to increase the number of transients. This is done by typing nt=32 (you may use any
number, but nt should be a multiple of 4).
Type e to eject the standard sample from the probe. Replace the standard sample with
yours, and insert your sample into the probe by typing i. The lower window has several tabs on
the right side. Click the one labeled 'Flags and Conditions.' Make sure the 'on insert' button is
checked under Autolock and Autoshim. You are now ready to begin acquisition.
3.
Data Acquisition.
Click the [Acquire] button.
If nt = 16 (or less), then click [Go, Wft].
If nt > 16, the click [Go, Periodic Wft].
The computer will optimize the lock signal and then shim the magnetic field (This
autolocking and shimming is done only if the sample has been changed since the last locking and
shimming.) When the locking and shimming are complete, data acquisition will begin. Progress
can be monitored by watching the top line, STATUS, in the ACQUISITION STATUS window.
Once the status is listed as Acquiring, you can monitor the number of transients (scans)
completed by watching the CT: item.
Once the acquisition is completed, the data will be weighted and fourier transformed, and the
spectrum will be displayed. If you initiated acquisition with [Go, Periodic Wft], then the data
will be weighted and fourier transformed after every 16 transients. You may process the
spectrum while additional transients are being acquired.
4.
Data Processing
Data processing involves weighting the data and fourier transforming the data. This is done
automatically if you follow the procedure above. If, after the data collection is done, you see a
spectrum, you can skip to Section 5. If for some reason you need to process (or reprocess) the
data, Click [Process], [Weight, Transform]. This will weight and fourier transform your data
and display the resulting spectrum. Any spectral processing you may have done should be
retained, although any weighting functions you may have applied will be over written.
5.
Spectral Processing.
There are several types of spectral processing one may wish to perform, these include:
phasing, expanding regions, integration and peak picking. These are accomplished while in the
[Interactive] mode. This mode can be entered by either clicking [Display] [Interactive] or by
typing ds in the command line. Generally, the manipulation will be more easily carried out if the
spectral window is enlarged. This is done by clicking [Resize] in the upper menu bar, followed
by [Interactive].
Displaying Spectral Scale.
To display the scale below the spectrum, either type dscale in the command line, or click
[Dscale] while in interactive mode.
Adjusting Vertical Scale.
There are two methods of adjusting the vertical scale of the spectrum, using the command
line or the mouse.
With the Command Line
Type vs=(value), where value is a number. The default value is 200.
With the Mouse
Place the pointer on a peak and click-drag the center mouse button up or down to increase or
decrease the scaling. Caution - doing this over the baseline will result in the scaling being
increase such that the noise in the baseline will be flush with you mouse pointer. To recover,
move the pointer to a peak, and click drag down until the scaling is correct (or use the command
line to set the vertical scaling).
Expanding Spectral Region.
To show the full spectrum, click [Full].
To expand (or zoom in on) a particular region, click the left mouse button to the left of the
region you wish to expand. This will bring up the left cursor. Right click on the right end of the
region to bring up the right line cursor. The region bracketed by the two line cursors can then be
expanded by clicking [Expand], which appears whenever both cursors are displayed. The left
cursor can be moved with the left mouse button, while the right cursor is moved with the right
mouse button. Bear in mind that if both cursors are present, when the left cursor is moved, the
right cursor with move with it.
Phasing.
The baseline of the spectrum should be flat and symmetrically disposed on either side of each
of the peaks, as shown in the spectrum on the right. If the baseline about the peaks is
asymmetrical, as shown in the left spectrum (esp. in the downfield peaks), then the spectrum
requires phasing.
2.4
2.2
2.0
1.8
1.6
1.4
1.2
1.0
0.8
0.6
0.4
0.2
0.0
SF: 300.08 MHz SW: 4500.45 Hz AQ: 1.50 seconds
TD: 16384 points
Scale units: ppm
2.4
2.2
2.0
1.8
1.6
1.4
1.2
1.0
0.8
0.6
0.4
0.2
0.0
SF: 300.08 MHz SW: 4500.45 Hz AQ: 1.50 seconds
TD: 16384 points
Scale units: ppm
Phasing is first applied to the right (upfield) portion of the spectrum, then the left portion.
Click the [Phase] button. Then click on the right-most peak(s) approximately halfway up
the window. That portion of the spectrum will become the active portion (blue), while the
remainder of the spectrum will become inactive (green). The phasing is adjusted by clicking (or
dragging) above or below the horizontal red line. Click above the horizontal red line. If the
phasing improves, continue clicking (or dragging) the mouse pointer higher above the line until
the active region is properly phased. If phasing worsens, click (or drag) below the line until the
active region is properly phased. If small movements of the mouse pointer result in large
changes in the phasing, use the right mouse button (fine adjustment) instead of the left button
(course adjustment).
Once the right most portion of the spectrum is phased, click on the left most peak(s)
approximately halfway up the window. The phase correction applied to the right portion of the
spectrum will then be applied to the entire spectrum and the left portion of the spectrum will
become the active portion (blue), while the remainder of the spectrum will become inactive
(green). Adjust the phasing in this region as you did in the right-most region. When the leftmost region is properly phased, again click on the right most peak(s). If necessary, apply further
phase corrections.
When phasing is complete, type ds to leave phasing mode and return to interactive mode.
Integration.
When in interactive mode, the second button of the lower menu toggles between No Integral,
Part Integral and Full Integral. Bear in mind that the button shows the next item in toggle
sequence, not the current mode.
Cutting the Integral Trace
Click the [Part Integral] button. This should result in a single green integral trace being
displayed above the spectrum. If the trace is broken, or shows only fragments, type cz. To "cut"
the integral trace into fragments, enter the resets mode by clicking [Resets]. Then move your
pointer to the left of the first (most downfield) peak. Cut the trace there by clicking the left
mouse button. The integral trace to the left will become dotted (turned off) while that to the right
will remain solid (turned on). Move the mouse to the right of the peak and cut the trace again.
Now only that portion of the trace between the two "cuts" will be solid (on). Repeat this
procedure for all of the peaks, cutting the integral trace on either side of each peak. For peaks
that are very close together, you may wish to integrate them as a single region. Exit resets mode
by typing ds.
Un-Cutting the Integral Trace
To undo individual cuts, place the pointer at the site of a cut you wish to undo and right click
the mouse. To undo all cuts, type cz (clear zeros). Exit resets mode by typing ds. You can
modify the cuts you have made by re-entering resets mode and making additional cuts, or
un-cutting the trace.
Assigning Integral Values
While in Part Integral mode, you can normalize (assign specific values) to your integration.
If you are in Part Integral mode, you should see your spectrum with the fragment integral traces
above each peak (or set of peaks). Place a cursor on one of the integral regionss by left clicking
with the pointer on that trace. Click [Set Int]. A message will appear giving the current value of
the integral and requesting a new value. Type the new value. The integration for that region will
be set to the value you typed and the other regions will be adjusted proportionately. You can
view the results by typing the commands vp=12 dpir. The values of the integral regions will be
written under the spectrum, so the spectrum must be moved up sufficiently for this task. vp = 12
moves the spectrum up 12 points. dpir will then Display Peak Integral Regions beneath the
spectrum, immediately under each of the regions.
Return to interactive mode by typing ds or clicking [Interactive].
Peak Picking
The VNMR software can automatically find and display the frequencies of the peaks in the
spectrum. To use this feature, you must first set a threshold. Only the frequencies of those peaks
above the threshold will be displayed
To set the threshold, click [Th]. A horizontal yellow line will appear. This threshold line can
be moved up or down with the left mouse button. View the results of the peak picking by typing
dpf (Display Peak Frequencies). If too many peaks are displayed, return to interactive mode
(type ds or click [Interactive]), raise the threshold and redisplay the results.
6.
Spectral Plotting.
To get to the plotting menu, click [Main Menu] [Display] [Plot]. Note that the commands
below only send the various bits of data to the plot buffer. To actually put ink to paper, you must
use the [Page] button (or page command) to send all the plotting info from the buffer to the
plotter to be printed. A few seconds after clicking this button, you should see a message that the
spectrum is plotting, and a few seconds later, you will hear the plotter start to hum.
The [Plot] button (or pl command) will send the spectrum to the plotter buffer. If an
integral trace is active in the display, then the integral trace is also sent to the buffer.
The [Scale] button (or pscale command) sends the scale to the buffer.
The [Params] button (or ppa command) sends a short list (approximately half a column in
length) of selected acquisition and processing parameters to the buffer, to be printed in the upper
left hand corner of the spectrum.
The [All Params] button (or pap command) sends a long list (approximately one and a half
a column in lengths) of the acquisition and processing parameters to the buffer, to be printed in
the left portion of the spectrum. Bear in mind that the list will overwrite the left most portion of
the spectrum.
The [Peaks] button (or ppf command) will print the peak frequencies above the peaks. Be
sure to set the threshold and preview the results with the dpf command (see Sec. 5, Peak
picking) prior to plotting peak frequencies.
Plotting Integral Values
To plot calculated integral values below the spectrum, type the command pir. There is no
button for this command. The spectrum must be at or above a vertical position of 12. This can
be accomplished (before plotting the spectrum) by typing vp=12. If the command dpir
worked, then the vertical position is fine.
7.
Exiting.
To exit and logout, first remove your sample and return the standard sample to the probe.
Make sure the spectrometer is locked on the new sample. If necessary, set up a [1H,CDCl3]
experiment, set nt=1 and click [Go, Wft] to force the spectrometer to lock and shim on the
standard sample.
Type exit in the command line to close the VNMR windows. When VNMR is closed
down, click the small EXIT icon just right of center on the CDE toolbar. Confirm that you do
indeed want to logout. When the login window appears, you are done. The monitor will power
down in about 10 minutes.