St. John Fisher College
Bruker DPX-250 FT-NMR Spectrometer
revision 2.08.2000, ljs
Routine manual spectrum
A. Logging on Note: All mouse clicks are done with the left mouse button unless otherwise specified.
1. Double click on "pchem" in the login window. Enter the pchem password, and hit enter on
the keyboard. If you want a clock, go to "find" in the toolbox window, then icon cat?, then
desktop tools?. If the "desktop" has two UNIX windows, proceed to step four.
2. To obtain a UNIX window, click on "desktop" in the toolbox window; release on "unix
shell". A new window will appear. Drag the mouse to move the window to a convenient
location near the top of the screen; click the mouse to make the window active. Make the
window as small as the clock or a small square; all it will be used for is to run the NMR
program, XWINNMR. [This will be called the main XWINNMR window.]
3. Repeat step 2 to open a second UNIX window. Move it off to the left hand side of the
screen. This window will most likely not be used during your NMR session; it is created so
that if a problem occurs during the NMR session, there is an open UNIX window through
which we can communicate with the computer. [This will be called the large UNIX
window.]
4. Move the cursor to the small upper UNIX window. Type "xwinnmr" to open the main
XWINNMR window. When prompted by a rectangle, position the XWINNMR window so
that a part of the larger UNIX window is still visible before clicking the mouse to activate
the XWINNMR window. (Covering the large UNIX window totally will prevent its use if a
problem should arise.)
B. Sample preparation
1. Your sample should have been prepared in a precision NMR sample tube using a deuterated
solvent. Use at least 0.5 mL solvent to get a good signal.
2. Insert the sample tube into the sample holder, adjust the depth of the tube using the depth
gauge, and wipe the tube and sample holder with a kimwipe.
3. Make sure that the black cap that covers the top of the magnet bore is off. If the cap is on,
take it off.
4. On the keypad, turn "Lift on/off" to on by pressing the lift key. ("Lock on/off", "spin
on/off", "sweep on/off" and other keypad lights should all be off.)
5. When you hear the swooshing sound that indicates that the lift air has come on, place the
sample tube plus holder into the magnet bore. Hold onto the sample tube until you feel
that the tube is being kept aloft by the cushion of lift air beneath it. You should be certain
that the tube is being supported by the cushion of air before letting go of the tube. Under no
circumstances should you let go of the tube unless it is supported by the cushion of air.
6. Turn "Lift on/off" to off. Listen for the lift air to slowly turn off and for the clunk that
comes as the sample tube settles into its place in the probe at the position inside the magnet
where the magnetic field is most intense and homogenous.
7. If you wish to spin your sample, turn "spin on/off" to on. [We have been told that spinning
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St. John Fisher College
Bruker DPX-250 FT-NMR Spectrometer
revision 2.08.2000, ljs
is unnecessary for 1H and 13C spectra.] While the sample is coming up to the spin speed
that is preset in the keypad, the spin light will blink. When the tube reaches a final, steady
speed, the spin light will be steady. To monitor the spin rate, press the "second function"
key and then the "spin meas." key. The keypad will display both the preset spin rate and the
actual spin rate. Press standby to remove the spin measuring function.
C. Locking and shimming
1. Type "rsh 5mmbbo". This command reads in default shim settings from a computer file
named 5mmbbo. (We have a 5mm diameter, broadband output probe.)
2. Type "lock". A list of solvents will be displayed. Click on the solvent used in your sample.
3. Click on the "windows" menu (at the top of the XWINNMR window) and release on
"lockdisp" to get a window that monitors the lock signal. When the instrument locks, the
lock signal will rise in the lock window and the lock light will glow steadily on the keypad.
4. The main shim fields to optimize are the Z and Z2 fields. To shim Z, press "Z" on the
keypad. This makes the keypad knob a Z-control. Rotate the knob in whichever direction
causes the lock signal to maximize. If adjustment causes the lock signal to move off the top
of the screen, press "lock gain" on the keypad, and use the knob to bring the lock signal
back onto the screen. Then press "Z" again to continue shimming. If an adjustment in z
only leads to a worsening of the signal, pressing "Z" will return the Z shim to its original
setting. Pressing any other key will cause your most recent adjustment to be saved.
Alternately press "Z" and "Z2", adjusting each until no further improvement in the lock
signal is seen. Press "Standby" on the keypad. Click on the top bar of the XWINNMR
window to bring it to the front of the screen.
D. Loading a preexisting set of parameters
1. Pull down the "File" menu and open a data set whose parameters are close to those you
want to use.
If you remember the name of a data set whose parameters you want to duplicate, e.g.
Schwartz 10 1, you can simply open that set with its parameters by typing "re Schwartz 10
1". Or, you can type "edc" (edit current data set) and input the name, expno, and procno
there. Once opened, these parameters are the ones that will be operative once an
experiment is begun. If you do not know of a pre-existing file, you can type "rpar" (read
parameters) and select "proton" which loads in standard proton parameters or "c13cpd" (cpd
stands for composite pulse decoupling) which loads in standard decoupled carbon
parameters.
2. Type "edc" (edit current data set) to put a new name, experiment number, and/or process
number on the data you will be generating.
3. Type "eda" (edit acquisition parameters). Input your solvent, and toggle "prosol" to true.
These two parameters must be set before running the experiment, and eda is the only place
to set them. However, eda displays all possible acquisition parameters, so it may be
overwhelming to search through it to check or modify other parameters for the experiment.
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St. John Fisher College
Bruker DPX-250 FT-NMR Spectrometer
revision 2.08.2000, ljs
The simplest thing to do is to leave "eda" after inputting your solvent and toggling prosol,
and type "ased" to display only the values of the parameters that are relevant for the pulse
sequence you have chosen. You may change them as desired in ased. Note that every time
you enter eda, the solvent can change, and prosol toggles to false; it is simpler to stick with
ased for the rest of your session.
4. Type "rga" (receiver gain adjustment). The spectrometer does a quick experiment on your
sample to find the optimum receiver gain to use in the real experiment. Ignore the scary
estimate of the time that the computer says this process will take. When the adjustment has
been made, the display will read "rga: finished".
5. If you wish to check the probe tuning, this is the time to do it. Go to the "acquire" window.
Type "wobb". Tune the probe to optimize the display. Type "stop" when done. Re-do
"rga".
6. Type "zg" (zero, go) to begin your experiment. To watch the FIDs (free induction decays)
as they are averaged together, click on the "acquire" menu and release the "observe FID
window". (You can enter the FID window before typing "zg".) When the experiment is
complete, the display will read "checklockshift: finished".
E. Processing the data
1. Type ef (exponential multiply, fourier transform) to smooth the FID (increasing signal to
noise at the expense of some line broadening) and Fourier transform it. To check the value
of the line broadening that will be used, before typing ef, type "lb" and either type in a new
value or accept the given value by hitting return.
2. At any point in the following, to change the displayed spectral width, click the left mouse
button with the cursor in the data field and use the right mouse button to mark the desired
endpoints of the spectrum. Click the left mouse button to return the mouse to its usual
functions.
3. a. Manually phasing the spectrum.
a. In order to phase the spectrum, it is helpful to be able to see the baseline clearly by
temporarily increasing the amplitude. Use the "*2" button to double the spectrum
amplitude and the "/2" button to cut it in half.
b. Enter the phasing mode by hitting the "phase" button. After increasing the amplitude
several times, click on "biggest". A dotted line will appear at the base of the highest
peak in the spectrum. This peak is the point where the zero order phase correction will
be applied.
c. Click and hold down the mouse button on the "PH0" button (zero order phasing). Roll
the mouse up and down to adjust the phase, mainly at the chosen peak. Release the
mouse button when the phasing of the chosen peak looks good. Click and hold down
the left mouse button on "PH1" button (first order phasing). Roll the mouse up and
down to further adjust the phasing, mainly at the end of the spectrum farthest from the
chosen peak. Release the mouse button when the phasing of the rest of the spectrum
looks good. You may need to alternate a few times between PH0 and PH1 to get the
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St. John Fisher College
Bruker DPX-250 FT-NMR Spectrometer
revision 2.08.2000, ljs
best final overall phasing.
d. Click on "return" and click on "save and return".
3. b. Automatically phasing the spectrum. Typing "apk" automatically finds the "best" phasing
parameters, which are then saved. Typing "pk" phases the spectrum using the phasing
parameters from the previously phased spectrum.
4. Calibrating the spectrum
5. Integrating the spectrum.
a. Enter the integrate mode by clicking on the integrate button.
b. If you wish your integrals to be scaled to a previously integrated spectrum, click on
the "lastcalc" button.
c. Click on the left mouse button while in the data field to change the mouse into a
cursor. Click the middle mouse button to anchor the cursor on the left and on the
right of each peak that you wish to integrate.
d. To choose a peak for calibration, click the left mouse button to remove the
anchoring function from the mouse. Move the cursor onto the chosen peak and
press the left mouse button. A star will appear at the top of the integral of the chosen
peak. Press the calibrate button and enter the value you wish for the chosen integral.
e. To change the slant of an integral, hold down the "slope" or "bias" button after
choosing an integral, and roll the mouse up and down until you are satisfied with the
integral shape.
f. Click on "return" and choose "save as 'intrng' & return" to save the integrals for
plotting.
6. Peak picking. Click on "analysis", choose "peak picking" and then choose "list".
7. Titling the spectrum. Type "setti" (set title). Activate the window that appears. Type in
your title, using backspace to correct mistakes. Click on "save" and then on "quit".
8. Plotting the spectrum.
a. After you have manipulated your spectrum so that it appears on the screen as you
wish to plot it, click on the "output" window. Choose "define/show plot region".
Choose "Retain CX, Auto-adjust Hz/cm". Hit "enter" after each of the three
parameters you are shown. Click of "okay" to the error message that comes on.
b. For no scaling (constant noise height), make sure that PSCAL is set to "noise" and
then set CY equal to the height (in cm) for the noise to be plotted.
c. Type, "plot" and hit "enter." (Or, click on the output window, choose "plot
commands", and "plot".)
F. Logging out
1.
2.
Click on the "file" toolbar and release on "exit".
Press the right mouse button and choose "logout".
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St. John Fisher College
Bruker DPX-250 FT-NMR Spectrometer
revision 2.08.2000, ljs
G. Removing your sample
1. On the keypad, turn "Lock on/off" to off. The lock light on the keypad should go off. Turn
off spinning the same way.
2. Press "Lift on/off". The light will go on, and you will hear the sound of the lift air come on.
3. Retrieve your sample.
4. Turn off the lift air by pressing the "lift on/off" button. The light will go off.
5. Replace the black cap on the magnet bore.
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