New users guide

OPERATING PROCEDURE FOR BRUKER AVANCE
(The steps marked * only need to be done if necessary)
*1. If you are the first user in the morning and if the overnight experiment is a 13 C, and has not
finished, you can stop the acquisition by typing “halt↵”, never type “stop↵”. In all other cases,
let the acquisition continue.
*2. Open the lock display window by selecting:
3. To eject/insert the tube:
a) Click “LIFT-OFF” to eject the tube.
b) If there is no sample or dummy coming out after your first attempt at “LIFT OFF”, ask
someone from the NMR lab to assist you. Do not try to push “LIFT OFF” again or to insert a
sample.
c) Place your tube in the spinner (there must be a little bit of resistance). Adjust the height using
the tube adjustment device. Wipe well the outside of your NMR tube and the spinner. The dirt on
the tubes accumulates inside the magnet and interferes with the rotation.
d) Put the sample in the hole at the top of the magnet and make sure that the tube does not
wobble. There must always be a flow of air.
e) Click on “LIFT-OFF” to insert the tube.
4. To lock and shim:
a) Check that the “FINE” button is alight.
b) Type lock .
c) From the list, select your solvent. (Look for the good lock signal, if there is more than one
deuterium signal in your solvent).
d) Always adjust the shims Z, Z2, X, Y to get the maximum height of lock line.
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On shim unit:
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To access to Z: press buttons On axis and Z
To access to Z2: press buttons On axis and Z2
To access to X: press buttons X and Z0
To access to Y: press buttons Y and Z0
On screen:
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Open the window by clicking on :
With the left mouse button, click on MAIN.
With the left mouse button, click on the shim to optimize by example, Z.
By clicking on step+/step-, with the left button of the mouse, optimize your
resolution until you get the highest lock line level. You can increase or decrease
the sensibility of the button step+/step- by moving the stepsize cursor. If the
height of the lock line is too high, decrease the value of “lock gain" or "lock
power". Select the function and click on button step+/step-.
When the resolution is optimized, then close the bsms control suite. Then the shim unit will be
reactivated.
If the resolution cannot be optimized, type “rsh↵” and with the left button on the mouse, select the
file which corresponds to routine. the probe used (ex. routine.qnp). These files are updated
periodically. Optimize again the shim Z1, Z2, X and Y.
5. To create a new experiment, type “edc↵” (Edit current data).
- Change the “name” of the experiment. The name must start by the characters of your login
name.
- Change the “expno” of the experiment.
- Change the “procno” of the experiment (use the number 1 to avoid confusion).
- “DIR” should be “D”.
- “USER” should be “chimie”.
- Click the left button of the mouse on the OK button.
6. Type “rpar probe.proton all↵” to recall the parameters for 1H spectrum.
ex.: “rpar bbfo.proton all↵” for a 1H spectrum.
* To see a list of all the experiments available type rpar probe.*
7. Type “rga↵”. The gain value is adjusted automatically.
*8.
- If required, change the value of “ns” if the sample is very dilute. Type “ns↵” and enter
the new value followed by ↵.
- To obtain a quantitative integration, type “d1↵” and enter 10 followed by ↵.
- To expand the spectral window, start by typing aq and noting the acquisition time “aq”.
Adjust “sw” to define the new spectral width and adjust “o1p” to define the middle of the spectral
window. Type back “aq” and put back the original acquisition time that you noted previously.
9. Type “zg↵” to erase everything there was in the experiment file and to start the acquisition.
10. Type “ft↵” when the acquisition is finished. To see the spectrum during acquisition, type “tr↵”,
wait until after the next scan and type “ft↵”. Follow the procedure describe in step 11 to phase the
spectrum. You can let the acquisition stop when the chosen value of “ns” is completed or you can
type “halt↵” before the end when the spectrum is satisfactory. Redo “fp↵” after each transfer and
at the end of the acquisition to get the final spectrum.
For a 13C spectrum, replace the command “ft↵” by “ef↵”and “fp↵” by “efp↵”. The signal to noise
ratio will be better.
icon with the left button of the mouse. The most
11. To phase the spectrum, click the
intense peak of the spectrum will be automatically identified. While holding the left button of the
mouse on the
icon and by moving the mouse, adjust the phase of the most intense peak.
Then, holding the left button of the mouse on the
icon and by moving the mouse, adjust the
phase of rest of the spectrum. When the adjustments are finished, with the left button of the
mouse, click on
the phase.
to return to the main menu. You can also type apk to automatically adjust
12. To automatically correct the baseline, type “abs↵”.
13. To define an expansion, in the spectrum window, click the left button of the mouse and
hold it down. Drag your mouse over the selected region and release the mouse button to
do the zoom. There are also some more zoom options:
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Exact zoom (define manually the window limits) :
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Zoom in centered in the middle of the window :
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Zoom out centered in the middle of the window :
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Smooth zoom centered in the middle of the window :
To see back the whole spectrum:
*14. The spectrum needs to be referenced. If this is not the case, expand the region containing
icon with the left button of the mouse. The cursor
the reference peak (see 13). Select the
moves on the spectrum and can be positioned at the top of the reference peak. Then click the left
button of the mouse. The value for this peak will be shown. Enter the new value, followed by↵.
15. To integrate the spectrum, define the area to integrate on the screen. Click the left button of
the mouse on the
icon to enter the integration subroutine.
Select
to select integration regions manually. Put your mouse cursor over the spectrum
and by holding the left mouse button down, drag your mouse over the desired region for
your integration. Just release the button to perform the integration. Repeat as many time as
necessary.
To calibrate the integration for a fixed number of protons, position the cursor on the corresponding
integral and click the right button of the mouse. Select calibrate and enter the desired value.
When all the spectrum has been integrated and calibrated, select the
menu.
to return to the main
16. To plot the spectrum, adjust the height of the peaks on the screen to the desired level. Click
on file-print. Select “print active window” and click on OK. Select the good printer and your
spectrum will be printed as seen on the screen.
To add or remove information on your spectrum right click anywhere on the screen and select
“spectra display properties”. You can now select the desired information.
You can also use the plot editor by using any of the (nucleus_routine) layouts.
17. To obtain a list of chemical shifts, type “mi” and define the minimum level in relative intensity.
Type “pps” to generate the list and see the chemical shifts of all your peaks appear on the
spectrum. Click on the “peaks” tab to see the list. Click on file export to export the file in the
desired extension.
18. To read an experiment on disk, type "re name expno procno". At the end of your experiment,
type “re junk 1 1↵”. Press “LOCK”, then “LIFT-OFF” to eject the tube. Put the reference at the top
of the magnet and insert by pressing “LIFT-OFF”.
19. Launch multiple experiments with multizg↵ or use the spooler.
a)
b)
c)
d)
e)
f)
Define each experiments using edc↵ (The experiments number need to be consecutive).
Recall the good parameters in each experiment (rpar or set commands)
Go back to the 1rst experiment.
Type multizg↵
Enter the number of experiments defined.
Multizg should now start and you should see the total acquisition time for all the
experiments.
INSTRUMENTS AV-300 AND AV-400 PJAB IN AUTOMATIC MODE
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Always use a good NMR tube with a minimum length of 7”.
Always filter your solution on cotton.
The required volume of solution is 0, 75 ml.
Preferably, use an NMR solvent with only one deuterium signal.
1. In the list, with the left button of the mouse, double click the same number as the number of
the holder with your sample.
2. Define the name of your experiment
3. Define the experiment number
4. Select your solvent
5. Select the experiment that you need on your sample. You can add many experiments by
clicking the ADD button. To start all experiments, select the number of the holder and click
on the SUBMIT button.
PROCÉDURE POUR LE AV400RG/AVII400
For all 1H experiments you can use the same procedure as the other AVANCE spectrometers.
So to recall 1H experiments:
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rpar bbfo.proton all 
rpar bbfo.cosy all 
rpar bbfo. noesy all 
rpar bbfo.tocsy all 
rpar bbfo.roesy all 
To define any experiment using other nucleus or to optimise a 1H experiment you need to type:
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set_proton 
set_protonhd 
set_c13 
set_c13ig 
set_dept 
set_hsqc 
set_hmbc 
set_p31 
set_p31coupled 
set_1hdec31pcw  (1H avec {31P} sélectif)
set_f19 
set_multi  (1H, COSY, HSQC, DEPT, 13C)
set_hdc  (1H, DEPT, 13C)
If you need any other nucleus just ask us and we will create the parameters set if possible.
Before starting your experiment you need to adjust ns and td0.
set_hdc will automatically create a 1H, a DEPT and a 13C experiments for you.
1. Type edc and define your first dataset (#1)
2. Type set_hdc  and the 3 experiments will be created with the correct parameters
(#1, #2 and #3)
3. Wait for the tuning and matching of the probe to finish.
4. Read each experiment and adjust rga  . Also adjust ns and td0 if necessary.
5. Read experiment #1 (re 1) and type multizg . You will be asked how many
experiments were defined. Type 3 and the 3 experiments will start one at a time
automatically.