Open Access Manual
NMR-Service LOC
Februar 2005
NMR-Service LOC
Tel: +41 1 632 29 33
Email: nmrservice@org.chem.ethz.ch
Open Access Manual for Superusers
1. Sample preparation
 Make a homogeneous solution of ca. 20mg in exactly 0.7ml of deuterated solvent,
giving a sample height of 4.5-5 cm. Avoid scratching solid samples from the wall
of flasks with a spatula. Spatulas contain nickel, which causes paramagnetically
broadened spectra
 Filter the solution through a small square of Kleenex, before transferring it to the
NMR-tube (see following pictures)
Kleenex
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Eject the dummy sample (manually on Gemini 3,4 or via software on Gemini 5,6
with the EJECT button). Let the ejecting air pressure on
Wipe your sample tube with the deer skin (Hirschleder)
Insert your sample tube into the spinner while you hold both in your hand
Adjust the height in the gage on the wall
Sometimes, the O-ring inside the spinner turbine gets so greasy from unclean
tubes, that it does not hold the tube strongly enough to maintain its position in the
spinner during transfer to the magnet (notify the NMR-Service, so that the O-ring
gets changed). Once adjusted in height, hold the sample at the
outside of the top of the spinner turbine, not on the top of the
NMR-tube itself.
Insert the spinner with the sample tube into the magnet (INSERT
button on Gemini 5,6, manually on 3,4)
Check the spinning indicator on the magnet leg (15-20 Hz, green
light steady, see the picture on the right)
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Right:
First put the sample
in the spinner then
put the spinner
in the gage for
adjustment
False:
Do not put the spinner
into the gage first!!
Do not put a tube
into a fixed spinner!!
2. Login and Setup
 Login by typing your username
 In the main menu, choose SETUP and NEW SAMPLE. Enter an alphanumeric
sample identification and choose the solvent from the solvent menu (less common
solvents are displayed under OTHER)
 Back in the setup menu, choose either H1, C13, F19 or P31. For combined
experiments, e.g. a sequence of H1, C13 and DEPT, select COMB.EXP. and the
corresponding sequence (H1+C13, C13+DEPT or H+C+DEPT)
 In the Acquire menu now, optionally adjust the time or number of transients by
selecting TIME/NT
 If you wish to do an experiment with variable temperature (max. 100°C for a short
time) contact the NMR-Service
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3. Locking and shimming
 Open the acqi-window with the ACQI button and select LOCK
 If the system has not locked, select LOCK OFF, increase lockgain and lockpower
until the sine wave appears. Change z0 slowly until the wave is a single step. (see
the pictures below). Then click LOCK ON and reset lockpower and lockgain to the
previous values
Not Locked
Locked


Select the SHIM button. Shim using mouseclicks on the –1+ or –4+ or –16+
buttons for ONLY z1 and z2 (left mouse=decrease; right mouse=increase until the
lock level is maximum
Click the CLOSE button
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4. Starting experiments
 Click the MANUAL GO Button
 If you selected a combined experiment, a chain of experiments is automatically
measured in sequence (eg.: H1 in exp1, C13 in exp2 and DEPT in exp3). Use
jexp1, jexp2, jexp3 etc. to switch between experiments
 Each finished experiment is automatically processed (wft: fourier transformation
and aph: auto phase correction) and can be inspected and plotted while the later
experiments are still acquiring
5. Processing the spectrum (read more under „The interactive dispay routine“)
 If you are not in the interactive menu, type ds
 Adjust phase if necessary
 Calibrate the spectrum on a solvent or on TMS at 0.00 ppm
 Adjust integral if necessary
 Adjust threshold for the line list
6. Plotting a spectrum
 Select RETURN in the interactive menu
 Click OUTPUT for canned plotting and printing or click PLOT if you want to
select individual elements of a plot (INT.REGIONS, SPECTRUM, SCALE,
PARAM or PEAKS. Send the plot to the plotter with PAGE
 Line listings and full parameter listings are obtained with the menu selections
PRINT, NEW PAGE, LINE LIST and ALL PARAMS. Send the plot with SEND
PAGE
7. Storing the data
 Go to main menu and click DATA STORAGE
 Click STORE ON DISK
 Type an alphanumeric filename, <enter>
8. Loading the data
 Go to the main menu and click on the file
 Click LOAD FROM DISK
9. Outlog
 Eject your sample, always insert the dummy sample and quit the instrument
typing outlog
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The interactive display routine
The spectrum window
The spectrum window can be toggled between full screen and standard size with the menu
button RESIZE (top row). If you use Resize while in the interactive mode, you have to type ds
or select INTERACTIVE to get back into the interactive display mode. If the spectrum
window is full size, you can bring the text output window (parameters etc. ) to the front (and
back again) with FLIP.
Mouse buttons
The left mouse button controls the cursor (or both cursors, if two cursors are displayed). The
right mouse button controls the right cursor, if displayed. In order to expand a region, click at
the left limit with the left mouse button, then at the right limit with the right button.
The middle mouse button controls the vertical size. Position the mouse in the area of the peak
or integral and click with the middle mouse button at the desired new height of the peak
(integral)
Attention: if you click over a region with noise, the spectrum gets blown up drastically in
vertical scale. In case of trouble, type in vs=180 to reset the highest peak to full screen again.
The submenus of the interactive menu
1. Cursor/Box
 Toggles between display of two cursors (called box) or one cursor
2. Full/Expand
 Toggle between display of full spectrum and expansion of the region between the
cursors
3. Integral on/off
 Toggle integral display on and off
4. Integral adj
 enter the interactive "integral adjust" submenu
5. Phase
 enter the phase submode. Click with the left mouse button near the largest peak to
define pivot and region for zero order phase correction. Adjust zero order phase
(frequency independent correction) moving the left mouse button (coarse adjustment)
or the right mouse button (fine adjustment) inside the box up or down near the
horizontal red bar (which defines the original phase setting). Click in another region of
the spectrum (outside the first box) to adjust the first order phase correction by the
same procedure. A third click outside this second box defines a new box for zero order
correction and so on. Leave the phase submode by clicking another button, e.g. thresh.
 if in trouble with phase correction, enter aph
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6. Thresh
 This displays a horizontal yellow line defining the peak picking limit in mm. Adjust
with the left mouse button, then select THRESH button again to leave this submode.
7. Scale
 Toggles display of scale on and off.
 In order to change from ppm to Hz enter axis='h', to get ppm back axis='p'
8. Return
 Leave interactive mode and go back to the display menu, e.g. for plotting and printing
The interactive integral adjust menu
1. Cursor/Box
 works as in the interactive display routine
2. Full/Expand
 works as in the interactive display routine
3. Full/Partial
 toggle between partial (if resets are defined) and full integral
4. Resets
 define reset points for integral with left mouse clicks. The odd numbered regions
that will not been shown in the partial integral mode are shown as dotted lines. Use
an even number of resets to get the correct partial integrals on display and plot.
5. Clear resets
 remove all integral resets
6. Lvl/Tlt
 Adjust level and tilt of integrals. Works exactly like the phase correction submode.
 Use bc to correct the baseline before adjusting the integrals. bc will not work for
spectra with very broad signals.
7. Return
 brings back the interactive display routine
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Calibration
Calibrate the spectrum on a solvent or on TMS at 0.00
ppm: put the cursor approximately on the signal, type nl,
then enter rl(...p). (eg. for CDCl3: rl(7.26p). If you
changed spectral width (sw) or transmitter frequency (tof)
manually, then you have to recalculate the correct
calibration: enter setref.
Calibrate an integral to the value 1 or 100: enter setint(x,y)
x: number of integral, y: value. E.g.: setint(4,100) means:
integral N° 4 (counted from the left hand side of the
spectrum) has a value of 100. The rest of the integrals will
change their values relative to the calibrated one.
Tetramethylsilan TMS
Insets
The inset command allows to display a part of the spectrum between two cursors as an
expansion in x or y or both. It displays its own submenu which allows to adjust the position of
the subspectrum relative to the full spectrum. Although the original (full) spectrum remains
on the screen, the display parameters are changed according to the inset. This means that after
inset, you have to recall the original spectrum display with r1 (see below).
Saving and recalling displays
At any time, the current display (actually the display parameters) may be saved by the
commands s2 to s9 and recalled later by r2 to r9. The standard processing macros use s1
internally to save the standard display (e.g., for 1H, -.5 to 9.5 ppm, automatically determined
phase and integral regions). Thus r1 recalls the standard display at any time during the
interactive display session.
Interactive plotting of expansions at a fixed Hz/ppm ratio
This can be done with the macro hex. Hz/cm is 10.0 by default, but other values can be
entered as argument hex(Hz/cm). Proceed as follows: position the cursors to enclose the
region you want to expand. Type hex. The left cursor is now shown where the right cursor
was. Reposition left and right cursors for the next region and type hex again. Continue until
all regions have been selected. Each region can be expanded in vertical direction
independently using the middle mouse button before typing hex for this region. After the last
region, you have to enter apage to send the last page to the spooler. Hex detects if the next
plot does not fit on the page and changes pages if necessary. If your selected region does not
fit on one page, an error message is displayed. If you want the peaks of the expansion to be
labelled in Hz, enter axis=´h´ and use hexf instead of hex.
Strongly tilted Baseline
Linear baseline correction (DC, drift correction) is part of the normal processing macros for
C13. This routine assumes that the left- and rightmost 10% of the spectrum contain only
noise. If a peak is located in these regions, the resulting baseline is strongly tilted. In this case
type cdc (clear drift correction) to get the non corrected spectrum, or measure the spectrum
with a larger sw such that the left and right 10% of the spectrum are free of peaks. In case of
proton spectra, the bc routine sometimes does not work correctly if the spectrum contains
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broad peaks or no regions free of peaks.
Troubleshooting Guide
NMR-Service: D314, 22933/26856, nmrservice@org.chem.ethz.ch
Known problems
 Locking and shimming is not possible
 Error message: RTP...
 Ejecting the sample via software does not work
 Spin On activation is not possible
 The yellow lock signal in the acqi-window is not visible or looks strange
 The black spectrum window is fluttering
 The screen is locked
 The acqi button is missing
 Broken tubes inside the probehead
 Spinner does not eject
 Irregular or no spinning
1. Locking and shimming is not possible
 Check your sample if some solids or fibers are floating in the sample
 Very concentrated samples (ca. >60 mg) lead to bad resolution and weak lock
signals
 Logout and do the setup again
 Is the lock button active?
2. Use su acqproc in following cases
 An RTP..-Error occured
 Ejecting the sample via software is not possible (on the instrument 5,6)
 Spin On activation is not possible, but the button is here
 The yellow lock signal in the acqi-window is not visible or looks strange
 The acqi window does not open

Proceedure:
-
-
open a terminal on the desktop:
 click with the right mouse button on the desktop and
choose Terminal from the Tool-Menu
type su acqproc , <enter>
wait 5 sec.
The status in the aqcstat-window switches to Inactive
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-
Push the red button on the console once (rebooting)
Wait 10 sec.
type su acqproc , enter
-
The status in the aqcstat-window switches to Idle
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logout
login and check if you are successful with a normal setup
if not, try the „su acqproc“-proceedure a second time
3. The black spectrum window is fluttering
 Enter exit in the command line of the VNMR-Software
 Click on the VNMR-Icon

4. Locked screen
 User-Login and Password for the Solaris-Environment and Locked Screen:
Login:
locnmr
Password:
locnmr1
5. The acqi button is missing
 Type acqi in the command line of the VNMR-Software
 If it doesn’t work, reset the Console with su acqproc
6. Irregular or no spinning
 In the acqi window, set the spinning rate to 20
 In the acqi-window, switch the spin button off and on. If you here a „click“ from
the magnet the spinning is activated
 Do not change the pressure settings or flow on the N2/Air supply; if the sample
does not spin with the standard settings, some parts inside the magnet might need
cleaning, a job that has to be done by the NMR-Service.
7. A broken tube was inside the magnet
 If, after the measurement, your tube comes out of the magnet broken, immediately
block the instrument from further use and call the NMR-Service directly. The
same holds if you cannot lift the tube out of the magnet for some reason. Do not
play around in this case, a new probehead costs Fr 50000.-!. Contact the NMRService by phone, email, or post a sheet on the door of the NMR-Service
(D314)
If nothing helps please contact the NMR-Service:
D314, 22933 / 26856 / 34734, nmrservice@org.chem.ethz.ch
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Useful Macros
set(´nucleus/method´, ´solvent´) *
The allowed nuclei are ´h´, ´c´, ´h´, ´c´, ´p´, ´po4´, ´f´, ´cf3´ as well as the combined methods
´hc´, ´apt´, ´dept´, ´capt´, ´cdept´, ´hcapt´, ´hcdept´.
setnt
For combined experiments, setnt asks for the number of transients to be accumulated for each
experiment in sequence.
settime
Works accordingly for the time in minutes of each experiment
gettime
Display the expected total time for chained experiments. For single experiments it is the same
as time.
tset(T in °C or ´n´ )
To set the temperature for variable temperature measurements use tset(i) where i is the
desired temperature in degrees °C. To reset the instrument to ambient temperature use
tset(´n´). The highest allowed temperature is 100°C! Ask for training before you use variable
temperature for the first time, the instrument can be damaged with improperly executed VT
experiments!
mango
This macro starts acquisition with the current parameters in the current experiment, or, if a
combined experiment like hc, cdept etc. was set up, it starts the acquisition of all experiments
as a queue. It assumes that locking and shimming have been done manually beforehand. After
acquisition, normal processing is done automatically and – if autosave was on at the time of
submission – all measured datasets are saved in the users directory automatically after
processing.
pnh1
do all the processing normally done for 1H-spectra in MENU mode. This macro is executed
automatically after acquisition, you need to enter it only in case of reprocessing.
pnc13, pnapt, pndept, pnp31, pnf19
work correspondingly for hetereonuclear spectra.
setref(´solvent´)
recalculate external reference vs TMS. Works only if the lock-solvent has been set correctly.
Precision is ca. ± 3 Hz compared to internal TMS.
mp(i,k)
copy parameters of experiment i to experiment k (neither i nor k have to be the current
experiment, and the current experiment is not changed to k in the process)
output
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a canned sequence of plot and print is done on the current plotter and default printer. This
includes apage, iprint, dll, ap, printoff.
hex(xx.x)
plots xx.x Hz/cm expansions of the spectral region between two cursors. Default is 10 Hz/cm.
May be used repeatedly, changes page automatically when the remaining page width is not
sufficient for the current expansion. Last page has to be sent explicitly with apage. Vertical
scale may be adjusted individually for each expansion. Spacing in x between expansions is 5
mm.
hexf(xx.x)
Same as hex but with peak labels on the expansions (set axis=´h´ if you want them in Hz).
hstore(´filename´)
saves the FID and parameters under filename inside the library of the current user on the hard
disk of the server. If no filename is given, entry of the filename is requested
hload(´filename´)
retrieves stored FID and parameters into the current experiment. If no filename is given, the
entry of the filename is requested. Use the menu Data storage to inspect the contents of your
directory.
towin(´filename´)
Send a copy of the dataset stored under ´filename´ to the group directory for BRUKER data
and convert it to BRUKER format. The converted dataset will be transferred to the group
directory by the system within 10 minutes, ready to be transferred to the Mac or PC of the
user. This macro works only if the dataset has been stored on the disk before with hstore or
autosave. If no argument is given, it will ask for a filename. If you don´t remember the
filenames use the menu Data storage.
a
In the interactive display routine, this macro enters the ds(´spwp´) submode where you can
shift and expand the spectrum with the mouse. Use ds or r1 to go back to the normal ds
display.
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