INTRODUCTION
to the Bruker Avance DPX-300
NMR spectrometer
Training and Operators Manual
Tufts University
Dept. of Chemistry
62 Talbot Avenue
Medford, MA 02155
by:
D. Wilbur
rev 1/13/04
Bruker Avance DPX-300 Training and Operator’s Manual
rev 1/14/04
CONTENTS
NOTE ON FORMAT: ....................................................................................................................... 3
GENERAL PROCEDURES FOR ALL SPECTRA .................................................................. 3
1.
2.
3.
4.
PRELIMINARY NOTES .............................................................................................................. 3
LOADING THE SAMPLE............................................................................................................. 4
LOCKING THE INSTRUMENT ..................................................................................................... 5
SHIMMING THE MAGNET ......................................................................................................... 6
RUNNING A 1H SPECTRUM ..................................................................................................... 6
5. SETTING THE PARAMETERS ..................................................................................................... 6
6. ACQUIRING THE SPECTRUM ..................................................................................................... 7
7. TRANSFORMING THE DATA...................................................................................................... 7
8. MANIPULATING THE SPECTRUM ............................................................................................... 7
9. PHASING THE SPECTRUM ......................................................................................................... 8
10. SETTING THE REFERENCE ...................................................................................................... 8
11. CHANGING SW AND O1 FOR INCREASED RESOLUTION .......................................................... 8
12. INTEGRATING THE SPECTRUM ................................................................................................ 8
13. PEAK PICKING ....................................................................................................................... 9
RUNNING A 13C, PROTON DECOUPLED SPECTRUM .................................................... 10
15. SETTING THE PARAMETERS ................................................................................................. 10
16. ACQUIRING THE SPECTRUM ................................................................................................. 11
17. PROCESSING THE DATA ....................................................................................................... 11
RUNNING A 13C DEPT SPECTRUM ..................................................................................... 11
18. SETTING THE PARAMETERS ................................................................................................. 12
19. ACQUIRING THE SPECTRUM ................................................................................................. 12
20.
PLOTTING ....................................................................................................................... 12
RUNNING A 2D 1H MAGNITUDE COSY SPECTRUM ..................................................... 12
21.
22.
23.
24.
SETTING THE PARAMETERS ................................................................................................. 12
ACQUIRING DATA................................................................................................................ 13
PROCESSING THE DATA ....................................................................................................... 13
PLOTTING ............................................................................................................................ 13
ADDITIONAL INFORMATION .............................................................................................. 14
25.
26.
27.
28.
NAMING AND MANIPULATING FILES .................................................................................... 14
REBOOTING THE COMPUTER ................................................................................................ 15
WHEN YOU'VE FINISHED WITH THE SPECTROMETER ............................................................. 15
FURTHER READING.............................................................................................................. 15
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29. ACKNOWLEDGEMENTS ........................................................................................................ 15
APPENDIX A--AVANCE FILE STRUCTURE ...................................................................... 16
NMR DATA FILES ...................................................................................................................... 16
OTHER FILES .............................................................................................................................. 17
APPENDIX B--XWIN-PLOT .................................................................................................... 18
APPENDIX C—PROBE TUNING ........................................................................................... 20
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Note on format:
The following format conventions are used in the Bruker Avance User’s Guide. To minimize confusion,
the same conventions will be used in this manual.
Unless otherwise specified, statements such as “click on calib” mean to move the cursor on top of the
calib button on the screen, and click with the left-hand mouse button. Consider the left-hand mouse
button the default; if another button is required, it will be explicitly stated.
Commands such as “Enter zg” mean to type zg followed by a return on the
keyboard. Commands must be followed by <return> before they are accepted.
Words written in bold Arial font, e.g., acqu, refer to buttons or pull down menus on the screen (items
that can be selected with the mouse). Multilevel menu choices written like this, Windows/lock, mean
choose the first menu choice by left clicking with the mouse. Choose the second menu choice from the
menu that appears when the first choice is made.
Words written in bold Courier font, e.g., edsp, refer to commands that can be typed at the keyboard.
Commands must be followed by <return> before they are accepted.
General Procedures For All Spectra
1. Preliminary Notes
A. This manual is a condensed and incomplete account of instrument usage. It is in no way a
substitute for reading the detailed instruction manuals available in the NMR room (M-02). Please get to
know them. This manual is written in a similar format to the Tufts AM-300 manual, to facilitate the
transition from the AM to the DPX.
B.
All users should sign the logbook before they do anything else.
C.
Log into the computer. The screen may be illuminated by hitting any key on the keyboard. You
should see a Welcome to IRIS window. Enter your user name and password. When the UNIX shell
window appears, type xwinnmr. The XWIN-NMR window will appear, as shown below.
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D. Only the active window will accept typing. To make window active, position the mouse cursor inside
it. To bring a window to the front, left click in its title bar.
E. Most commands are accessible from the menu bar. Alternatively, any command may be typed into
the command line below the spectrum window. Most commands are the same as the AM-300.
F. Parameters may be changed by typing the abbreviation for that parameter followed by the (return)
key (hereafter <rtn>. The computer will respond by popping a window with the current value of that
parameter. Typing the new value of the parameter followed <rtn>by will replace the old value with the
new value. Alternatively, groups of parameters can be edited with various ed commands. For example,
eda presents a window of all acquisition parameters, edp presents a window of all processing
parameters.
G. Sample control is provided through the BSMS (Bruker Smart Magnet System) control panel. To
access the BSMS Panel choose Windows/BSMS Panel from the menu. Lock, Shim, and Sample
panels are similar in appearance to the hardware buttons on the AM-300, except control is through a
slider bar and +/- button, rather than through the knob. For all buttons the left mouse button decreases
the value, the middle button increases. Step size is changed by left (decrease) or right (increase)clicking
on the :2/*2 button
2. Loading the Sample
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A. The probe should contain a sample at all times. When you arrive at the instrument with your research
sample, you should remove the standard sample from the magnet and replace it with your sample as
follows:
From the XWIN-NMR menu choose Windows/BSMS panel. Then click on the Shim button
-Click on the LOCK button to unlock the instrument. The color of the button will change from yellow to
gray
- Click on the SPIN button to stop the spinning of the sample The color of the button will change from
yellow to gray
- Click on the LIFT button. The standard sample should rise out of the probe on a stream of air. Remove
the standard sample from the top of the probe. Remove the standard from the spinner.
-Place your sample tube in the appropriately sized spinner and adjust the precise depth of the tube within
the spinner by using the depth gauge. Note that the depth gauge should be set at 10mm regardless of the
tube size for a 10 mm probe. (and at 5 mm gauge for a 5 mm probe). Note: 10 mm tubes cannot be run in
a 5 mm probe. For best shimming set tube 1mm below the appropriate line to assure a uniform sample in
the active region of the probe.
- Place your sample in the top of the probe. Do not release the sample unless you are sure it is supported
on the air current.
- Click on the LIFT button again. Your sample should slowly lower into the tube as the air stream
decreases. Click on the SPIN button.
B. The rate of the sample spinning should be 20-25 rps. To check this:
-Press the Sample button on the BSMS panel. Then click on the SPIN MEAS button on the Sample
panel that pops up. To change the spin rate, click on the SPIN RATE button, and usethe slider bar to
change the value.
3. Locking the Instrument
A. To display a swept lock signal, choose Windows/lock from the XWIN-NMR menu. You should
now see a continuous wave deuterium NMR spectrum of your solvent. This should be a trace across the
screen with the signal in the middle of it.
B. To lock the sample, type lock, then click on the solvent from the list that pops up. Lock power,
phase, and gain will be adjusted automatically.
C. The lock can also be adjusted manually, using the buttons on the Lock panel from the BSMS panel.
Note: Appropriate power and gain levels are different from the AM-300.
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4. Shimming the Magnet
A. To obtain a high resolution spectrum it is essential that all parts of the sample are exposed to the same
magnetic field. The homogeneity of the field is generally assessed by noting the intensity of the lock
signal, the more intense the signal the better the field. In practice, the shims most likely to require
adjustment are the spinning ones, namely Z Z2 and Z3 shims, and the non-spinning shims X and Y. To
adjust the homogeneity by hand (often adequate for routine spectra and almost always faster than by
automated computer shimming) you must first make sure that the lock trace is visible. If it has gone off
the screen during the locking procedure it can be brought back by lowering the LOCK GAIN level. A
sample procedure follows:
- Click on the LOCK GAIN button. Use the +/- button to adjust the lock gain until the trace is in the top
two squares of the grid. Press the Z button. Use the +/- button to maximize the lock signal. Change the
step size if needed. Repeat for the Z2 button. Continue to alternate between the these buttons maximizing
the lock signal each time until no further improvement can be seen. You may have to adjust the Lock
Gain if the trace goes off the screen.
-If the sample must be shimmed to highest standards, adjust the non-spinning shims by pressing the SPIN
button and waiting until the sample stops spinning. SPIN RATE can be used to monitor this. Raise the
lock level by adjusting the lock gain until the level is in the upper half of the screen. Now press the X
button and use the +/- button to adjust the lock level to maximum. Then press the Y button and repeat
this procedure until no further improvement is possible. Start the sample spinning again by pressing the
SPIN button and repeat the Z and Z2 shimming as above.
Running a 1H Spectrum
5. Setting the Parameters
A. From the XWIN-NMR menu choose File/New. A edc window will appear containing the file name
parameters. Enter a new NAME. Generally only the Name parameter needs to be changed. NOTE: The
first time you use XWIN-NMR you will need to change other parameters to EXPNO=1, PROCNO=1,
DU=datanmr, User=<username>. Click on SAVE
B. Data files containing typical parameters for a proton spectrum are stored in the hard disk for easy
access. To retrieve these:
Choose File/Copy/parameters from file from the menu, or type rpar. A list of standard parameter
files will appear. Use the scroll bar to access the entire list. Click on proton. In the next window that
pops up, click on Copy All.
Type eda to edit acquisition parameters. Always change Prosol to True by clicking on its value,
which loads all default pulse lengths and also check that the solvent is correctly identified, otherwise
calibration will be off. IMPORTANT: Failure to set Prosol to True will result in all pulse lengths not
set by you will be of zero length and rga will go off scale trying to find a signal.
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Change any other acquisition parameters desired, then click on SAVE. A complete list of acquisition
parameters and their meaning can be found in the manual XWIN-NMR Software Manual Part 2:
Acquisition, p A-39-A59. Ones you might want to change are
TD (time domain size)-Defines the number of data points of the fid.
NS (number of scans)
P1 (pulse length in microseconds)
SW, SWH (sweep width in ppm, Hz)
AQ (acquisition time in seconds)
RG (receiver gain)
B. You may wish to tune the probe before beginning acquisition. See Appendix C of this manual.
C. The last parameter to be set is the receiver gain (rg) which adjusts the gain of the signal coming out
of the probe. This will vary from sample to sample. To set this gain type: rga (receiver gain adjust).
The computer will automatically take a few sample pulses and alter the RG between each. When the best
value is found, the computer will type rga: finished. You may see this value which the computer
has selected by typing: rg. If you want this value then type: <rtn>. If you wish to select another
number then type in the new number and then type <rtn>. Do not increase the value, but you may
decrease it.
6. Acquiring the Spectrum
A. To start the acquisition type zg to zero the memory and go (start the acquisition). You can watch the
progress of the acquisition by choosing Acquire/observe fid window from the menu, or by typing
acqu.
B. The acquisition will automatically end when the number of scans taken equals ns. However if you
wish to stop it prematurely or abort the run then you will have to click on the STOP button to the left of
the FID in the acquisition window.
7. Transforming the Data
A. A complete description of processing parameters and their meaning can be found in the manual
XWIN-NMR Software Manual Part 1: Processing, Chap 2,6
B. The time domain data can be processed by typing bc, then em, then ft (or type ef to do all three at
once).
C. It is not necessary to wait for the acquisition to end before transforming the data. Type tr to transfer
the data to disk at any time during the acquisition. Once written to disk, the data can be transformed.
Time domain (fid) and frequency domain (spectrum) data are always stored in separate files. All data
acquired so for can be processed while the acquisition continues in the background.
8. Manipulating the spectrum
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A. The spectrum can be expanded vertically and horizontally using the mouse, clicking on the buttons to
the left of the spectrum. *2, /2, *8, /8 multiply or divide the vertical scale by 2 or 8. To expand the
horizontal scale, left click anywhere in the spectral window. Then middle click on the desired expansion
limits. Left click again to unlock the mouse from the expansion. To expand the vertical scale by an
arbitrary amount, left click and hold the double arrow button to the right of /8. Move the mouse
vertically until the peaks are desired height. Release the mouse button. For more extensive
documentation on spectrum manipulation, see the XWIN-NMR Processing manual, chapters 2,3.
9. Phasing the Spectrum
A. The spectrum will usually not have all the signals upright in an absorption phase. To correct this type
apk (automatic phase korrection). For spectra with well separated narrow lines, apk will usually work
well.
B. If the automatic phase correction does not work well, click on the phase button to the left of the
spectrum, then click on biggest. A marker will appear under the biggest peak in the spectrum. Left click
and hold the PH0 button. Move the mouse vertically until the largest peak is phased correctly. Release
the mouse button and click and hold the PH1 button. . Move the mouse vertically until the other peaks
are phased correctly. Release the mouse button.
10. Setting the Reference
A. The spectrometer cannot provide an exact chemical shift without being calibrated to a standard
(usually TMS). Click on the calibrate button to the left of the spectrum. A small arrow will appear on
the spectrum. move the arrow to the reference peak with the mouse, and click the middle mouse button.
A window will appear with the current frequency value. Enter the reference frequency. A chart of
chemical shift values for solvents is on the console.
11. Changing SW and O1 for Increased Resolution
The default parameters display the spectral range 16 to –4 ppm. This range can be changed for greater
resolution. Click the left mouse button somewhere in the spectral window to tie the cursor to the
spectrum. Position the cursor at the left limit of the desired spectral width. Click the middle mouse button
to set a marker at this frequency. Move the cursor to the desired right hand limit and click the middle
mouse button to expand the spectrum. The expanded region now appears in the window. Click the left
mouse button to release the cursor from the spectrum. Click on sw-sfo1 while the expanded region is
displayed. This adjusts sw so that it has the same value as the expanded region and also adjusts o1 (and
thus sfo1) so that the carrier frequency lies in the center of the expanded region. (You can verify these
changes by checking the eda table.) Notice that by reducing the spectral width, the acquisition time aq
is increased while the parameter fidres is reduced. Finally, now that the acquisition parameters are
optimized, it is a good idea to repeat the automatic receiver gain adjustment (rga). Notice that since the
spectral width has been changed, it may be necessary to readjust the phase correction.
12. Integrating the Spectrum
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A. It is often useful to integrate 1H spectra. The simplest way to define the integral range is by entering
abs. The command abs performs an automatic baseline correction and also automatically defines the
integral ranges. The integrals will not appear on the screen, but will appear on the plot.
B. To display the integral on the screen:
Choose Analysis/Manual integration from the menu, or simply click on the integrate button of the
button panel at the left side of the XWIN-NMR window. Additional buttons, like those that control
vertical and horizontal scale for the spectrum, will appear in the lower left. The upper part of the button
panel is identical to the standard layout, and allows you to shift and scale the integral data on screen. In
addition, there are three special sections headed by current:, all:, and mouse:. The command buttons in
these sections work on the current integral marked by the user, on all integrals on the screen, and on the
mouse sensitivity, respectively.
Defining integration regions
Move the cursor into the data area of the XWIN-NMR window. Click the left mouse button. The cursor
is now bound to the spectrum, and moves along the spectrum trace when you move the mouse. It can be
released from there by clicking the left button again. Clicking the middle button will mark the current
position (the mark can be removed using the right button). Clicking the middle button a second time at a
different cursor position will define the area between the mark and the current cursor position as the
integration region, and the corresponding integral trace is displayed along with the value of the area
under the integral. By default, the first integral region defined will be assigned the value 1.0. This
procedure can be continued for all desired regions, and need not proceed left to right. Click the left
button to release the cursor from the spectrum when you are finished.
In order to mark one of the defined integrals as current integral, move the cursor into the data area of the
XWIN-NMR window. Click the left mouse button. The cursor is now bound to the spectrum, and moves
along the spectrum trace when you move the mouse. Select the integral you want to make the current
integral by moving the cursor under it, and release the cursor by clicking the left button again. The
integral will be marked with an asterisk. All button panel commands in the section current: can now be
applied to this (and only this) integral.
To calibrate the integrals, mark an integral as the current one, then click on calibrate. Enter the integral
value in the dialog box.
When all integral regions have been defined, click on return. Click on save as ‘intrng’ and return to
save the regions to a disk file.
13. Peak Picking
The most straightforward way to produce a peak list is through the command line. First display the Y
axis in cm, if it is not already displayed. The Y button to the left of the spectrum window will toggle the
y-axis, the YU button will change the units from cm to absolute. Choose the region for peak picking by
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setting the parameters f1p and f2p to the ppm values for the left and right limit, respectively. (If the xaxis is in Hz, use f1, f2 instead of f1p, f2p.) Set the parameter mi to the desired minimum
intensity in cm. Type edo and check that CURPRIN is set to hplj5l. The command pp will produce
a peak listing on the printer. Use pps to print to the screen.
14. Plotting the Spectrum
A straightforward way to plot 1D spectra is by using most of the plotting parameters found in the plot
parameter file standard1D. Read in the file by choosing File/Copy/parameters from file from the
menu, selecting standard1D from the menu of parameter file names, and then selecting plot from the
menu of parameter file types that appears. Then click on Copy. This sets the plotting parameters to
values appropriate for most 1D spectra. More information about plotting parameters can be found in
Appendix B of this manual and in Appendix C of the Avance Users Manual ‘1D and 2D Plotting
Parameters’. For basic 1D spectra no changes need to be made within the parameter menu edg itself;
however, the spectral region and the integral range must be defined, and the spectrum title must be
written. To select the spectral region (full or expanded) to be plotted, first make sure the spectrum
appears as desired on the screen, and then click DP1and simply hit return in response to the following
three (3) questions:
F1 = <return>
F2 = <return>
Change y-scaling on display according to PSCAL?<return>
You may change the values of F1 and F2 if you wish.
Other plot parameters can be changed by typing edg (edit graphics) and changing the values, mostly
yes/no, which determine whether integrals, parameters, etc appear on the plot. The edg window is
analogous to the DPO command on the AM-300. Some plot features have a button labeled ed. Clicking
on this button will open another window, with parameters that control the position and style of these
features. See Appendix C of the Avance Users Manual for the meaning of some of these parameters. If
simply editing the yes/no parameters in the edg dialog box will not give the plot you want, it is usually
easier to use XWIN-PLOT, rather than to change other plot parameters. XWIN-PLOT is a graphical plot
layout program described in Appendix B of this manual.
Next create a title for the spectrum. Enter setti to use the editor to open the title file. Write a title and
save the file. The title must end with a <return>.
To preview the plot, as it will appear on paper, type view.
To plot the spectrum, type plot (provided the correct plotter is selected in
edo).
Running a 13C, proton decoupled Spectrum
15. Setting the Parameters
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A. From the XWIN-NMR menu choose File/New.
B. Data files containing typical parameters for a carbon spectrum are stored in the hard disk for easy
access. To retrieve these:
Chose File/Copy/parameters from file from the menu, or type rpar. A list of standard parameter
files will appear. Click on C13CPD. In the next window that pops up, click on Copy All.
Type eda to edit acquisition parameters. Always change Prosol to True by clicking on its value,
which loads all default pulse lengths and also check that the solvent is correctly identified, otherwise
calibration will be off. IMPORTANT: Failure to set Prosol to True will result in all pulse lengths not
set by you will be of zero length and rga will go off scale trying to find a signal.
Change any other acquisition parameters desired.
C. You may wish to tune the probe before beginning acquisition. See Appendix C of this manual.
D. To set receiver gain type: rga (receiver gain adjust). The computer will automatically take a few
sample pulses and alter the RG between each. When the best value is found, the computer will type out
rga: finished. You may see the value which the computer has selected by typing: rg. If you
want this value then type: <rtn>.
16. Acquiring the Spectrum
A. To start the acquisition type zg to zero the memory and go (start the acquisition). You can watch the
progress of the acquisition by choosing Acquire/observe fid window from the menu, or by typing
acqu.
B. The acquisition will automatically end when the number of scans taken equals ns. However if you
wish to stop it prematurely or abort the run then you will have to click on the STOP button to the left of
the FID in the acquisition window. If you wish to save data already acquired, type tr to transfer the data
to the disk before clicking the STOP button.
17. Processing the Data
A. All data processing including Fourier transform, phasing, peak picking and plotting is done just like
proton.
B. It is not necessary to wait for the acquisition to end before transforming the data. Type tr to
transfer the data to disk at any time during the acquisition. Once written to disk, the data can be
transformed.
Running a 13C DEPT Spectrum
Three DEPT spectra, with final H1 pulses of 45, 90, and 135 deg, can be used to assign the multiplicities
of all carbons in the spectrum. Dept 45 spectra have signals from all protonated carbons, with peaks
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upright. Dept 90 spectra have only CH carbons. Dept 135 spectra have both positive and negative peaks.
The positive peaks arise from the CH and CH 3 groups and the negative peaks from the CH 2 groups.
18. Setting the Parameters
Before running a DEPT spectrum, acquire a normal C13CPD spectrum. This spectrum will be stored as
EXPNO 1, under whatever name you choose. Although three DEPT spectra can be acquired separately,
using parameters for DEPT45, DEPT90 and DEPT135, it is easier to collect all three at once using an
automation program. The AU program deptcyc will set up, acquire, and process three DEPT spectra,
with final H1 pulses of 45, 90, and 135 deg, based on the parameters in this C13 spectrum.
19. Acquiring the Spectrum
Type deptcyc to begin the AU program. An informational dialog box will appear. Read it and choose
OK. Answer the following questions.
Enter number of cycles
10
(this can be changed, if desired)
Enter first expno
2
(accept default value)
Enter NS per cycle
16
(accept default value)
Enter DS per cycle
2
(accept default value)
Enter 13c pulse width
10
(accept default value)
Enter 1h pulse width
7.2 (accept default value)
Enter 13c pulse power attenuation
-5
(accept default value)
Enter 1h pulse power attenuation
0
(accept default value)
Enter 1h CPD pulse width
24
(accept default value)
Enter CPD pulse time
135 (accept default value)
Enter typical J value
135 (accept default value)
Suppress cycle number message
n
(accept default value)
The product of NS per cycle and number of cycles should equal the number of scans needed for a normal
C13 spectrum.
Three spectra will be acquired, stored in EXPNO 2,3,4. Each spectrum will be transformed, and phase
corrected according to the parameters in the normal C13 spectrum, stored in EXPNO 1.
20.
Plotting
The three DEPT spectra can be plotted individually, just like normal 1D spectra. To plot all three on one
piece of paper, use the XWIN-PLOT program described in Appendix B of this manual.
Running a 2D 1H magnitude COSY Spectrum
A. Before running any 2D spectrum, first acquire a 1D proton spectrum, and readjust sw and o1 to give
a frequency range about 10% larger than the range of chemical shifts in your sample. If all of the peaks
are in the range 1-5 ppm, there is no point in wasting time and disk space acquiring data outside this
range. If you wish to plot a 1D spectrum alongside your 2D plot, do not overwrite this spectrum. Note
the values of sw, o1p, and rg
21. Setting the Parameters
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A. From the XWIN-NMR menu choose File/New. Data files containing typical parameters for a COSY
spectrum are stored in the hard disk for easy access. To retrieve these:
Chose File/Copy/parameters from file from the menu, or type rpar. A list of standard parameter
files will appear. Click on COSY45SW. In the next window that pops up, click on Copy All.
Type eda to edit acquisition parameters. Always change Prosol to True by clicking on its value,
which loads all default pulse lengths and also check that the solvent is correctly identified, otherwise
calibration will be off. Enter the values of sw, o1p, and rg found for the 1D spectrum. The sw
value must be entered in both the F2 and F1 columns.
22. Acquiring Data
A. To start the acquisition type zg to zero the memory and go (start the acquisition). You can watch the
progress of the acquisition by choosing Acquire/observe fid window from the menu, or by typing
acqu.
23. Processing the Data
Enter xfb to multiply the time domain data by the window functions and perform the 2D Fourier
transform. This is the 2D equivalent of ef. For magnitude COSY, a sine-type window function is
selected by default to suppress the diagonal peaks relative to the cross peaks. Such a window function is
also resolution enhancing, which is appropriate for a magnitude mode 2D spectrum. By de-emphasizing
the beginning of the time domain signal, the sine-type window function eliminates the dispersive tails of
the magnitude signals and so enhances their resolution.
Type sym to symmetrize the spectrum. Since COSY spectra are inherently symmetric, this will eliminate
some artifacts.
.
Adjust the contour levels
The threshold level can be adjusted by placing the cursor on the vertical scale button (looks like up and
down arrowheads), holding down the left mouse button, and moving the mouse up and down.
Since this is a magnitude spectrum, click on +/- with the left mouse button until only the positive peaks
are displayed. The optimum display (both the threshold and which peaks are displayed) may be saved by
clicking on DefPlot.
24. Plotting
Before plotting, type edo, and verify that CURPLOT and CURPRIN are set to the desired plotter
(Currently only hplj5l).
A straightforward way to plot 2D spectra is by using most of the plotting parameters found in the plot
parameter file standard2D. Read in the file standard2D by choosing File/Copy/parameter file from
from the menu, selecting standard2D from the menu of parameter file names, and then selecting plot
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from the menu of parameter file types that appears. Then click on Copy. Equivalently, simply enter
rpar standard2D plot. This sets most of the plotting parameters to values which are appropriate
for most 2D spectra.
More information about plotting parameters and the file standard1D can be found in Appendix C of the
Avance Users Manual ‘1D and 2D Plotting Parameters’. To select the spectral region (full or expanded)
to be plotted, first make sure the spectrum appears as desired on the screen, and then click DefPlot and
answer the following questions:
Change levels = n
Display contours = y
If you want a 1 D spectrum alongside the contour plot, type edg to edit the plotting parameters.
Click the ed next to the parameter EDPROJ1 to enter the F1 projection parameters submenu. Edit the
parameters from PF1DU to PF1PROC as follows:
PF1DU
datanmr
PF1USER
<username>
PF1NAME
<name of 1D file>
PF1EXP
<EXPNO for 1D file, usually 1>
PF1PROC
<PROCNO for 1D file, usually 1>
Click SAVE to save these changes and return to the edg menu.
Click the ed next to the parameter EDPROJ2 to enter the F2 projection parameters submenu. Edit the
parameters from PF2DU to PF2PROC to have the same values as above.
Click SAVE to save these changes and return to the edg menu.
Click SAVE to save all the above changes and exit the edg menu.
Next create a title for the spectrum. Enter setti to use the editor to open the title file. Write a title and
save the file.
To plot the spectrum, simply enter plot (provided the correct plotter is selected in edo). A complex
contour plot may take several minutes to write to the plotter.
Alternatively, you may use XWIN-PLOT to plot the 2D spectrum. XWIN-PLOT is described in
Appendix B.
Additional Information
25. Naming and Manipulating Files
NMR data files are stored in /datanmr/data/<user>/nmr/<filename>. Details of the data directories are
given in Appendix A. Files can be deleted or renamed with the File/delete or File/rename menu
choices. Since the SGI O2 computer runs under UNIX, standard UNIX commands, such as pwd, cp,
rm, mv, ls can also be used from a Unix shell window on the desktop.
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Data files are not routinely backed up. You are strongly encouraged to back up your important data to
the Zip drive.
26. Rebooting the Computer
Rebooting the computer requires the root password. Fortunately, the SGI O2 is much more stable than
the Aspect 3000. If you think the computer needs to be rebooted, contact David Wilbur or Larry
Aulenback.
27. When you've finished with the spectrometer
1) Remove your sample and insert one of the standards.
2) Lock the instrument on that sample. Shim by adjusting Z and Z2.
3) Exit the XWIN-NMR program by choosing File/Exit from the menu.
4) Log Out by Choosing Desktop/Log Out from the Toolchest in the upper left corner of the screen.
28. Further Reading
The following manuals are kept in the NMR Room. All of these manuals are stored on the SGI disk, in
Adobe Acrobat format. The directory names for each of the manuals is also listed. Each chapter is a
separate file, named similar to the chapter title.
Avance User’s Guide ver 2.0 <962507> (see especially Chapters 1-4)
/u/prog/docu/english/avance/pdf
XWIN-NMR Software Manual Part 1: General Features and Data Processing (see especially
chapters 1-3)
/u/prog/docu/english/xwinproc/pdf
XWIN-NMR Software Manual Part 2: Acquisition (see especially pp A37-A59 for a complete list
of acquisition paramenters and their meaning.)
/u/prog/docu/english/ xwinproc /pdf/acquire.pdf
XwinPlot Software Manual
/u/prog/docu/english/xwpman/pdf
The documentation files can be read from any PC with Adobe Acrobat software. The documentation
files can be copied to a Zip disk, or copied via FTP. The IP address of the SGI is 130.64.4.40. See Dave
Wilbur if you need help transferring files or getting a copy of Adobe Acrobat Reader.
29. Acknowledgements
This manual is a rewrite of the manual Introduction to the Bruker AM-300 NMR Spectrometer, Training
and Operators Manual by M. D’Alarcao, D. Parkinson, C. Amass. All sections were rewritten to apply
to the DXP-300. Some sections were taken directly from the Bruker documentation.
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Appendix A--Avance File structure
NMR Data Files
All NMR data is saved to the disk in a named file. The named "file" referred to in the File/Open menu
is really a directory, containing many different files.
When a new data set is created with the File/New menu in XWIN-NMR, the directory
/datanmr/data/<USER>/nmr/<NAME>/<EXPNO> is created, where <USER> is your login name,
<NAME> is the name you give to the data set, <EXPNO> is an experiment number used when you do a
series of experiments on the same sample, such as 1H, then COSY. The following files are created.
acqu
Text file containing current acquisition parameters. If a parameter is changed, it shows
up here immediately
acqus
Text file containing acquisition parameters at the time the fid or ser file is written.
fid
Binary file containing fid as 32 bit integers, created after zg. File is 4*TD bytes long.
ser
Binary file containing all fids of a 2D acquisition as 32 bit integers, created after zg. File
is 4*TD bytes long. Data directory will contain either a fid or a ser file.
pulseprogram
A copy of the pulse program.
format.temp
Text file controlling format of the parameter printout.
pdata
Directory for processed data
The pdata directory contains the following files, in the subdirectory <PROCNO>
meta
Text file containing plot parameters in JCAMP-DX format
meta.ext
Text file containing plot parameters in JCAMP-DX format.
proc
Text file containing processing parameters in JCAMP-DX format. If a parameter is
changed, it shows up here immediately
procs
Text file containing processing parameters in JCAMP-DX format. This file is rewritten
each time the processed data is changed.
1r
Binary file containing 1D real spectrum, created after ft. File is 4*SI bytes long.
1i
Binary file containing 1D imaginary spectrum, created after FT. File is 4*SI bytes long.
1rr, 1ii
Binary file containing 2D spectra
title
Text file containing the plot title (created by setti command)
intrng
Text file containing integral ranges.
int
Text file containing integral values.
If XWIN-PLOT was used to plot the data, the following files may be found
parm.txt
Text file of parameters, used by XWIN-PLOT
peaks.txt Text file of peak intensities, used by XWIN-PLOT
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Other Files
/u/exp/stan/nmr/lists/
pp
cpd
probeheads
solvents
bsms
Pulse programs. Can be edited with edpul.
Composite pulse decoupling programs. Edit with edcpd.
List of probeheads used by prosol command. Edit with edhead command.
List of solvents used by prosol command.
directory containing shim files
/u/prog/au/
src
bin
Source code for all AU programs.
Compiled AU programs.
/u/conf/instr/spect/
uxnmr.conf
Created by cf command.
uxnmr.par
Created by cf command.
users
Directory containing permission files for each NMR user
prosol
Directory containing solvent and probe pulse lengths in files named like
CDCl3.10
nuclei
Nucleus table. Can be edited with cf command
bsmsdisp.calibr Contains min and max values of all parameters in BSMS display
/u/prog/docu/english/xwinproc/pdf
procall.pdf
acqall.pdf
au.pdf
XWINNMR processing manual in pdf format. Accessible from Help menu.
XWINNMR acquisition manual in pdf format. Accessible from Help menu.
XWINNMR AU program manual in pdf format. Accessible from Help menu.
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Appendix B--XWIN-PLOT
Although the plot parameters within the edg command provide great flexibility in plotting, managing all
of the parameters can be overwhelming. To simplify the task, Bruker has provided a point and click
plotting program called XWIN-PLOT. This is a brief introduction to XWIN-PLOT. Refer to the XWINPLOT manual for further information
XWIN-PLOT is a fully object-oriented, interactive WYSIWYG plot editor for creating high quality
printouts of NMR data. XWIN-PLOT is built on two basic concepts: Layouts and data set portfolios. A
layout describes all the attributes of graphic objects, e. g. position, size and color, but does not contain
any NMR related data. A portfolio is a list of NMR data files that can be imported into the layout to
produce a plot.
Starting XWIN-PLOT
Type xwinplot in the XWIN-NMR command line. To create a new layout, choose File/New from the
menu. To load an existing layout, choose File/Open from the menu. Several standard layouts are
available in /u/plot/layouts/*.xwp. Any of these can be loaded by typing +/<name>.xwp as the file name,
where <name> is the name of the layout.
Creating a 1D spectrum object
Click on the 1D spectrum icon. Place the mouse cursor at the upper left edge of the layout window and
press the left mouse button to place the spectrum object on the drawing. Hold the mouse button and drag
to the lower left portion of the spectral window. Multiple spectrum objects can be created to plot
expansions or a series of related spectra, such as DEPT. The contents of each object can be changed
independently (see below).
Creating a contour plot object
Click on the contour plot icon. Place the mouse cursor at the upper left edge of the layout window and
press the left mouse button to place the spectrum object on the drawing. Hold the mouse button and drag
to the lower left portion of the spectral window.
Creating a parameter list
First click on the attributes command button, and change the font size to 10 point. Then click on the
parameter list icon, and left click on the drawing at the desired upper left corner of the parameter list.
Editing NMR objects
To edit an object, first select it by left clicking one of the marking mode icons (a box of small green
squares) then clicking on the desired object. Then click on the Edit or 1D/2D Edit command button on
the tool bar. The Edit dialog window allows setting options such as axis, integrals, etc. The 1D/2D
Edit dialog window allows adjusting vertical or horizontal scale with interactive buttons, like the ones in
XWIN-NMR. Any object can be moved by middle clicking and holding, while dragging the object to the
desired location. Spectral objects can be resized by dragging one of the green boxes.
Creating non NMR objects
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XWIN-PLOT is also a drawing program that can draw boxes, text windows, arrows, etc. Click on Basic
to access the icons. Refer to the XWIN-PLOT manual for further information.
Saving the layout
If you want to save the layout for use with other data sets later on, choose File/Save As in the menu. A
file selector will appear where you can enter the name of your layout. Layout files have the extension
.xwp, and are stored in your home directory. In case XWIN-PLOT was started from within XWIN-NMR,
information about the layout filename will be saved in the current data set parameters.
Inserting data into layout objects
By default, all NMR objects in the layout will be derived from the current data file in XWIN-NMR. This
data must have been acquired or created with XWIN-NMR before it can be referred to in XWIN-PLOT.
If data is missing, the plot editor will display a warning message. To create parameter and peak lists,
choose XWIN-NMR/XWIN-NMR Interface from the menu, then use the command buttons that appear.
NOTE: The parameter and peak files used by XWIN-PLOT are different from those used for plotting
within XWIN-NMR. They must be explicitly created for XWIN-PLOT.
To change the data file that applies to any object, select the object, and click the Data command button.
A list of data files, called a portfolio will appear. If the desired data file is in the portfolio, choose it and
click Set. If it is not in the portfolio, click Edit in the portfolio, choose the data from the search box,
click Append. Click Apply after all the data you need is added to the portfolio. This procedure applies
to all NMR objects whether they are spectra, parameter lists , or titles.
Plotting the Spectrum
Before printing, select the Options/Printer Setup entry in the menu. Check that the printer type is set
to HP LaserJet 5L, paper size to Letter. You can also set margins (Offsets) in the Printer Setup dialog
box. To print your layout, choose the File/Print option in the menu. Printing will commence after
clicking on the Print button in the print dialog window. Depending on complexity of the layout it will
take a while for a document to print, so be patient. You should see a flashing green light on the printer.
You can continue to work with XWIN-PLOT or XWIN-NMR while printing is in progress.
Predefined Layouts
Several predefined layouts are available in /u/plot/layouts/*.xwp. Any of these can be loaded by typing
+/<name>.xwp as the file name, where <name> is the name of the layout.
1D_std.xwp 1D spectrum, with parameters and integrals
1D_1expan.xwp
1D spectrum, one expanded region, with parameters and integrals
cosy_std.xwp
Contour plot, with 1D on top and left side, with parameters
DEPT_std.xwp
Three spectra, for DEPT 45, 90, 135, with parameters
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Appendix C—Probe Tuning
Probe tuning must be matched to the sample in order to minimize pulse widths and maximize sensitivity.
Although the effects are small for routine proton spectra, they can be dramatic for more complex pulse
sequences. Although the tuning changes between different organic solvents usually do not justify the
effort to tune, if you are changing from an organic solvent to water or D2O, retuning the probe is usually
worthwhile. If you are starting a long experiment, you will want to check the probe tuning.
The wobb command allows you to tune and match a probe in an easy way even when the coil is heavily
mistuned and mismatched. First copy the parameters for the nucleus you wish to observe.
Now enter the acquisition window by clicking Acquire/Observe fid window and start the wobble
routine by clicking on Acquire/Acquisition parameter setup/Tune probehead. Alternatively
enter acqu and then wobb via the keyboard. The acquisition is started and after a few seconds the
wobble curve is displayed and refreshed continuously. A vertical line is drawn at the center frequency
(SFOx) to provide optical information on the frequency which is to be tuned. The horizontal axis of the
coordinate system is scaled in MHz and labeled accordingly. Useful information like nucleus, tuning
frequency, frequency of the minimum of the wobble curve and wobble width, is displayed in the
information window. Simultaneously the LED display on the preamplifier is set and refreshed
accordingly (See “Preamplifier operating panel” on page 64.). The wobble curve shows a dip downwards
which changes while you turn the tune or match knobs of the probe. Example displays are shown on the
next page.
1. Turn the tune knob (tune sliders on the indirect probe) so that the dip moves towards the center of the
screen. Keep on turning until the dip is exactly in the center across the vertical line.
2. Turn the match knob (match sliders on the indirect probe) so that the dip becomes deeper. Keep on
turning until the base of the dip is at a minimum. This occurs at the zero level line for most probes.
3. On most probes the matching influences the tuning and vice versa, so repeat steps 1 and 2 until the dip
is exactly in the center of the screen and its base at minimum level. Then the probe is tuned and matched.
When you are finished with tuning and matching stop wobb by activating the stop button or by entering
stop via the keyboard.
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Figure 2 Examples of wobb display
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