Department of Chemistry NMR Facility
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Acquiring a Spectrum Using ICON-NMR on the Bruker500
Correct Login Procedure and Restarting Information---Security is tighter on this machine which dictates some attention to matching the user to who started XWIN. You must be logged into your UNIX account. Note: If the Bruker300 is down and the Bruker500 is handling its jobs then you may login as advanced with the supplied password and run iconnmr.
Signing Up for Use---Use Netscape Calendar. See the NMR manager for specific directions.
READ IN A PARAMETER SET---To bring up a long list of parameter sets, type rpar or if you already know the name of the specific parameter set you want, you can simply type; for example, rpar csd.ezproton all or rpar PROTON all in the pink command line area. If running an experiment that involves two nuclei both must be tuned. In the is case recall an experiment that involve both nuclei (i.e. C13CPD involves 1H and 13C) When a new parameter set is recalled you must always type eda
and scroll down about half way down the window and change the solvent to what you
are using and change PROSOL to true. Click Save to exit from the acquisition list.INSERTING YOUR SAMPLE ---First you need to take the current sample out of
the magnet and replace it with your sample. Type ej. Remove previous sample. Insert
your sample into the depth gauge so that the bottom of the tube rests on the white disc.
Remove your sample from the depth gauge and put your sample into the sixpack on top
of the magnet. (DO NOT PUT THE DEPTH GAUGE IN THE MAGNET!!!!!) Type
ij to insert sample. Start spinning by typing ro and answering yes and then making sure
ate is at 20 Hz. You can also control lifting and spinning by typing bsmsdisp and clicking on the button SHIM. There are buttons here that control lifting, spinning and
shimming. It is highly recommended you acquaint yourself with the BSMS display.
On the Avance 500, you also have the option of using the BOSS keypad to remove,
insert, spin and shim your samples. On the keypad, you can simply hit the Lift Off/On
button to activate or deactivate the Lift air. (Top row of buttons first from left) Spinning
is controlled by the spin button (top row third from left).LOCKING AND TUNING---First recall some starting shims by typing rsh
filename. Use 5mm.tbi.cdcl3 for CDCl3. Next, type lock. A list of solvents
abbreviations will be displayed. Select your solvent from the list. You can also type
lock "solvent abbreviation" if known (i.e. lock cdcl3 for locking onto cdcl3) On the 300MHz NMR: tuning is handled automatically for you. On the 500MHz NMR: You will need to tune the probe to each nuclei you are observing, starting with the lower
frequency and moving up. Typing a then wobb will display the tuning curve. The NMR
manager will need to show you how to tune the probe. Make sure to type or click on
stop otherwise you will get an error message saying there is already an acquisition
running.VIEW THE LOCK SIGNAL---Open the lock display by typing lockdisp by
selecting Lock from the Windows from the main top menu bar. A new window will
open and you should see a red and white trace moving across the display window. You
will need to observe this window while you are shimming.SHIMMING---You should have already read in a starting shim parameter set in
step 5. If it is not already open, open the Shim panel by selecting it from the BSMS
display (must type bsmsdisp to display the SHIM panel).. (NOTE: If the Shim panel
items all appear “grayed out”, you will need to turn on the shim panel by selecting “turn
on” from the display submenu of the BSMS panel). Adjust the z and z2 shims ONLY
to maximize the lock trace (do not adjust any other shims). First, click on the shim you
want to adjust and then place your red arrow on the +/- bar at the bottom of the shim
panel. You can then adjust your shims by using the left and middle buttons to increase
or decrease the shim value. You can always go back to the original value of the shim
you are working with by reclicking its shim button. If the lock trace goes off scale, you
can bring it back into view by clicking on the Lock Gain button and adjusting it until the
lock trace drops down in the lock display window. Then continue to adjust the z and z2 shims until you are satisfied (you can also change the step size of your adjustment to
make coarser or finer adjustments by factors of 2 by changing the stepsize in the bottom
right corner of the Shim panel). When you have finished shimming, put the shim panel
away by selecting Close Shim Panel from the BSMS panel. Close the lockdisplay by
using the quit button in the lower right corner of the display (note: do not close the
lockdisplay by any other means). Put the BSMS display panel away by selecting
Display, then exit. On the Avance 500, you also have the option of using the BOSS
keypad to shim. On the keypad, you can adjust z1, z2, z3, etc. by activating both the
ON AXIS button (lower left) and the selected shim. When you have finished shimming
on 500, set the keypad to STD BY.STARTING ICON-NMR---If only XWIN-NMR is open type iconnmr in the pink text field (there is a menu option under Window in the main menu if you prefer menus). If only the desktop is displayed then follow this sequence:
1) Open a shell by going to the Tool Chest on the desktop and choosing Desktop-->Open UNIX Shell.You will be prompted by icons during this process.
2) At the prompt type in xwinnmr
3) In the command line of xwinnmr type iconnmr1. ROUTINE SPECTROSCOPY---Obtain a login ID and password from the NMR Lab Manager. Click on Routine Spectroscopy and scroll down to your login ID and double click. nEXT, Enter your password and press enter.
2. INJECT/EJECT---Three important reminders for this operation:
The first window you are presented with allows you to eject the sample currently in the machine and allows you to insert your sample. Click on Insert New Sample and wait till you hear air escaping from the top of the magnet. Remove the tube and spinner assembly that is lifted up and replace with your tube and spinner assembly. Fist you must insert your sample into the spinner and set the correct height using the depth gauge on the cabinet above the sample preparation area. Clean your tube and spinner with a Kimwipe and insert into the magnet. There are pictures detailing this process in the lab. Once your sample is being held at the top of the magnet by air click OK in the pop up window.THERE IS A HIGH POTENTIAL FOR DAMAGING THE NMR IN THIS PROCEDURE SO YOU MUST SEEK TRAINING FROM AN AUTHORIZED USER BEFORE INSERTING YOU SAMPLE INTO THE MAGNET. NEVER TOUCH THE TUBE AND SPINNER WITH BARE FINGERS. MAKE SURE THE YOU HEAR AIR COMING FROM THE MAGNET BEFORE YOU INSERT YOUR SAMPLE. 3. EXPERIMENT---Click on the Data Set Filename icon. Type in or choose from the pull down menu a file name then click OK
4. SET SOLVENT---Choose you solvent from the list and click OK.
5. SET EXPERIMENT---Choose the experiment you wish to execute. A normal proton is named PROTON. See the NMR lab manager or someone with experience if you wish to try a new a different sequence. You can enter a plot title here if you wish.
Before starting you can investigate the acquisition and processing parameters. Go to the Parameters menu option and choose which parameters you wish to edit. A few acquisition parameters that are routinely changed are:
a. NS – number of scans. Typically:
PROTON 16b. SW – size of window in ppm
gCOSY 1 to 4
gHMQC 4 to 8
gHMBC 8 to 16
C13CPD 1k to 20k depending upon probe and concentration
C13APT 1k to 20k depending upon probe and concentrationPROTON to encompass all peaks of interest (sw = max ppm - min ppm)c. TD – number of points the FID is sample with.
gCOSY The F1 and F2 columns need to be identical to the value used in the 1D proton experiment.
gHMQC The F1 column needs to be identical to the value used in the proton experiment. The F2 column need to be 250.
gHMBC The F1 column needs to be identical to the value used in the proton experiment. The F2 column need to be 250.
C13CPD 250
C13APT 250PROTON 64k for a 20 ppm window and 32k for a 10ppm windowd. O1P or O2P – center of SW in ppm
gCOSY The F1 column needs to be 2K The F2 column need to be 128, 256 or 512 depending upon desired resolution.
gHMQC The F1 column needs to be 2K The F2 column need to be 128, 256 or 512 depending upon desired resolution.
gHMBC The F1 column needs to be 2K The F2 column need to be 128, 256 or 512 depending upon desired resolution.
C13CPD use default
C13APT use defaultPROTON calculate using o1p = sw/2 + min ppm. sw determined by: sw = max ppm - min ppme. If TD is changed for any experiment then the processing parameter SI needs to be set to ½ of the TD value.
gCOSY The O1P needs to be identical to the value used in the proton experiment
gHMQC The O1P needs to be identical to the value used in the proton experiment. The O2P needs to be 110.
gHMBC The O1P needs to be identical to the value used in the proton experiment. The O2P needs to be 110.
C13CPD 110
C13APT 110You can also choose Show approximate experiment time to see what effects your changes made.
6. START---Click on start to initiate the experiment.
7. PROCESSING---To look at the spectra in detail in XWIN-NMR go to File-->Exit ICON-NMR then File-->XWIN-NMR. To process go to step 11 in the XWIN-NMR instructions.
8. EJECTING SAMPLE---The easiest way to eject your sample is to open XWIN-NMR by the steps outlined in step 7 and type ej to eject you sample and type ij to insert the standard sample. If you are running another sample then just type ej and remove your sample and then type ij and insert NO sample. Your sample will be insert in step 2 above.