Department of Chemistry NMR Facility
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Acquiring and Processing a Proton Spectrum in XWIN-NMRIf you are working with a spectrum acquired by ICON-NMR start at step 11.
If you want to process spectra on the PC start here.1. GETTING STARTED---There are several ways to enter XWINNMR:A. If you are in ICONNMR, exit to XWINNMR (if you have privileges).2. CREATE A FILE WHERE YOUR DATA WILL BE STORED---Select File, then New (or type edc). Edit the file name and the experiment number and user to your icon login name. Make sure the disk unit is /x. Click Save.
B. I f you are in an Unix shell, you will need to login with the correct ID and password. Next, type xwinnmr (small letters, no spaces) to bring up the XWINNMR window.
C. If you are starting from a blank desktop go to the Tool Chest (upper left corner) and click on Desktop then choose Open Unix Shell. You will need to login by typing "login your ID". Next, enter your password then at the prompt type xwinnmr.
3. 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. 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.
4. 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 rate is at 20 Hz. You can also control lifting and spinning by typing bsmsdisp and clicking on the button SHIM. There are button 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).
5. 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 move 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.
6. 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.
7. 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.
8. ACQUIRING YOUR DATA---Type rga and when it is finished then type zg. You will now begin to collect data. (Note: You can observe the FID by selecting it under the Acquire menu or typing a---you can return to the 1D window when the FID is finished by clicking on the return or by typing return. Typing any of the processing commands when the acquisition is done will also automatically switch back to the 1D window. If you need to stop the acquisition and save your data, type halt. The command stop (either typed or selected on the acquisition window) will end the acquisition without saving the data. Changing acqusistion parameters such as the sweep width (sw), center of window (o1p) can be accomplished by typing eda and finding the parameter. Talk the NMR manager about the various parameter to change.
9. PROCESS YOUR DATA--- When your acquisition is finished, type ef (this is a combination of the commands em + ft) to apply an exponential multiplication and to Fourier transform your data. You can also select this option under the Process, then special processing, then sequential operations submenu. As an alternate here, you can also type efp which performs em + ft + pk (this performs a phase correction based on last phase correction performed ---i.e. this is useful if you are running a series of spectra and want to apply the same phase correction to each).
10. PHASING YOUR DATA---You have several options here but the two most common (i.e. simplest) to use are: (1) Automatic which you invoke by typing apk or by clicking Process followed by Auto Phase correction. The corrected spectrum will then be displayed. Option (2) Manual phase correction can also be selected from the Process menu or more simply by clicking the phase button on the left side of your screen. First multiply your spectrum by 2 until you can see the baseline clearly. You may chose to phase using the biggest peak in the spectrum or you may select a peak of your own choice. Some people prefer to phase first on the leftmost peak in your spectrum. The choice is up to you. If you choose biggest, the largest peak in the spectrum will be automatically selected and an initial phasing will be performed. If you wish to phase on another peak, select cursor and then select the peak upon which you want to phase (you should see a vertical dashed line on the screen). Click on ph0 and then while holding the left button down, adjust the phase by pushing the mouse forwards and backwards. Click on ph1 and while holding the left button down, phase the spectrum at a point far from your original pivot point. For example, if you choose to phase on the far left peak, pick a point on the far right of the spectrum. When you have finished phasing, click return and save.
11. EXPANDING REGIONS OF YOUR SPECTRUM---Click the left mouse button to attach your cursor to the spectrum. Click the middle mouse button once on each side of the region to be expanded. Click left mouse button again to detach from spectrum.
12. CORRECT THE BASELINE (optional)--- Type abs. Note ---if you use this command, it will automatically do your integration but most of the time it is unsatisfactory.
13. SET THE REFERENCE PEAK (MANDENTORY)---Expand the region around the desired reference peak as described above and then click Calibrate. Attach the cursor to the spectrum by clicking the left mouse button. Put cursor on desired peak and click the middle mouse button. Enter the reference frequency.
14. INTEGRATE YOUR SPECTRUM---Select the Integrate button at the left of your screen. If you used the abs command above, you must first click Delete under the all section to remove the integral file created by the abs instruction. Next, attach the cursor to spectrum by clicking left mouse button. Apply integration by clicking middle button before and after each peak to be integrated. Give plenty or room to establish a flat baseline before and after each integral. To set the area of an integral to a specific value, select the desired integral as the current integral (double click on the integral). Click Calibrate and enter the desired value for this integral. Click return and select save as ‘intrng’& return. If you ever want to modify your saved integral click on Integrate and then under File choose read intrng.
15. SET UP PLOT PARAMETERS --- Expand the region you want to plot and click on DP1 or type dpl1. Press enter 3 time to respond to the questions. Type pscal preg. This command will make the tallest peak in your defined plot region cy centimeters in height. Usually one sets cy to 10 cm by typing cy 10. In summary, one usually one types pscal preg and then cy 10 for "normal" spectra. You can type pscal global and cy 10 and then tallest peak in your entire spectrum will by scaled to 10 centimeters in height. Using pscal global or preg will sometimes make it impossible to print small peaks in the presence of larger peaks, to rectify this type pscal preg and then cy 0. With cy set to 0 the scaling you see on the screen will be used to plot. Type view to see if the scaling is to your satisfaction.
Detailed description: (Note: the vertical scaling of your plot is controlled by a combination of two parameters: CY and PSCAL. If CY >0 and PSCAL = global, then the highest intensity in your entire spectrum serves as the reference intensity to which all other peaks will be scaled. If PSCAL is et to preg, then the highest intensity in the plot region (as you define it) serves as the reference. If CY = 0, then the spectrum will be plotted with exactly the same vertical scaling as you set up on the display. If CY = -N, the spectrum will be scaled relative to the last spectrum plotted with CY>0 with a factor N applied; i.e. CY=-1 would be scaled according to last spectrum.) First, you can click plotreg to show current region to be plotted. If it is what you wanted, proceed. If not, then you will need to define the plot region and there are a variety of ways to do so. Probably the simplest way is as follows. Set CY=0, set PSCAL = preg. When you have expanded your spectrum to display the desired region (as described in #11 above), click on DP1 and the plot limits will be set to the current limits (just hit in response to the questions). Or you can set PSCAL = global, CY= 10. (the units are in cm), click on DP1 and hit return in response to the questions. Note: you can also set CY interactively under the utilities window, but in that case, PSCAL must be set to global.
16. PRINTING CHEMICAL SHIFTS ON THE SPECTRUM OR AS A LIST ---To do your peak pick, click on utilities, select MI (or type setmi) and move horizontal line such that any peak maxima below are not picked and any maxima above are picked. Click left button to set mi to that point. You can also set the MAXI parameter if you wish (found through the Utilities button). Peak picking will not pick any peak outside the limits defined by MI and MAXI. Click return to exit from the Utilities menu if in the Utilities mode. To change the units from the default value of Hz to ppm, type plunit, click on ppm. You can also simply type plunit ppm or plunit Hz. To print the peak values on the screen type plabels yes and then plcolor blue. You can also find these parameters by typing edg. You should type view to see if the correct peaks are be picked for plotting if you choose to print them on the plot.
Type pp to print peak listing or select Peak Picking from the Analysis menu, followed by print peak list. From that submenu, you can also select pps to view the peak list on the screen
17. PLOT YOUR SPECTRUM---You can plot directly from XWINNMR with use of the plot command (the older plotting program) or you can exit to XWINPLOT (a “what you see is what you get” plot editor) and create your own templates and plot from there. (If you wish to use XWINPLOT, refer to the XWINPLOT manual. You have lots of plot parameters, which can be viewed and modified in XWINNMR by typing edg (edit graphics). To plot from XWINNMR, follow Step 15 above. In order to avoid wasting paper, you should preview your plot before actually printing it. You can do this by typing view; a copy of your plot will appear. After previewing your plot, click quit to exit the preview mode. Type or click plot to plot your spectrum.
18. FINISHING UP---To remove your sample from the magnet, you have several options: On the 300, you may: 1) go back to ICONNMR (i.e. type iconnmr in the pink command line area or invoke ICONNMR from the Windows menu) and remove your sample via the normal iconnmr routine; or 2) you can select Windows, then BSMS display, then Sample. Turn Lift on. Remove your sample and replace with the standard sample. Turn Lift off; or 3) type ej in the command line window to eject your sample, replace it with the standard sample and type ij to insert the standard sample. On the 500, you may: 1) select Windows, then BSMS display, then Sample. Turn Lift on. Remove your sample and replace with the standard sample. Turn Lift off; or 2) type ej in the command line window to eject your sample, replace it with the standard sample and type ij to insert the standard sample; or 3) on the keypad, select LIFT ON-OFF, wait for your sample to come up, replace it with the standard sample and reselect the LIFT ON-OFF key. In any case, you should always relock on the standard sample solvent (CDCl3).Note 1 –To call up old data files in XWINNMR, click on File, then Open, then select dir. The current month's data is is /x and data as of August 1, 2001 are stored in /x/archive. You will get a list of files under the current user account from which you can select the data file you created in ICONNMR or a previous run of XWINNMR. As another option, you may select Search from the File menu. You will get a list of files for all users from which you can select your file. The command diro will give an owner list of files. The directories /y and /y/archive have the same format as discussed above but are for the SGI machine you are NOT using. Here is the directory structure:
On either machine think about it in this way:
Present month and this machine /x
Present month the other machine /y
Past month and this machine /x/archive
Past month and the other machine /y/archive