Open Access Manual for Superusers

Transcription

1 NMR-Service LOC Tel: 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 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 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) 1

2 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 2

3 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 3

4 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 4

5 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 5

6 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 6

7 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 broad peaks or no regions free of peaks. 7

8 Troubleshooting Guide NMR-Service: D314, 22933/26856, 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 8

9 - 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 - logout - login and check if you are successful with a normal setup - if not, try the su acqproc -proceedure a second time 9

10 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 !. Contact the NMR- Service by phone, , or post a sheet on the door of the NMR-Service (D314) If nothing helps please contact the NMR-Service: D314, / / 34734, nmrservice@org.chem.ethz.ch 10

11 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 a canned sequence of plot and print is done on the current plotter and default printer. This includes apage, iprint, dll, ap, printoff. 11

12 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. 12