Routine Use of the Varian Mercury
Contents
1. to Acquire Data Using VNMR Commands and Menu Buttons Click Setup If this button is not visible click Main Menu to find it Then select the observe nucleus and solvent This can be done with the two routine buttons H1 CDCI3 or C13 CDC13 or with the Nucleus Solvent button for less common combinations Certain more sophisticated experiments DEPT etc are available under the Sequence button If you want to change any parameters such as sweep width sw number of scans nt or delay time between pulses d1 type the parameter and value such as sw 4000 ret Type su ret This loads the hardware with the parameters you have selected You will note a Shim button under Setup but the standard autoshim routines are not very good Note that doing an autoshim may ruin your careful manual shim Please do not click the button since our machine does not have this excellent capability See the notes in the above section if you want to do good autoshimming using method allzs If you have locked and shimmed manually and don t want the machine to do so type alock n Ret Then initiate the acquisition with the Acquire button which offers several choices note that if you want to do Wft you must first set the exponential multiplication factor lb usually lb 0 1 or 0 2 for proton nmr 1 or 2 for C13 nmr TSRI Varian 200 User Manual MGF 6 1 03 Routine Processing In Glide processing is o2. TSRI Varian 200 User Manual MGF 6 1 03 Routine Use of the Varian Mercury 200 NMR Spectrometer Nomenclature e VNMR or vnmr refers to the nmr program that runs the spectrometer e CDE is Common Desktop Environment the operating system window that the computer boots into It has several useful utilities e Glide is the Varian menu driven program for taking spectra it is typically the easiest and most restrictive way to do so Name refers to a menu button marked Name these can appear on the at the top of the screen when using Glide just below the area reserved for typing commands these are vnmr menu buttons or in a pop up menu under discussion gt Name2 means that you click on the Name1 button to reveal the button which you then also click e Ret or ret means pressing the return key e VNMR commands can be strung together with spaces in between such as pl pscale page to plot a spectrum with x axis scale e Remember UNIX and VNMR commands are case sensitive Locking and Shimming Please note that the instrument is very sensitive to magnetic field homogeneity Poor signal strength and false multiplets are common if shimming is not good Set up your experiment in Glide or by selecting parameters and typing su Ret see Routine Data Acquisition below Acqi gt Lock turn spinning off turn lock off eject sample lower new sample turn spinning back on tu
3. btained from the convenientlhy labeled Process button Ignore FID number input the desired line broadening value 0 1 for H 1 or 2 for C higher numbers for spectra with broader peaks Click process to do weighted Fourier transform and automatic phase correction Automatic phase correction may be separately applied by typing aph Ret If you are not using Glide the Process menu button takes you to self explanatory buttons which you can use to see the FID adjust weighting factors and transform Usually you will use the Weight Transform button Alternatively the wft command can be used The spectrum you see can be manipulated using the regular menu bar commands while still in Glide To expand the spectrum click on the left limit with the left mouse button the right limit with the right mouse button and then in the A TT button does not appear click a gt Aas gt and then re set the right limit with the right mouse button The display can be expanded to fill the screen with the Resize menu button Flip toggles the bottom parameter display window on and off To phase click Phase on the vnmr menu Click on the right side of the spectrum then hold the mouse button down and adjust the phase Then click on the left side of the spectrum and drag to adjust phase Go back to the right if necessary Click the button to end and save the changes Useful tip to see the effecgt of phasing on the entire spe
4. ctive gt Th threshold button Click on the spectrum with the left mouse button and move the line to the desired cutoff height Click Return when done To set a reference place the cursor on the line to be referenced Click the Main gt Display gt Interactive gt Ref menu button and follow directions Printing Plotting Put what you want to plot on the screen Glide provides _ button which is easy to use Alternatively gt Display gt gets you a list of buttons This is a menu of options click on all that apply and then click on Page to get everything to come out Usually you use Plot Scale to plot the ppm scale and to get peak picking to print the computer will report the number of peaks at this point and get printouts of the parameters on the spectrum Click to send these instructions to the printer and get your printed spectrum These commands are also available by typing them in pl plot pscale plot the scale pir put integral values below plot pap put parameters in the upper left hand corner ppf plot peak frequencies on top of spectral display pll plot line listing on the spectral display or separate page page print out the spectrum pleosy 12 1 3 1 is a standard COS Y plotting command To plot an inset display the wide limit spectrum you want to plot save the current display with the sl command plot the current spectrum using line commands such as
5. ctrum instead of just the highlighted part type phasing 100 before you begin To adjust the vertical scale hold the middle mouse button down and drag the mouse up or down Clicking above or below the baseline also adjusts the vertical scale If you are integrating this will adjust the integral levels Integration is controlled by a menubar button Main Menu gt Interactive gt that has three states no integral full integral entire spectrum without breaks and partial integral with breaks Integral break points are automatically set by Glide and they are often quite good To set your own be in partial integral mode and use the following remove all break points with cz command remove individual break points by clicking Resets and then putting the cursor next to the break point and pressing the right mouse button Keep clicking that button to remove all break points to insert break points click resets menu button then put cursor at desired point and click with the left button To adjust the level and tilt of the integrals click the LvI TIt button Then hold the left mouse button down on the spectrum and move the mouse up or down to adjust level the right mouse similarly adjusts tilt Click Return when done To set an integral value position the cursor in the integral and click a TSRI Varian 200 User Manual MGF 6 1 03 Peak Picking is done by selecting Main Menu gt Display gt Intera
6. pl pscale pir page place two cursors around the region you want to inset type inset Ret Move the inset into position by dragging with the right mouse Vertical position can be changed by clicking on the cursor line with the Center button Vertical scale of the inset is changed by clicking in the inset display with the center mouse button The width of the spectrum is adjusted by dragging with the left mouse button To customize plot appearance and create pict files for graphics export use jdesign routine See Getting Started manual or MGF for more information jplot is the command to plot from the plot design program Saving your data If you did not specify a filename in Glide your data has probably not been written to the hard drive To do so type svf Ret The computer will prompt you for a file name which will actually be the name of a subdirectory in your user directory containing the FID processing parameters etc To load saved data back into VNMR use the rtf command Note that svp and rtp save and retrieve parameters only TSRI Varian 200 User Manual MGF 6 1 03 Archiving your data Log into the NMR computer from your lab Macintosh users will find Fetch particularly helpful and copy your data files to your own media Zip or Jaz drives are excellent Data will be purged from the computer at regular intervals Make sure you are on the NMR users e mail mailing list send your e mail address to mgfinn scrip
7. ps edu so that you will receive notice before your data is zapped Data can also be compressed for storage All nmr data is in the form of directories containing several files a recreation of the spectrum in VNMR requires all of these files To transform a directory which cannot be compressed into a single file which can be compressed issue the unix commands gt tar cvf inad tar inad fid puts directory inad fid into a single file inad tar gt tar xvf inad tar restores file inad tar to whatever it was created from in this case the directory inad fid Compression can then be done with the CDE file compression utility In File Manager expansion of the compressed file is done by double clicking on the file z file When you are done e Lock and shim the standard CDCI sample e Always exit VNMR before logging out e Exit VNMR by typing exit Ret or by clicking on the Main Menu gt More gt Exit button e Log out by holding the right mouse button down and selecting Log out Never Do These Two Things If the computer hangs up call M G Finn 4 8845 the Research Computing help desk 4 9369 or Stephanie Gates in Research Computing 4 9363 Other helpful numbers Macintosh help 4 9366 Matt or 4 9330 David TSRI Varian 200 User Manual MGF 6 1 03 Useful Notes VNMR commands nt number of scans transients sw sweep width Hz dg displays current parameters ft Fourie
8. r transform with no weighting wft weighted Fourier transform applies lb value Note you can set a weighting function resolution enhancement or s n enhancement with the button or the wti command Zero filling is done by setting fn number of points in Fourier transform to 2 np np number of points in FID Do this whenever you are using resolution enhancement cd returns you to your home directory To retrieve data into VNMR two methods exist 1 issue the vnmr command listenon then open File Manager from the CDE menu bar Find your desired data file in your directory data files are stored in export home username vnmrsys data and double click on it B in VNMR type rt Ret The system will prompt you for the file name You can then process the data as usual
9. retty fast on these buttons so you can make adjustments quickly You can make additional shim adjustments by clicking the SHIM button until Z1 Z5 shims are shown typically it is necessary to further adjust only Z3 Click Close and you re done shimming Note the standard auto shimming routine is not very good You can do good auto shimming takes 3 5 minutes by typing in the vnmr command area method allzs Ret shim Ret after shimming is done type method z1z2 Ret To save your own shim settings for a particular type of sample that you may use again type svs Ret and the system will prompt you for your desired shim file name To allow unlocked spectra to be obtained in Glide issue the command in no TSRI Varian 200 User Manual MGF 6 1 03 Routine Data Acquisition Click Glide then the big Glide Setup button Select the experiment and solvent use the right mouse button to click on the buttons to show the available choices Be sure to type in a file name if you want to save the data in your directory on disk and put comments in the box at the bottom Click Setup to finish this window Click the Glide Acquire button Select the parameters displayed then click Do The machine will acquire the data It is not possible using Glide to do something else while data is in acquisition unless you open an entirely new vnmr session See MGF to learn how to do this Alternative Method
10. rn lock back on If shim is likely to be way off load standard shim parameters by typing the following vnmr commands rts filename ret shim files have the same name as the solvent cdcl3 c6d6 acetone d20 etc su ret Adjust Z0 lock power and lock gain to the values in the table below lock power and gain can be higher if the sample is highly concentrated has undissolved stuff floating around or has nondeuterated solvent mixed in Note however that lock power can be so high as to saturate the signal and reduce the lock signal You know you are saturated if you reduce lock power and the lock level goes up TSRI Varian 200 User Manual MGF 6 1 03 Solvent Lock Power LockGain Z0 eoc B3 a oo CDe 16 25 900 D O 18 26 1100 acetone d 16 25 1000 CD CN THF d DMSO d pyridine d CD 0D toluene dg Shim A screen showing the lock level coarse bar on top fine bar under this and a set of shims Z1 Z2 Z1C Z2C should appear If other shims are showing click the toggle button marked SHIM until the above four shims are shown Adjust only Z1C and Z2C to maximize the lock level Adjust lock gain or lock power to put the signal back on scale if it goes over 100 Note that the left mouse button accomplishes the adjustment shown on the button 4 or 16 for example clicking on these with the right mouse button sends the value the other way 4 or 16 The response is p
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