Operation Procedure
Detailed Configuration and Procedural Steps to Acquire NMR Data
Varian 300 MHz is
only capable of observing
1H,
19F,
13C, and
31P, but due to hardware constraints it is not capable
of experimen
ts such as
19F decoupled
13P. The instrument has an ‘AutoSwitchable’ probe run in 4 NUC Mode. In
this configuration it does not have the broadband capabilities. However it does not
require the user to tune the probe. The instrument has
variable temperature capabilities. The spectrometer is ideally suited for quick 1D spectra but is fully capable of many of
the more sophisticated multiple dimension experiments. It does not use the same software as the Unity 400 and 500 MHz NMR's but VNRMJ. The following details procedure uses the same Varian commands used in VNMR 6.3C. However, the walkup protocol do not require extensive knowledge of these commands.
1. Login to the host computer with an assigned user identification. Access is forbidden without an account. No Exceptions. Please see adminstrative staff for training.
If the VNMR program running on login, a message may indicate vp does not exist. The previous user from forgot to type exit before logging off. Type restart in VNMR to close the current program, then reopen VNMR.
2. Click on the Spectrum icon at the bottom of the screen on the CDE toolbar, or right mouse-click the background and select VNMR.
3. The program will automatically change to the user's personal directory. A prompt will ask to load bestshim (answer yes or no). Selecting ‘no’, may require loading of any other shim set using the rts command (a previously saved a shim file has been made with the svs command). Example: rts(‘my_own_shim_file’) will load a shim file previously saved as ‘my_own_shim_file’. If ‘setup complete’ doesn’t appear in the status window in the bestshim macro doesn’t run, type reset in VNMR The macro reset will automatically stop and restart the acquisition daemon. If reset does not work, open a terminal window and type su acqproc once or twice (once to go from Idle to Inactive in the acquisition status window, and once more to restart the acquisition daemon).
4. Click [main menu] [setup] and choose the desired nucleus and solvent then type su.
5. Click the [Acqi] button. The Acquisition window will open. If the [Acqi] button is not visible type acqi in the input window. If the Acquisition window still does not open, perform an su acqproc or reset as described above. In the acquisition window click [LOCK].
6. Properly position the sample (i.e. center the solvent volume) using the depth gauge located near the magnet leg. Note that shimming the sample is easiest when the proper volume (0.7 mL) is used.
7. Click [eject], remove the standard, then place the sample on top of the magnet bore tube. Click [insert], wait until there is a click, then click SPIN: [on].
8. Adjust Z0 until the sample is on resonance then click LOCK: [on] to lock the sample. Use the highest power but do not excessive power will cause saturation. A lock power of 26 is about right for CDCl3 . Adjust the lock phase to maximize the lock signal.
9. Click [SHIM] to open the shimming window. Adjust the Z1 and Z2, start with ±64 and also use ±16. If the spectrum is going to be crowded (lot of resonances lines) for publication-quality spectrum, adjust Z1-Z5 as well.
10. Click [CLOSE]. Save shims, using the svs command.
11. The standard parameters will load the default sweep width (sw), pulse width (pw), and several other 'standard' values. Change: nt (the number of transients) to collect. To change nt, type nt=4 (or any other number). The block size is bs (default is 16 for proton). This parameter determines how often the data is written to disk. To change this value type bs=8. During long runs, this parameter allows the user to monitor the progress by typing wft (weight, Fourier transform) after the message “exp1: BS 1 completed” is displayed. Display group paramaters (dg) displays the current parameters in a ‘text window’. View the current pulse sequence with the command (dps).
12. Type ga (submit the experiment, acquire data, and perform a Fourier transform on the result) to start collecting the spectrum. If a message appears about an autogain failure appears, type pw=pw/2 ga. Repeat as necessary. Sample with too high a concentration will produce the autogain failure message.
13. Simple processing commands: aph will automatically phase the spectrum. Or click [phase] to manually adjust the phasing with the mouse. vsadj will adjust the vertical scale vs. vs can be automatically adjusted using the middle mouse button. ds will display the spectrum again and exit the phasing mode, The following adjust the vertical scale and display the scale: vsadj dscale.
14. Reference the spectrum, first locate the solvent resonance or some other reference line (such as TMS). By clicking with the left mouse button on one side of the peak and then clicking with the right mouse button on the other side of the peak then click [expand] to expand this region of interest. Place the cursor on top of this resonance and type nl (nearest line). Now type rl(7.27p) (for chloroform) or whatever ppm shift is appropriate for that resonance. The command dscale will display the entire scale.
15. Spectrum Integration: Click [partial integral] to display the integral line. Type cz to clear all resets (zeroes) already in memory. Click [resets] and use the left mouse button to define those regions for integration. The right mouse button can be used to undo mistakes. The parameter is is the integrals scale and can be adjusted using the middle mouse button while in integral mode. Type ds to regain cursor control. Place the cursor over the desired region and click the [Set int] button. A query asks for an integral value. Type ds dpir (display peak integral regions) to get the integral values displayed underneath the spectrum.
16. To perform peak picking: Click the [Th] (threshold) button to interactively define a threshold with the mouse. dpf will display the peaks in ppm. dpfhz will display the peaks in hertz. Type ds to erase the displayed ‘peak picking.
17. To add text to the spectrum: Type text('sample_date…') (single quotes required) to put in whatever text (in this case sample_date…) to be displayed in the upper left hand corner of the spectrum. To plot the text use the macro pltext. Other positioning options are available. Type man(‘pltext’) to learn more. Another option is the macro gettext. This will open a small easy-to-use text editor, which will easily allow text on multiple lines.
18. To plot the spectrum, string together any of the following plotting commands followed by page: pl will plot the actual spectra. pscale will plot the scale below the spectrum. pir will plot the integral amplitudes below the spectrum (defined earlier in step #15). pirn will plot normalized integral amplitudes below the spectrum. pap will plot out ‘all’ acquisition parameters. ppa plots a more easily understood version of pap. ppf plots the peak frequencies in ppm (above the spectrum). ppfhz plots the peak frequencies in hertz. pldate plot the current date and time in the upper right-hand corner. pltext will plot the text defined above (in step #17). page will dump the plot buffer to the plotter. Example: pl ppfhz pscale pltext page will plot the spectrum, peak positions (in Hz), the reference scale, and text.
19. Type svf save data to a file. The command rt will allows retrievial of a file. The system default to the user's home directory, if not, type gohome.
20. Click [acqi] (type acqi in the Input Window if the button is not present). Click [lock] spin [off] lock [off] [eject]. Get a sample. Click [insert], [close]. Type exit at the VNMR command line. Click on EXIT on the CDE toolbar and confirm the logout.
21. Please sign and time stamp the logbook and note any problems with the instrument.
Detailed Configuration and Procedural Steps to Acquire NMR Data with VNMRJ are given elsewhere.