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Nuclear Magnetic Resonance Facility

Instructions For Operating The Varian Unity 300 MHz NMR Spectrometer

1. Sign your name, date, time and type of experiment you are going to run in the logbook. Please make a note of any problems you encounter-no matter how trivial they may seem.

2. At the VARNMR LOGIN: prompt type your username (such as cds, cdup, jbw, etc.). The login name will be the name of your research group. Passwords are no word for all user accounts. After entering the password the VNMR window will appear after a few seconds.

3. Click on Main Menu then File followed by Set Directory. Choose the Home button.

4. To setup an experiment you can display the experiment library by typing explib or by clicking on the workspace button. Type j1 to go to experiment 1. Next choose the Setup button and choose the appropriate nucleus and solvent button. If you are going to run a routine 1D experiment like 1H or 13C{1H} in CDCl3 then click on those buttons and then type SU. For nuclei and solvents other than these choose the nucleus/solvent button and then choose the desired nucleus. If the nucleus doesn't have a defined button then click on other and type in the nucleus (such as Si29, Pt195, B11 etc) then follow with the choice of solvent and su. You can also setup the experiment by typing in setup(nucleus,solvent) manually. When you want to run an experiment other than a standard 1D experiment choose from the list of optional experiments by clicking on the choose Select Pulse Sequence option. A new set of buttons will appear listing several 1D and 2D experiments such as INEPT, DEPT, COSY, HETCOR, etc. Just click on the one that you want to run. After you have chosen the type of experiment then type su.

5. To insert your sample type I for insert or E to eject it. Typing rts('std') su. To open the lock/shim display window click on acqi button. The window should appear. To display the FID type df.

For interactive lock and shim adjustments in the acqi window use the mouse to make adjustments in this window. To lock the sample increase the Lock power and Lock gain so that you can see a signal (sine wave pattern). A setting of about 45 for the lock gain and lock power should be sufficient to see the signal. Turn spinning on and Lock off. Adjust Z0 incremental until you are on resonance(wave pattern become straight line) and then click on the Lock on button. The sample should now be locked. Decrease the Lock power and Lock gain to maintain the lock so that it is not saturated (approx. settings: lock power = 36 and lock gain = 40) and the lock level is approximately 40-80%. Adjust the Lock phase to get the maximum signal. Keep the spinning rate set at 20 Hz.

Click on Shim button for interactive shimming. A course and fine meter display will show the current lock level. Use the mouse to adjust the shimming by small increments (X1) or large increments (X32). Maximize the lock level by adjusting Z1 and Z2. You should have to adjust Z1 and Z2 only to increase the value as high as possible. You can manually shim then choose an automatic shimming routine by clicking on the shim auto option. Choose the L > M quality and the Z1-Z2 shim option. Click on the start button when you are ready to start the auto shimming. When the auto shimming is completed be sure the lock level is approximately 50-80% then click on the close button to close the Acqi window.

6. To setup and tune the probe be sure that you are in the appropriate experiment number that has the correct frequency for the nucleus that you want to observe (i.e. you have already gone through the setup procedure and typed SU). There are 2 channels on the Unity-Plus system: 1 and 2. Channel 1 will always be the observe channel and channel 2 will be the decouple channel. For example if you are going to run a 1H , 13C, or 31P experiment then you will tune channel 1 for those nuclei. For almost all applications you will not have to tune the probe for 1H UNLESS you will be working with very polar or ionic solutions or you are going to run an experiment that requires precise tuning. If this type of situation should arise then see Rensheng Luo for instructions on tuning for proton. If you are going to run a 13C{1H} or 1H{31P} experiment then you would tune carbon or proton, respectively on channel 1 and proton or phosphorus, respectively, on channel 2.

Certain nuclei will require connecting a different coil (the standard configuration uses the 1/4" WL 60-130 MHz coil) or insertion of tuning rods (such as Silicon which uses the cap stick #20). Table 4 shows the frequency range for nuclei and the rod required. The other available coils are used for 45-65 MHz (1/4" WL) and 20-40 MHz. For most experiments you won't have to change the current configuration. Please see Rensheng Luo for instructions if you need to change the configuration.

Connect this cable in the front of the tune interface part of the magnet leg labeled Probe J5321. The red light will flash. Change the channel position to 1. Adjust the attenuation so that the reading of the signal on the meter is on scale. Manually adjust the match/tune1/tune2 screws to the approximate settings listed on the card taped to the magnet support. Start by adjusting the tune 2 screw to minimize the meter value. Then adjust interactively the match/tune1 screws until the signal on the meter is minimized. Adjust the attenuation to 8-9 to see the full minimization. The meter should read < 20 at an attenuation of 8-9 when the tuning is completed. When the tuning is completed set the atten back to a setting of 6 and the channel position back to 0. If you forget to do this the experiment will not run. Re-connect the cable form the front of the tune interface connection Probe J5321 to the B Band probe connection at the blue filter on the back of the unit. IF the probe is not tuned properly then this will result in possible damage to the probe and a poor signal to noise ratio. In addition, if the decoupler channel is not tuned properly then inefficient decoupling will result. Once you have the probe tuned then you can change acquisition parameters as needed then start your acquisition.

7. The acquisition parameter menu can be displayed by typing dg. The parameters are changed by typing in for example nt=256 followed by return. To enter any parameters that are designated by letters then you must put single quotes before and after the parameter (for example dm='yyy' or gain='n'). When you are ready to start your experiment choose the Acquire button. Choose go or go, wft (the latter will perform a wft after each collection of bs) or go, periodic wft (this will automatically perform the wft command after each BS is collected). The show time button will tell you how long the experiment will take. The experiments can be started by typing in the words go or ga and the time for the experiment can be displayed by typing in the word time. The Varian Unity Plus has a 2 MHz NMR module that allows the users to look at a large display window of up to 2,000,000 Hz (but gives poor resolution).

8. Temperatural control experiments to use the styrofoam dewar to cool the vt coil with liquid nitrogen. DO NOT USE DRY ICE/ACETONE BATH for cooling. It will dissolve the styrofoam container. Type vttype=2 then temp=xx (i.e. temp=-20, values are in degrees C) su to set the temperature. After the temperature reaches the value, type vttype=0 su. The temperature is displayed on the lock level meter unit next to the computer monitor.

9. To process the data, type wft. Type aph to perform the automatic phasing or choose the phase button the click on the left mouse button and drag the mouse until the desired level of phasing is obtained. Type ds to get out of the manual phasing mode. The middle mouse button adjusts the intensity of the spectrum. Drag the mouse to make smaller changes and click on the middle mouse button to make larger changes-above peaks to move up in intensity and below the top of the peak to decrease the intensity. The left cursor on the mouse will display one red cursor line and the right mouse button will place a second cursor on the screen. Choose the expand button the expand a defined region shown by the two cursors. The full spectrum can be shown by the full button or by typing f.

To integrate the spectrum first click on the integrate button. Choose partial integral or full integral then:
1. type cz to reset the integral values, cdc to cancel drift correction and dc to apply drift correction.
2. type intmod='partial' to display integral peaks (no baseline)
3. click on Next then Resets buttons
4. type z or click on left mouse button on left side of farthest left peak to cut the first integral

Type z or move the mouse to the right side of the peak and click on the left mouse button to define the other side of the integral. Repeat this for all peaks of interest
5. type vp=12 to move the spectrum up to allow for plotting the numerical integral values
below the peaks.
6. click the center mouse button to adjust the intensity of the integrals.
7. enter ins='x' where x is a numerical value that you wish to assign to the integral value
8. type dpirn to display the numerical value of the integrals.

To set the threshold for the peak picking choose the th button. Move the left mouse button to set the position of the threshold line. Type dpf to display the peaks found on the screen. To inset a spectrum first type s1 to save the current setting then display two cursors around the region that you want to inset then type in the word inset (for plotting see below). To return to the full spectrum type r1. If you forget to type in the s1 command in the beginning then to get back to the original spectrum you must change the following parameters: wc=400, sc=400 vp=0 then ds to display the full spectrum.

10. To save the spectrum it is best to type out a text command. The text command allows one to designate a filename and a description that will be associated with the dataset file. To enter a text command type in text('abc=description of data') where abc is the filename that you will save the data under and the written portion after the = sign is a personal description of the sample, notebook page, solvent etc. that you choose to enter for the sample under study. Next be sure that you are in your home directory by typing pwd. It should display a directory string of either /home/group or /exports/disk2/group where group is your research group name which is the same as your login name (i.e. cds, cdup, jbw, etc.). If you are not in your home directory then click on the file button, then choose set directory button and then the home button. It should now display your home directory on the top of the display screen. To save the data type svf('abc') where abc is the filename that you assigned to the dataset. There is a 10-12 character limit for the filename. This creates a directory for your data with a .fid suffix that contains raw data (fid), processing parameters, acquisition log, and text file. To retrieve the data type rt('abc') or click on the file button, then choose set directory button and then the home button to display your home directory. Find the dataset of interest and click on it then choose the load button from the menu bar options. Type wft to transform the data then display it or su to use the parameters to collect new data from these starting parameters.

11. To plot the spectrum choose the plot button from menu bar. Choose the appropriate options for plotting such as plot, params, scale, peaks etc then follow with page when finished. If you want to plot the integrals they must be displayed on the screen before you click on the plot button. to plot the numerical integration values you must type in pirn. The plot commands can also be typed in manually and in a string if separated by a space in between commands: pl pscale ppf pap pirn page. When plotting an inset region first send the plot commands for the full spectrum but do not click on or type in page. Define the inset region (see above) and type in or click on the plot commands for the inset region. When you have completed the inset region and are now ready to complete the plotting then click on or type in page.

12. Under the setup menu bar option there are several sophisticated 1D and 2D experiments available by choosing the select pulse sequence button. Please schedule time with RL for individual instruction on how to run more advanced experiments.

13. In the event that you would have to turn on or turn off the computer and electronics cabinet-PLEASE follow the sequence listed below. If the computer is shut off incorrectly or rebooted improperly you run the risk of corrupting or destroying files. This is true for nearly all UNIX based computers! To turn on the system: Flip the switch on the back of the electronics cabinet on and wait 10 seconds then push the green button next to the on/off switch (both are located at the back of the cabinet on the right side). Next turn the differential box on (it is the unlabeled box located on top of the computer and just underneath the CDROM drive). Turn on the CDROM drive next and the computer and monitor last. To turn off the system reverse this sequence.

14. To finish using the Varian Unity Plus NMR spectrometer first eject your sample by the e command and stop the air flow with the i command.

To exit VNMR you must follow these steps. MAKE SURE THAT THERE ARE NO EXPERIMENTS RUNNING. If there is an active experiment (you can check by moving the mouse over to the far right of the screen and hold down the right mouse button to get a popup window-choose acquisition status. A window will appear that tells you if an experiment is running and if so how many transients have been collected. If no experiment is running it will say that it is idle. If there is an experiment running stop it by typing sa or aa or click on the abort acquisition button. Once you have determined that no experiments are running then move mouse out of the VNMR window and Hold the right mouse button down and choose the exit option from the pull down menu. It will ask you to confirm that you want to exit. The VNMR Login: prompt should then appear. Be sure to sign out in the logbook. If you have any questions or problems when your are running experiments please contact Rensheng Luo (x5330)