Stanford University Chemistry Department NMR Laboratory Policy Guide

     The instruments in the Department NMR Laboratory are available for use by “Qualified Operators” in accord with time constraints posted for each instrument. In general, use is restricted to shorter time slots during prime time hours (08:00 to 18:00) with longer experiments performed at off peak hours as much as possible. The management reserves the authority to make exceptions to this policy when, it its judgment, it is necessary or desirable to do so. Exceptions to this policy must be approved by the director of the facility, Dr. Stephen Lynch.


     Qualified Operators are persons who have received instruction from a TA (initial instruction is normally done by one of the TAs- Sushant Malhotra, Brian DeChristopher, or Matt Kiesewetter, and then have successfully completed a check out on the instrument with Dr. Lynch at which time the user will be given his/her own account. Before being awarded his/her own account, a user can use an instrument with help from a member of their lab; however, the lab member must be present, or both users NMR privileges will be suspended. All users will be checked-out on the Inova 300 first in order to become acquainted with the software before using any other instrument. The check out involves demonstrating the ability to use the instrument properly, including changing samples, finding the deuterium lock signal by adjusting the Z0 offset and ‘locking’ on that signal, adjusting the lock power, lock gain and lock phase; adjusting shims to obtain satisfactory resolution; setting a reference signal; and printing the proton spectrum with integral set for the number of protons in a specific signal. The spectrum should be plotted with the integral, identifying text, parameter list and integral list followed by correct log out procedure. When this is successfully completed, the operator will be given an account and password on the instrument and a permit to get a key to the NMR Lab (17A) for access after hours. Passwords and keys are not to be shared with others who have not yet become qualified operators. However, qualified operators are encouraged to assist operators who are not yet qualified by logging in for them and being available to help them if needed. Persons found to be using someone else’s password will be cause for that password to be changed. The owner of that password will be unable to access the instrument until they see the Lab Manager to get their password restored. Once a user is completely with the software, a user can be checked-out on the Mercury 400 or Inova 500 for passwords on both instruments. Check-out will be done by Dr. Lynch. In general, the Mercury 400 and Inova 500 are to be used for higher sensitivity/better resolved 1H NMR, higher sensitivity 13C NMR, variable temperature NMR, or basic 2D NMR. In addition the Mercury 400 is useful for 19F or 31P, while the Inova 500 can be used to detect nearly any nucleus detectable by NMR. Further information is listed here:

NMR tubes – Sample Volume

     The probes on superconducting magnets have close tolerances and are sensitive to NMR tube quality and sample volume. Only high quality tubes should be used. The so-called “Thrift” or “Throw-away” tubes can be sufficiently out of tolerance as to cause damage to a probe. Tubes heated above 100 degrees in a drying oven may become warped or bent. There is a high probability of spinning side bands or other spectral degradation with these “bargain” tubes and with overheated tubes which have become warped. For routine work, tubes of a quality at least equal to Wilmad 507PP tubes (5mm od) should be used for routine work. For best results with critical samples (2D or NOE experiments) tubes of quality equal to or better than Wilmad 528PP are recommended. Tubes that are 7” long are OK in all systems. Longer tubes may be desirable if the tube is to be sealed off in a flame. Tubes with chipped or cracked edges constitute a safety hazard and should not be used. Tubes shorter than 6 ¼” should not be used. A filtered volume of 0.6 ml is recommended for 5 mm tubes. Smaller volumes require much more adjustment of shims and can easily take more time to shim than to collect the data. The absolute minimum volume is 0.4 ml, but shimming will be difficult.


Logbooks / Problems

     All the instruments have accounting software that maintains a chronological log of instrument use. In addition the systems have paper logbooks. Users are requested to enter their name, research group, start and finish times, nucleus, and temperature if other than ambient temperature was used. If problems are encountered, a description of the problem should be entered in this logbook. It is helpful to NMR personnel to be able to contact persons who have experienced a problem in order to know what needs to be fixed.


Saving / Archiving Data

     Files may be saved in your home directory on any instrument. As of now, there are no disk space problems, so the data will be there indefinitely. Data can be transferred to a personal computer and written to CD which will likely be directly readable in NMR CD drive, but at least will be readable by personal computer and transferred back to NMR lab computer. 


Logout / Stand-by Conditions

     Before log-out, operators should return the instrument to stand-by conditions for proton acquisition in CDCl3 solvent with the deuterium lock engaged and shims set for the standard sample. This is especially important if you have used a solvent other than CDCl3.

     On the NMR systems it is important that all acquisitions be halted (“aa”) and the vnmr program be exited (by typing “exit” in the command line or using the mouse to select [Main Menu], [More], and [Exit] buttons before exiting UNIX. To do otherwise may corrupt your user file which will require help from NMR personnel to restore it. 



     Be very careful inserting and removing sample tubes in the spinner turbines to avoid loss of important samples and possible cut hands. The tubes have very thin walls and are easily broken. In the event a reference sample is broken (outside the probe) please leave a message for the TA or Lab Manager so that the sample may be replaced. If any sample gets broken (outside the probe) please clean up in an appropriate manner for the material and dispose of the broken glass and sample in proper places. If an injury results, it must be reported to the Departmental Safety Officer in the main office (121 Mudd). If the injury is serious, have someone take the injured party to Emergency.

     If any sample gets broken in the probe, it is important to the performance of the NMR to get it cleaned up as quickly as possible. Notify the TA in charge of the instrument (by phone or in person). The sooner the matter is addressed the less likely there will be permanent damage. For samples broken in the probe please leave a note on the instrument keyboard warning users not to use the instrument. Include your name and your lab and home phone numbers so we may get additional information if needed. Minimum information needed: name and structure of compound if known, or at least class of compound, name of solvent, toxicity of material, other solvents which dissolve it, special precautions in handling it if toxic. This is important for those of us who will need to clean it out and for the probe shop if we have to send it in for repair.


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