A Data Processing computer is available in the lab. Data can be transfered from Spectrometer computers to this computer for further processing and viewing in TopSpin. This computer also has its own IP address to facilitate data transfer to another computer. Details of operation are posted next to it.
Sample volume should be a minimum of 250 uL for a Shigemi tube, 180uL for a 3mm/5mm tube, or 500 uL for a regular NMR tube. Insufficient volume may cause bad shimming result, and consequently poor resolution of NMR spectrum.
The NMR sample should be homogeneous, free of air bubbles or precipitate. Spin, filter, and/or sonicate the sample if necessary.
High salt condition should always be avoided if possible, as well as high paramagnetic ion concentration.
High quality NMR tubes should be used at BioNMR facility, in particular for the 800 MHz spectrometer.
For volatile organic solvent, or long term use sample, sealing the sample NMR tube with material such as parafilm is highly recommended. NMR cap itself works OK to seal aqueous sample.
For aqueous samples,
D2O concentration should be equal to or higher than 7%.
NaCN 0.02% is recommended for sample buffer to prevent bacterial growth.
For protein samples, minimum concentration of 1 mM is highly recommended for efficient NMR measurement.
Labeling your NMR tube. All samples must be labeled with sample content, solvent, and user initials. Avoid writing directly on the NMR tube since the ink can be erased easily by mistake. Using a labeling tape/tag is recommended.
1. All the adjusting knobs are color coded for different nuclei.
2. If you don't see the dip in the wobb window, first you may try adjusting T or M. Second you may increase the sweep width in Wobb window to 10 or 20 MHz.
The following are general steps to set up a 2D experiment.
Please choose IconNMR from the left side panel for details
Put samples with spinner in the carousel sampleholder, and record the corresponding positions of all samples.
In TopSpin, type "iconnmr" to open IconNMR interface.
Select "IconNMR Automation", then select user.
Double click the holder number which has your first sample.
Change/edit the following information if necessary(1) Disk and Name: By default, Disk is the current TopSpin address, something like Topspin3.5pl6, but you may want to change it to the address where you usually store NMR data, such as TopSpin 3.0. The name will be a data folder under your account
(2) Experiment number: Check the data folder first. You may set any number but make sure it won't overwirte any existing important data..
(3) Solvent: it should be the deteurated solvent in the sample.
(4 )Experiment: Please read carefully the description of the experiment to make correct selection.
(5) Priority: not necessary to set it if you submit the experiment in your desired order.
(a) Acquiision parameters. You may click on icon to edit a set of specified parameters. Or go to the top menu bar and select /parameters/Edit all acquisition paramenters, which is open the AcquPars window in topspin. After editing, you can click on Return to IconNMR to go back to Automation window. Note that you may set temperature here (TE). When IconNMR automation starts, a window will pop up asking you whether you want temperature be regulated.
(b) Locking, Shimming options. You may change the settings by clicking on . I recommend NOT to tune and match X-channels, if you will adjust it before starting the automation.
(9) Click on “Add” to add more experiments to this specific sample. Right click the experiment, you may also see "Iterate" option, which allow you to copy the same experiment including customized parameters.
The “Copy” option allows you to copy the already set-up experiment to the next holder number/sample, and then edit only what is necessary. Repeat this step to cover all the holder numbers that have samples. Use "Delete" option to remove entries that have no samples.
Review all the experiments that have been set up. Highlight the holder number, then click “Edit” will allow you to modify that experiment.
Highlight the holder number then click on “Submit” to add the experiment to the queue one by one. You may highlight multiple holder numbers at once.
Click “Start” to run the queued experiments. You may still any experiment that has not been running yet.
At the end, you must quit the automation mode by clicking on the stop icon “” . After that, you can set up single experiments in TopSpin window, which is the "manual mode".
1. Open Filezilla, go to File/Site manager, choose New Site, put in information such as host name/IP, user name and password, and then select Connect or OK to finish the site setup.
2. In Filezilla main window, click on the icon "open the site manager", and choose the remote computer you want to access.
3. If all the information in the site-manager was correct, you should be able to see files from the remote computer.
4. To transfer files, go to the desired file directory on both local and remote sites, click and drag the target files from one site to the other.
Note that some directories may not have access permission in a Linux computer.
Possible Filzezilla related issue
Problem: NMR data transferred by FilleZilla can not be opened in TopSpin
Cause: The ser file may have been altered during transfer. If so, in the desination folder you will see that it has a different size.
Solution: Go to FileZilla Client menu, Edit/Settings/Transfers/File Types, change Default Transfer Type to "Binary", and uncheck Treat files without extension as SCII file. Then re-transfer the data.
You may use the following procedure to validate the setting temperature, ranging from 282K-330K. Temperature correction is routinely checked by the facility Note that temperature correction is usually being enabled which should not be altered by users.
CP800 NMR Spectrometer is equipped with a special CPQCI probe which can run high temperature experiments. To set up a high temperature experiments, you need to know the followings:
The CPQCI probe has operating temperature range from 5 °C-135 °C.
Use a ceramic spinner for experimental temperature higher than 50 °C / 323 K.
To run a low temperature experiment, such as at 5 °C, you may need to set BCU / Chiller power to MAXIMUM in temperature control window.
Non-uniform sampling (NUS) is a method of acquiring data using less time than the conventional NMR methods. The method can also be used to improve resolution if experiment time is limited. For details on how to use NUS, please read NUS manual from TopSpin 3.2 program. The following is a brief guild of NUS paramenter set up.
1. Click AcquPars, and change FnTYPE to non-uniform_sampling.
2. Go to NUS section, set NusAMOUNT[%]. The amount is usually 50% or less, and make sure NUSLIST is set automatic.
3. Run the experiment as usual.
4. To process the spectrum, go to ProcPars page, and at NUS section, set MDD_mod to either cs or mdd (cs may give better result). Then, process the data as usual.
3D NUS Data phasing
(1) Using a third party software to process data if available, such as hmsIST or Mnova
(2) TopSpin method.
(a) It is highly recommended to acquire a 2D plane first in conventional mode to determine the phase correction.
(b) You may read the first FID, "reser 1"; determine the phase for f3 from this 1D spectrcum. If the experiment is ET or Echo Anti-Echo, you need to add or subtract 90 degrees from the phc0 value determined from the 1D.
(c) The indirect dimonesions should not require a phase correction.
Safety Policy Environment and Safety in Biomolecular Nuclear Magnetic Resonance Facility, University of Maryland, College Park: Responsibilities, Risks and Liabilities:
Staff members, Teaching Assistants, and Users will expose themselves to strong magnetic fields (maximum of 14 Tesla) from the NMR superconducting magnets, while they are working around the spectrometers. To the best knowledge of the NMR community, no known health hazard has been reported when one is exposed to such field, in the past twenty years. However, there is no guarantee that future findings may show otherwise.
Any person with metal implants, such as heart-pacers, should not work or enter the NMR labs. The strong field and the radio frequencies of NMR spectrometers are known to interfere with heart-pacers.
Keep all loose metal objects at least ten-foot from the magnets. The strong magnetic field attracts any loose paramagnetic metal objects nearby. The collision force is so strong that it can induce a structural collapse of the magnet, which in turn causes spontaneous boil-off of the super-cold liquids in the magnet. A person around the collision (magnet) can be injured.
Use proper procedure and obey safety policy when dealing with liquid nitrogen and liquid helium. Then superconducting magnet contains liquid nitrogen and liquid helium. Contact with these cold liquids will cause severe burns to the body. Safety policy must be complied with during transportation and refilling of the magnet with these liquids. During the refilling of liquid helium, the operator must be very careful and always maintain proper balance when stepping up to the platform (no more than 3 feet in height). Falling from the platform could lead to body injuries.
The prospective users should read ‘responsibility, risks and liabilities’ and fully understand the potential danger, implication and risks described. The staff members in the NMR facilities, the Department of Chemistry and Biochemistry or the University of Maryland is not responsible or liable for any possible misshape caused by any user negligence. By reading this, the users will behave responsibly and follow all the proper procedures as described in this form and the published NMR facility policy of the department.