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MSU NMR Problem Solving Guide

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This guide was written for VNMR6.1C, but will work on versions up to VnmrJ3.2. If there is a difference between the old software and new version, it will be noted. Please contact facility staff if your issue is not covered by this guide.

 

Broken Tube in the Magnet:

THIS MUST BE REPORTED AS SOON AS POSSIBLE TO MINIMIZE DAMAGE TO THE PROBE. DO NOT ATTEMPT TO REMOVE SAMPLE! PLEASE CONTACT NMR STAFF IMMEDIATELY (CALL 792, 386, OR 387). IF STAFF IS UNAVAILABLE, LEAVE MESSAGE AT 386 OR 387. ALWAYS LOG-OFF OF THE INSTRUMENT AND HANG A SIGN ON MONITOR STATING; 'BROKEN SAMPLE: DO NOT USE INSTRUMENT'.

Console is unresponsive to Commands (This is only for instruments running old software. For New software issues including VnmrJ not starting or VnmrJ starting but no icons, see below):

1. With the right mouse button, click once on the Solaris desktop background to reveal a menu.  Click on Programs or Tools, then over to select Terminal… A Terminal window will pop-up.


2.  In the Terminal window, type ‘su acqproc’ and hit Return.  You will get a message indicating that acqproc is being ‘killed’.  Also, in the ACQUISITION STATUS window in VNMR, STATUS should now read “inactive”.


3. Proceed to the NMR console, which is the big grayish box.  See below for location of reset button for various instruments.

4. Push the reset button.

LOCATION OF RESET BUTTON FOR EACH INSTRUMENT
Instrument (floor)
Reset Button Location
Mut: UnityPlus-500 (sb) In the big grayish box to the right of the computer (left for Mut).  Open the left door and look for a large red button on the middle right. 
Maat & Imseti: UnityPlus-300 (1st) Open the left door of the console. Look for a large red button on the middle right. 


5. Wait for at least 40 seconds.


6. In the terminal window type su acqproc and hit Return.  This will take a few moments.   Look at the ACQUISITION STATUS window in VNMR.  Wait for STATUS to read “idle”.


7. In the VNMR command line (i.e. where you usually type e), type su and hit Return.  The NMR should now be ready for use. 

 

Console is unresponsive to Commands (This is only for instruments running NEW software. This includes Mut (500, B8), Anubis (500, B7), Ra (300, B8), Isis (600, B7), and the NMR's in room 125. For Old software, see above):

1. In the command line, type abortallacqs. The instrument status will go to Inactive. Wait for the status to return to Idle, then type fixshims. You will need to turn spinning back on and reestablish lock.

If the above fails, use the following procedure:

1. With the right mouse button, click once on the desktop background to reveal a menu.  Click on Terminal… A Terminal window will pop-up.


2.  In the Terminal window, type ‘su acqproc’ and hit Return.  You will get a message indicating that acqproc is being ‘killed’.  Also, in the ACQUISITION STATUS at the bottom of VnmrJ, STATUS should now read “inactive”.


3. Proceed to the NMR console, which is the big grayish box.  Open the left door and look for the blue ethernet connector on the middle far left. Just above that connector is a small red button with the label 'reset' above it.

4. Push the reset button.

 

5. Wait for at least one minute.


6. In the terminal window type su acqproc and hit Return.  Wait a few moments.   Look at the ACQUISITION STATUS window in VNMR.  Wait for STATUS to read “idle”.


7. In the VnmrJ command line (i.e. where you usually type e), type fixshims and hit Return.  The NMR should now be ready for use. 

VnmrJ program is unresponsive or does not open (This is only for instruments running NEW software (VnmrJ2.2 or higher). This includes Mut (500, B8), Anubis (500, B7), Ra (300, B8), Isis (600, B7), and the NMR's in room 125. For Old software, see above):

If after clicking the VnmrJ icon the program doesn't start within 30 seconds, please contact the NMR Facility to have your account activated on that machine. Please include your account name and the instrument you were trying to use (this includes the datastations as well).

If VnmrJ opens but does not display any icons or menu items or gives 'variable undefined' errors, please do the following:

  1. Exit VnmrJ.
  2. Right click on the Desktop and select Open Terminal.
  3. In the terminal window, type cd and hit <Enter>.
  4. Type cd vnmrsys and hit <Enter>.
  5. Type rm lock* and hit <Enter>.
  6. Restart VnmrJ.

 

Can't Lock on Sample: (PDF version)

This can be caused by several problems. Common reasons and their solutions are listed below:

Common Reasons for Inability to Lock
Cause
Result
Solution
No deuterated solvent No deuterium signal to lock on. Use a deuterated solvent like CDCl3.
Shimming is very poor The signal is so broad that it is not well observed. Type fixshims to get a good start.
Suspended particles This causes line broadening, which makes the signal intensity weaker. Filter your sample.
Too concentrated There is little deuterated solvent to get a lock. Especially problematic when using CDCl3. Dilute your sample or use a solvent with more deuteriums (e.g. C6D6).
Improperly gauged When injected, the sample is not in the coil. Eject sample and ensure that the sample resides between the white lines on the gauge.
Lockpower is too low The sample is not receiving enough rf signal to flip the deuterium spins. Increase lockpower to 80% of max before trying to lock.
Lockpower is too high (for multi-resonance samples) With solvents having more than one deuterium resonance (e.g. CD3OD, THF-d8), high lock power will cause all resonances to be excited. This makes locking on a single resonance difficult. Reduce the lockpower by 20 and find the lock signal. If you see the signal with 'bumps', reduce lockpower further.
Lockgain is too low The signal from your sample is not amplified enough for you to see the signal. Increase Lockgain to maximum.
  • If the above table does not resolve your problem, try locking on a pure sample of C6D6.
    • Once you are able to lock on the benzene-d6, shim as well as you can.
    • Replace the benzene-d6 sample with your sample and attempt to lock.
    • Still can't get a lock? Contact the staff at 792

I Can't Access a Workspace (e.g. exp1, exp2) or, for New software, VnmrJ screen is mostly blank and you get exp0:

  • The usual message you will get is,'foreground processing is active.'
  • A locked experiment is a result of improper logging-off by a user or a program crash. Remember to always exit VNMR prior to exiting the User session!
  • To unlock and gain access to an experiment:
    • Type unlock(#,'force'), where # is the number of the locked experiment. For example, I try to access exp1 by typing jexp1 and I get the 'foreground processing is active' message. I would then type unlock(1,'force'). Exp1 is now available.
    • For the new software, always try unlock(1,'force') first.

I Can't Eject my Sample:

  • This is usually a result of a failure in the acquisition computer. You need to see if the acquisition computer is active.
  • Look at the ACQUISITION STATUS window and see if the Status is Idle, Acquiring, or Inactive.
    • If it is Acquiring, type aa. If you get the message similar to,'no experiment is active', you will need to reboot the acquisition computer. Use the procedure for a unresponsive console. Click here to view reboot procedure.
    • If it is Inactive, you will need to reboot the acquisition computer. Use the procedure for a unresponsive console. Click here to view reboot procedure.
    • If it is Idle, try typing exit. Wait about 1 minute. If you are not exited from the VNMR program, you will need to reboot the acquisition computer. Use the procedure for a unresponsive console. Click here to view reboot procedure. If you are exited, click on the VNMR icon and type su, then try ejecting again. Still can't eject? Try to reboot the acquisition computer. Use the procedure for a unresponsive console. Click here to view reboot procedure.
  • If rebooting does not work, contact the NMR staff at 792!

Poor Shimming: (Click HERE to get a more detailed procedure for shimming. PDF format)

  • Poor shimming or more properly, poor lineshape, can be a result of many factors. Below is a list of common causes and their remedies:
Common Reasons for Poor Shimming
Cause
Result
Solution
No deuterated solvent No deuterium signal to lock on and, thus nothing to shim on. Use a deuterated solvent like CDCl3.
Initial shimming is poor Your peaks are very broad. Type fixshims to get a good start.
Suspended particles This causes line broadening, which makes the signal intensity weaker. Filter your sample.
Too concentrated Concentrated samples can be viscous, which will cause line broadening. Dilute your sample.
Too little solvent When injected, the sample is not properly positioned in the coil and the liquid/air interface is 'seen' by the coil. This will make shimming very difficult. Add more solvent.
Improperly gauged When injected, the sample is not properly positioned in the coil and the liquid/air interface is 'seen' by the coil. This will make shimming very difficult. Eject sample and ensure that the sample resides between the white lines on the gauge.
Cheap, old, or stored in hot oven NMR tube Poor quality NMR tubes are either very slightly out-of-round and/or have uneven wall thickness. This results in a flucuation in the field and thus poor line shape. Throw away the NMR tube and get a tube that is, at the very least, rated for the field you are using. We recommend the Wilmad 528 series as a minimum.

 

  • If shimming problems are not resolved, contact the NMR staff at 792.

Poor Signal/Noise:

  • Signal/Noise (S/N) improves as the square root of nt. Increasing the number of scans will improve S/N up to a point. Maximum improvement in S/N occurs early in the experiment. Diminishing returns are acheived with larger number of scans.
  • Increasing concentration is an obvious fix if you have enough sample. But be careful not to get too concentrated because linebroadening will occur at higher concentration.
  • Many of the same problems with poor shimming result in poor signal/noise. If you don't get better S/N after trying the shimming procedures, contact the NMR staff.
  • If you are using either of the UnityPlus-500's, make sure that the probe is tuned correctly. The tuning procedures are posted on the magnets. Some hints are listed below:
    • Tuning hints: (tuning procedure for a Switchable BB probe is available here)
      • Be sure that you setup the correct experiment (e.g. Setup=>C13,CDCl3 for carbon) and type su after setup.
      • Be sure to carefully follow the instructions on the magnet.
      • Do NOT force the tuning rods. They are FRAGILE. If you feel resistance when turning the rod, you probably have reached the end and should turn the rod in the opposite direction.
      • Always start tuning by turning the shorter rod (Red for Proton. Gold for Carbon).
      • In general, you need only turn the shorter of the two rods for either Proton or Carbon.
      • If you need to turn both rods, start by turning the shorter one until you get a minimum on the meter. Then,…
        a. Turn the longer one (Blue for proton. Black for Carbon) in a direction opposite to what you turned the short rod. Turn the long one to the minimum and continue turning in the same direction until the meter reading goes up a bit (5 with the lower knob set to 60).
        b. Now turn the short rod to minimize the meter reading and continue turning in the same direction until the meter reading goes up a bit.
        c. Return to the long rod and turn to minimize. Turn past the minimum as before.
        d. Repeat for both the short and long rod until the meter reading is minimized.
        e. If this process does not lead to a minimum, try reversing the directions you were turning the rods.

The Computer Screen is Blank:

  • Try moving the mouse to see if the screen saver is activated.
  • Make sure the monitor is turned on.
  • Turn off the montor and turn it on again.
  • If this does not fix the problem, contact the NMR staff at 792.

The Temperature is too High/Low (OLD software):

  • Type vttype?. If the reponse is 'vttype =2', proceed to next bullet. If not, type vttype=2 su.
  • Type temp, click RESET, wait until VT controller has reset, and set the temperature in the pop-up window by dragging the slider.
  • If the temperature is still incorrect, contact the NMR staff at 792.

The Temperature is too High/Low (NEW software):

  • Click on View, Parameter Panel.
  • Click on Start tab in Parameter Panel and click Spin/Temp.
  • Move the Temperature slider to 25 and click Regulate Temp.
  • If this does not work, proceed to the magnet and push up on the black connector with the thick black cable hanging from the underside of the probe.
  • Return to the computer and click Reset VT Controller. Wait for the reset to complete, then click Regulate Temp.
  • If the temperature is still incorrect, contact the NMR staff at 792.

The VNMR Screen Colors are Terrible (OLD software only):

The odd colors for your VNMR interface are usually a result of having too many windows/applications open. Since VNMR is generally the last to be opened, it is given the last dregs of color available, which turn out to be pretty awful. You should close all unnecessary applications prior to running VNMR.

  • TO FIX THE DISPLAY COLORS OF VNMR:

    I. After logging-in to the session and prior to running VNMR, close all windows that pop up (e.g. Netscape, Solaris Registration, Terminals, etc.).
    a. If you have the Solaris Registration window open every time you log-in, you can disable it by clicking More Information=>Never Register=>Never Register.
    II. Click on the VNMR icon. The colors should be fine. If not or if you want your own colors, do the following:
    a. Type color. A color palette will appear.
    b. Click on the button for the item you wish to change the color (e.g. background, spectrum, etc.) and then click on the desired color.
    c. When completed, enter a filename for the name color scheme and click save. If you want this new scheme to be the default, save the file as DEFAULT.

My Sample is not Spinning (OLD Software):

  • Check to make sure that spin is turned on by clicking Acqi=>LOCK. Check the spin setting at the bottom of the window. Adjust the spin rate to 20. To the right of Spin:, click off, then click on. If it still is not spinning, then...
    • The most common cause of this problem is a dirty spinner or a improperly gauged sample.
    • Eject the sample and clean the spinner with a Kim wipe and ispropanol. Make sure you clean the narrow portion of the spinner.
    • Regauge the sample. IMPORTANT: Always hold the spinner and sample at the fat part of the spinner. Holding the sample and not the spinner may cause the spinner to slip, which will make shimming difficult.
    • Insert the sample. If it still does not spin, contact the NMR staff (792 or leave message at 386 or 387). Please fill out a NMR Incident Report.

My Sample is not Spinning (New Software):

  • Check to make sure that spin is turned on by clicking on View, Parameter Panel.
  • Click on Start tab in Parameter Panel and click Spin/Temp.
  • Move the Spinner slider to 25 and click Regulate Speed.
  • If this does not work, then...
    • The most common cause of this problem is a dirty spinner or a improperly gauged sample.
    • Eject the sample and clean the spinner with a Kim wipe and ispropanol. Make sure you clean the narrow portion of the spinner.
    • Regauge the sample. IMPORTANT: Always hold the spinner and sample at the fat part of the spinner. Holding the sample and not the spinner may cause the spinner to slip, which will make shimming difficult.
    • Insert the sample. If it still does not spin, contact the NMR staff (792 or leave message at 386 or 387). Please fill out a NMR Incident Report.

My baseline rolls or is not flat (for 2D Spectra, see the Processing, phasing, and plotting 2D phase sensitive data Handout):

  • There are several possible causes of this problem:
    • Too high receiver gain can cause severe distortions to the baseline that cannot be corrected. If this is the problem, you should of seen the error message 'Reciever Overflow' or 'ADC Overflow' during the experiment. The easiest fix is to enable autogain (default setting) by typing gain='n' and rerunning the experiment. Arrayed experments like pulse width determination or kinetics do not allow autogain so you must set it manually. Type gain=gain-6 and rerun the experiment (one scan will be sufficient to check for errors). If errors still occur, reduce gain and repeat experiment. Continue with command until no error is shown. If you've reduced the gain to the minimum and still get an error, reduce the pulse width (e.g. type pw=pw/2).
    • If your spectral window is too narrow, peaks outside that window will be 'folded' or aliased because they were not properly sampled (they need to be sampled at twice their frequency, see Nyquist theorem). These peaks will typically appear as out-of-phase peaks folded into the opposite side of the spectrum. For example, my spectral window is set for 10 ppm to 0 ppm and I have a carboxylic acid with a peak at 13 ppm. Since the 13 ppm peak is outside my window it will appear as a distorted peak at 3 ppm (0 ppm +(13 - 10 ppm). To correct this, increase the spectral window by typing setsw(upper desired ppm #,lower desired ppm #) [e.g. type setsw(15,0)].
    • A rolling baseline can be a result of improper phasing due to a failure of autophasing (usually because the S/N is too low for the automation to work properly). You should reset the phasing parameters and start over. Type lp=0 rp=0 to return zero- and first-order phasing to their initial positions. Follow the manual phasing procedure detailed here.
    • A crooked but flat baseline is due to a slight offset in the quadrature detectors. To correct, type f full cdc dc. This will make the edges of the spectrum horizontal. Do not use if you have a peak at the edge of the spectrum. You'll need to increase the spectral width and repeat the experiment.

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Last Updated:  August 1, 2013   - WebMaster
URL: http://www2.chemistry.msu.edu/facilities/nmr/index.html
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