Max T. Rogers NMR-Guide

MTR Resources

THIS GUIDE REFERS TO SOFTWARE, VNMR 6.1C, THAT IS ONLY USED ON ONE INSTRUMENT AT THE FACILITY. WE ARE NO LONGER SUPPORTING THIS SOFTWARE. IF YOU ARE LOOKING FOR GUIDES FOR THE LASTEST SOFTWARE THAT IS RUNNING ON ALL OTHER LIQUID-STATE INSTRUMENTS, PLEASE GO HERE.

Welcome to the User Resource Guide for the Max T. Rogers NMR Facility at Michigan State University. This guide will help you navigate the facility and use the instruments for standard and advanced NMR techniques. Please choose the desired experiment or technique from the list below or scroll down the page to browse listings.

How do I....
 
  Run a 90-Degree Pulse Width Calibration

 

Note: Bold text represent boxes you should click. italic text represent text you should type and hit RETURN.

Getting an NMR Account: (available to MSU community only)

Preparation of Samples: (pdf version)

Reserve and Logging-in to an Instrument:

 

To log-in to an instrument: Back to Top

 

Insert and Lock on a Sample:

Main menu screen

picture of the Acqi window

picture showing appearance of the Lock window when the sample is not locked

A note about using the Acquisition window:

ADJUSTING LOCK AND SHIM VALUES: You can adjust any of the levels in two ways:

1. Using the right mouse button, click and slowly drag the slide button in the darker gray box next the bracketed numbers. Dragging to the left will decrease the number, dragging to the right will increase it.

2. Place the pointer on the button containing '-number+' next the value you wish to change. Clicking the left mouse button will decrease the value by the value named in the button. Clicking the right mouse button will increase the value. For example, next to Z0, I place the pointer on '-16+' and click the right mouse button. The value will change from -1488 to -1472.

 

 

 

picture of locking process when the user is close to on-resonance

picture of step wave indicating a locked sample

Back to Top

Shim and Save your own Shims for Later Use:

  • Shimming your sample:

  • Saving your own shim values:
  • Retrieving your shim values:
  • Back to Top

    Run a Simple 1D Proton or Carbon Experiment: (for a handy Quick Guide, click HERE)

    VNMR Command
    Description
    Typed Example
    nt
    number of transients: Sets the number of transients (scans) to be acquired. You should always select a multiple of 4 (e.g. 4, 8, 128). The larger the number of scans, the better the signal to noise.

    nt=16

    default setting for 1H,CDCl3

    bs
    block size: Directs the acquisition computer, as data are acquired, to periodically store a block of data on the disk.

    bs=8

    sets the block size to 8 scans. If you are acquiring 1000 scans (nt=1000), you can view your spectrum after 8 scans by typing wft.

    ga
    submit experiment to acquisition and FT the result: Performs the experiment described by the current acquisition parameters and Fourier transforms (wft) the result.

    ga

     

    wft
    weight and Fourier transform 1D data: Performs a Fourier transform on one or more 1D FIDs with weighting applied to the FID.

    wft

    usually used if you stop the acquisition prior to completion or when loading a saved FID.

    aph
    automatic phase of rp and lp: Automatically calculates the phase parameters lp and rp required to produce an absorption mode spectrum and applies them to the current spectrum.

    aph

    usually gives well phased spectra

    f
    full: Sets the horizontal and vertical control parameters to produce a display on the entire screen.

    f or full

    vsadj
    Automatic vertical adjustment: Automatically sets the vertical scale, vs, in the absolute intensity mode so that the largest peak is at the requested height.

    vsadj

    resets the vertical scale to fit on the screen

    dscale
    Display scale below spectrum or FID.
    dscale
    aa
    abort acquisition: immediately aborts the acquisition.
    aa
    sa
    stop acquisition: stops acquisition after acquiring current transient.
    sa
    su
    submit a setup experiment to acquisition: Sets up the system hardware to match the current parameters but does not initiate data acquisition.
    su
    svf('filename')
    Save FIDs in current experiment: Saves parameters, text, and FID data in the current experiment to a file.

    svf('H1_070703')

    saves the FID as a file named H1_070703

     

    Spectra are generally referenced to the residual protio signal from the deuterated solvent. Click Solvent Reference to determine the chemical shift for your solvent (CDCl3 is a singlet at 7.24 ppm, acetone is a pentet at 2.04 ppm). The standard parameters that you chose to setup the experiment referenced the spectrum to a preset value. This value will be close to the correct chemical shift of your solvent as long as you specified the correct solvent during setup.

  • Find your solvent peak: Type dscale. Locate the region for your solvent peak and expand it. For deuterochloroform, the region would be around 7.24 ppm. Expand on the desired region; click the left mouse button at the left-most point of the desired expansion (you will see a red line) then click the right mouse button on the right-most point of the expansion (you will see two red lines denoting the region to be expanded) and click Expand. To expand further, click the left mouse button then the right and click Expand. (To return to the full spectrum, click Full.)
  • Reference your solvent: With the left mouse button click at the top of your solvent peak. Type nl. This brings the cursor to the top of the nearest peak. Type rl(solvent chemical shiftp) (e.g. rl(7.24p) for CDCl3 or rl(7.15p) for benzene-d6 or rl(2.04p) for acetone-d6). Remember for multiplets like acetone-d6, reference the middle peak.
  •  

  • Integrate your Spectrum:
  • Given ample time for the induced magnetization to relax (5*T1), peak areas are directly proportional to the number of protons responsible for the given peak(s), thus making it possible to determine the relative number of protons in a given system. Deviation from a direct relationship can be due to insufficient time for complete relaxation. Usually sp2 hybridized centers will have longer T1s then sp3 centers and thus you may get integrated values for sp2 centers that are less then they appropriate. To reduce this phenomenon, increase d1 (e.g. d1=30). A flat baseline and consistent, level integrals are very important.

    Integration Quick Reference
    If you want to...
    then you should do this...
    Clear integral resets
    Type cz
    Increase spectrum size when in integration mode

    Type vsadj for vertical scale adjustment to maximize the largest peak in the region.

    If you need to increase further, click Full Integral => No Integral and adjust the peak height using middle mouse button. Turn integral on by clicking Part Integral.

    Increase integral size
    Whenever the integrals are displayed, the middle mouse button controls the size of the integrals. Clicking on the screen above the integral will increase the integral to that position. Clicking below the spectrum will decrease all integrals by a half.
    Change integral position
    Type io=30 or appropriate value.
    View integral values
    Type vp=12 dpir
    Perform a baseline correction
    Type bc

     

     

  • Peak Picking: Note: Any time you want to replot the peak values, type ds first to redraw the spectrum without the old peak values.
  • Peak Picking Quick Reference
    If you want to...
    then you should do this...
    display all peaks
    Type dpf
    display only positive peaks

    Type dpf('pos')

    increase sensitivity on peak picking
    Type dpf(0). The default is 3; any value greater then that will decrease sensitivity.
    clear peak labels
    Type ds.
    set peak threshold
    click on Th and use left mouse button to drag the threshold line (yellow) to the desired height.
    display a peak list
    Type dll. The peak list will apply in the gray window below the spectrum window. If you can't see the gray window, click Flip.
      Peak picking is important because it allows you to print the peak locations and calculate coupling constants. The yellow line designates the threshold below which no peaks are picked.

  • Set your peak threshold: With the full spectrum displayed, click Th. You will see a yellow line across the screen. Using the left mouse button, click and drag the yellow line to the level just below the smallest peak you wish to have displayed.
  • Display peak labels: Type dpf or variant (see Table above). If you need greater peak sensitivity, type ds dpf(0). You are now ready to print your spectrum!
  • Printing Quick Reference

    String together any of the commands listed below in any order followed by page to print what you want. Whatever is displayed on the screen will be printed.

    For example, I typically use: pl pscale pll pltext(150,150) pir page.

    Command
    Action
    pl

    print spectrum

    pscale
    print scale
    pll
    print line list, which includes frequency in Hertz for calculating J-values
    ppf
    print peak frequencies
    pir
    print integral values (vp must be greater than 10: type vp=12)
    pltext
    print text. To plot in the upper right corner, type pltext(150,150), this is necessary when you are printing a peak list (i.e. pll).
    pap
    print all parameters
    Back to Top
  • Acquire a 1D Carbon Spectrum:
  • Back to Top

    Determine number of protons attached to each carbon (DEPT):

    Distortionless Enhancement by Polarization Transfer (DEPT) is an experiment that utilizes a polarization transfer from one nucleus to another, usually proton to carbon or other X nucleus, to increase the signal strength of the X nucleus. Furthermore, by varying the length of the last proton pulse from 45 to 135 degrees, the multiplicity of the carbon or X nucleus can be determined (i.e. depending on the pulse the signal for a methine, methylene, or methyl will either be a positive, negative, or null signal. See table below). Addition and subtraction of the various DEPT spectra will give the multiplicity of each carbon. Remember, since quaternary carbons have no attached protons, they will show no signal.

    Relative Intensities from DEPT
    Spectrum #
    Pulse Angle
    C (quaternary)
    CH (methine)
    CH2 (methylene)
    CH3 (methyl)
    1
    45
    0
    0.707
    1
    1.06
    2,3
    90
    0
    1
    0
    0
    4
    135
    0
    0.707
    -1
    1.06

    Back to Top

    Determine 1H-1H connectivity (COSY): (PDF Version available here!)

    COrrelation Spectroscopy (COSY) is a 2D NMR technique which gives correlations between J-coupled signals by incrementing the delay between two 90 degree proton pulses. The resulting 2D spectrum is generally displayed as a contour plot (see below), which is similar to a topographical map. When looking at a contour map, you are actually looking down at a cross-section (slice) of a 3D-image of an NMR spectrum. The usual 1D spectrum is traced on the diagonal of the plot and any peaks that are not on the diagonal represent cross-peaks or rather correlation peaks that are a result of J-coupling. Thus, by simply tracing a rectangle using the diagonal and cross-peaks as vertices you will know which protons are coupled to each other. Standard COSY experiments require phase cycling to remove unwanted signals and thus can be quite time consuming. This can be circumvented using gradient selected COSY (gCOSY), which utilizes pulsed field gradients to destroy unwanted z-magnetization and hence their associated signals (axial peaks). Quality gCOSY spectra can be acquired in as little as 10 minutes! All our instruments except the Gemini-300 and the VXR-300 are equipped to do gradient selected spectroscopy.

    a picture of a COSY spectrum as obtained on an Inova-300

    Back to Top

    Run a Homonuclear Decoupling (HOMODEC) Experiment: (PDF available here)

    This is a simple and quick means of determining if two resonances are coupled. The HOMODEC experiment is most effective for relatively simple spectra where the couplings are, at least, somewhat resolved. The experiment consists of irradiating a selected resonance with a low power decoupler, which will eliminate any couplings to that resonance. By comparing the resulting spectrum to that without decoupling, it is easily determined which resonance(s) are coupled to the irradiated peak.

    1. Acquire a 1H NMR spectrum. For a procedure, click HERE.
    2. Type HOMODEC. This enables homodecoupling.
    3. Type ds to display the spectrum and expand around the desired resonance you wish to irradiate (i.e. the one that you want to determine coupling).
    4. Click on Cursor and place the cursor on a position in the spectrum that contains no peaks within 0.3 ppm. This is a reference spectrum.
    5. Type sd. This resets the decoupler offset to the cursor location.
    6. Expand and place cursor on your desired peak to be decoupled and type sda. Repeat using sda for all peaks you wish to decouple.
    7. Choose your number of scans and type ga.
    8. Type wft ds(1) vsadj and, if necessary, manually phase. Ignore the irradiated peak because it will not phase correctly.
    9. If the irradiated peak is still positive and contains splitting, you may want to increase the decoupler power. Type dpwr=30 and repeat the experiment. Do not increase dpwr above 40.
    10. Type vs=vs/#, where # is the number of spectra in the array. For example, if you did one reference and 2 decoupled spectra, type vs=vs/3.
    11. Type f full dssa. This displays the spectra in a vertical stack.
    12. Expansion is the same as with 1D spectra, but you must type ds first.
    13. To plot all stacked spectra, type pl('all') pscale pltext page.
    14. To plot selected spectra, type pl(1, #) pscale pltext page, where # is the number of the spectrum. For example, if I wanted to print the reference and the third spectrum, I would type pl(1,3) pscale pltext page.

    Run a 31P, 19F, 11B NMR or other heteronucleus:

    *Portions of this page were adapted from procedures by Long Lee and Kermit Johnson.


    Last Updated:  April 27, 2015WebMaster
    URL: http://www2.chemistry.msu.edu/facilities/nmr/how do i.html

    Home - NMR Staff - Instruments - How do I... - What do I do if...

    Tip of the Week Archives - NMR-Reserve -  Sign-up Rules - Handouts