Use older Varian software (vnmr6.1C)

This guide is provided 'as is' and refers to long discontinued NMR software used for Varian Unity, Unity-Plus, and Mercury systems. 

Insert and Lock on a Sample:

• To insert your sample:

  • In the VNMR window type e to eject the reference sample. Remove the reference sample and spinner by gently grabbing at the spinner and lifting straight up. Remove the reference from the spinner.
  • Insert your NMR tube in the spinner and place in the NMR gauge so that the tube touches the bottom of the gauge. While holding the spinner, raise the NMR tube until the solution is centered about the two white lines (named NMR coil limit in picture below). For proper sample preparation, see the Preparation of Samples section.

  

  • Remove the spinner and sample from the gauge by grabbing the fat part of the spinner and gently place in the upper barrel of the magnet. IMPORTANT: MAKE SURE THAT EJECTION HAS BEEN ACTIVATED, YOU WILL HEAR THE NITROGEN GAS PURGING (I.E. A HISSING SOUND)! IF NO GAS IS HEARD, TYPE e AGAIN. IF IT IS STILL NOT WORKING, CONTACT THE NMR STAFF AT 792.
  • Type i to insert your sample. You are now ready to Lock on your sample!

• To Lock on your sample:

  • Type fixshims to load the default shim set, which is updated regularly, or retrieve your own shim values. Wait for the instrument to beep prior to moving to next step.
  • On the Main Menu screen, click on Acqi (see picture below). If Acqi is not on the menu screen, type acqi.

• You will now see a small pop-up window titled ACQUISITION (see picture below for example).
• Click on Lock.

• The Acquisition window will now show the lock signal plus the lock controls (see picture below). If the spin is off, turn it on by clicking on to the right of SPIN. Adjust the spin rate to 20 Hz. If it doesn't spin, see What do I do if... my sample is not spinning.

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.
   • If your sample is already locked, skip ahead to adjust lockphase. If not, you will probably see a straight yellow line in the lock window, a lock level below 10, and NOT LOCKED in the corner (as in the picture above).
   • Turn off the lock by clicking the off button to the right of LOCK. You should never adjust Z0 when the instrument is locked.
   • Increase lockpower to about 80% of maximum and lockgain to maximum.
   • Using the slide bar for Z0, slowly drag it in one direction and look for the yellow line to become wavy (i.e. a sine wave as pictured below) then become a step and stop. If you didn't find it, try the other direction. You still couldn't find it, see What do I do if... I can't lock on my sample.

   

   • Now that you have the step , turn the LOCK on by clicking on to the right of LOCK:. You should now get a step wave as shown below. Your lock level will be not be steady because there is too much power being supplied to your sample. You will need to reduce lockpower until the lock level remains constant.
   • Reduce lockpower to the appropriate value. For deuterated chloroform, 25 is good; for deuterated benzene, acetone, DMF, DMSO, 15 is good. A good lock level is from 30 to 80. If your lock level is at 100 even though you reduced the lockpower, reduce lockgain. You will lose lock if you allow the lock level to drop below 15. When this happens, increase the lockpower and wait a few seconds for the lock to be reacquired.

• Adjust lockphase in units of 4 so that the lock level is as high as you can get it. When adjusting lockphase and/or shimming, it is best to always adjust until the level drops on both sides of the maximum. This ensures that you have found the peak level.
• Your sample is now locked and ready to be shimmed!

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Shim and Save your own Shims for Later Use:

• Shimming your sample:

  • If you haven't already, in the VNMR window (activate by clicking in the text box), type fixshims or retrieve your own shim values. Be careful about using your own shim values. If we change the probe, these values will not give good shimming. Also, due to changes to the spectrometer and its environment over time, old shim values will be less and less useful. We update the default shims (accessible through fixshims) regularly.
  • In the acqi window (the window pictured above), click on SHIM. The window will now look like:

  

  • Start out using manual shimming. To select, click on manual to the right of SHIM:

    • You want to optimize the lock level. This is represented by the values listed at current lock level and by the horizontal bars. You will try to get the bars to increase to the right as much as possible. Don't worry about the color, just try to make them increase to the right by first adjusting the course Z shims (Z1C and Z2C) then using the fine controls (Z1 and Z2). A few instruments don't have Z1C and Z2C. For those instruments, start with Z1 and Z2 using -64+. A quick procedure is:
      • Start with Z1C using -1+ or Z1 using -64+. Right click on the button repeatedly and watch the lock level. If it is increasing, continue until it is as high as possible. If it is decreasing, use the left mouse button on -1+ (or -64+ for Z1) to increase the lock level. If you reach a lock level of 100, reduce the lock gain (located at the bottom of the acqi window) until the level is around 30.
      • Repeat with Z2C using -1+ or Z2 using -64+ until lock level is optimized.
      • Return to Z1C (or Z1) and reoptimize. Do the same with Z2C (or Z2) and repeat with Z1C, Z2C until no significant change in the lock level occurs.
      • Now repeat the procedure using Z1 and Z2 using either -4+ or -16+.
      • If completed, click CLOSE to end shimming session and to exit ACQUISITION window.
    • If time permits, you can now autoshim.
      • Click auto to the right of SHIM:. From the available choices, select Z1,Z2,Z3.
      • Click Start and allow the instrument to optimize the shims. This will take several minutes. Autoshimming will be complete when the Stop button changes to Start. You can stop at any time by clicking Stop.
      • Click CLOSE to end shimming session.
    • Your sample is now shimmed and you're ready to acquire a spectrum!

• Saving your own shim values:

  • After you have done all the work to optimize your shims, save them.
    • In the VNMR window type svs('filename').

• Retrieving your shim values:

  • Type rts('filename') su.

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

Before beginning to run an experiment, you should be familiar with some of the basic VNMR commands.

Full list of common VNMR commands (PDF file)

VNMR commands (the most important for present purposes)

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

 

• Acquire a 1D Proton Spectrum: (Click HERE for 1D Carbon)

  • Before beginning make sure you know how to prepare a sample, reserve NMR time, and log-in to a spectrometer.
  • Lock and shim according to standard procedure.
  • Close the acquisition window by clicking Close in the upper left-hand corner.
  • In the VNMR Main Menu screen, click on Setup =>H1,CDCl3 for deuterated chloroform. This selects the standard proton parameters. If you are not using CDCl3, click Nucleus,Solvent => H1, then choose your solvent. If your solvent is not on the list, click Other and type in your solvent (e.g. THF). If you get an error message, just select a solvent that has a chemical shift similar to your desired solvent. For a list of common NMR solvent chemical shifts, click here.
  • Select the number of scans: The default setting is 16 (i.e. nt =16). If you need more scans, type nt= #, where # is the number of scans you desire. Note: nt should be a multiple of 4 in order to reduce artifacts (specifically, to reduce quadrature images). If you are acquiring many scans, you may wish to set the block size to 4 or 8. To do this, type bs=4. With bs set to 4 scans, the resulting FID will be stored after ct=4 and you can Fourier transform (wft) or save these data [svf('filename')].
  • Start the acquisition: Type ga. The instrument will automatically check the spinning, adjust the gain, acquire the spectrum with nt scans, and Fourier transform (wft) the result. When it's finished, you will hear a beep and see the resulting spectrum, which will generally not be correctly phased. An incorrectly phased spectrum will have an uneven baseline as in the spectrum below.

  

  • Save the FID: Type svf('filename'), where filename is your designation for that FID (e.g. svf('dh321_1H'), which contains my initials, lab book page number, and the nucleus). Now you are ready to process your data!
• Processing 1D Proton Data: This may be done at the instrument or at one of the workstations (two are located in room 204, two in the Data Processing Center in room B-8, and one in room 538). We prefer that you use the workstations for processing data so that others can use the instruments for data acquisition. Log-in and spectral processing are the same on the datastations as on the instruments. For those users with one username for all instruments, access to the different spectrometers is acheived by typing logon in the VNMR command line and following instructions on screen.

  First you should phase your spectrum.

• To automatically phase the spectrum: Type aph. This should give a well phased spectrum with a flat baseline as in the picture below. In phasing, you are attempting to adjust the spectrum such that the baseline on either side of every peak is even and does not deviate significantly from the horizon line.

• If automatic phasing does not fix poor phasing, you may need to phase it manually.
  • Manual Phasing: Click on Phase (second row middle of Main Menu options buttons. If you don't see it, click Main Menu => Display => Interactive => Phase). Type lp=0 to reset the First-Order Phasing to zero. Increase the scale using the middle mouse button such that the base of the biggest peaks are clearly visible.
    • Adjust Zero-Order Phasing: Using the left mouse button, click on the middle of the largest peak on the right side of the spectrum and drag the mouse either up or down. You will notice the phase changing for the selected peak. If the baseline is becoming even, continue to drag the mouse until it is as even as you can get. If the baseline is getting worse, drag the mouse in the opposite direction. If you come to the edge of the spectrum window and it's still not phased properly, click Phase again and continue to drag in the same direction as previous starting from the opposite edge of the window (i.e. I dragged the mouse up and came to the top of the window, so I click Phase and begin dragging up from the bottom of the window).
    • Adjust First-Order Phasing: Using the left mouse button, click on the middle of the largest peak on the left side of the spectrum and drag up or down. Proceed as with Zero-Order phasing; remember, you are trying to get the baseline even. Once you get it as good as possible, return to the right side of the spectrum and rephase the biggest peak again. Repeat until optimum.

• Reference your Spectrum:

  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

• View and Level your integral: click Part Integral in the Interactive Menu (If you don't see this button, click Main Menu => Display => Interactive => Part Integral). You will now see a stepped green line across the entire screen. Type f cdc dc and hit Return. If your integral trace does not have a flat baseline, you will have to adjust it manually. Click on Lvl/tlt. With the left mouse button click on the left-most integral (step) and drag up to increase the slope or down to decrease it. You want the slope of the integral to be zero at the left edge of the integral trace. Click on the right-most integral step and drag it in the appropriate direction such that the overall slope of the integral is as near zero as possible (i.e. a flat line between peaks). When done click on Box.
• Reset integral for individual peaks: Type f. Expand around a desired region for integrals. Click on Resets. Starting from the left-hand side and using the left mouse button, click on the baseline around each desired peak set (e.g. a triplet, quartet). Integrated areas will have a solid green line and unintegrated areas have a dashed line. Once completed with a section, click Full, expand around the next region of interest and click Expand => Resets. Repeat process of setting your individual integrals. If you want to change a single reset point, place the cursor over that point and click the right mouse button. If you make a mistake and need to start over, type cz to clear the integral reset points. When you are done, you can type bc; this is a baseline correction based on the integral regions that are nulled in your spectrum, but be careful because a simple bc can cause significant dips around the peaks. To undo the bc, just type wft.
• Reference your integral: Look for a peak that you think you know the number of protons (e.g. a singlet around 2 ppm could be an acetate group and therefore should be 3 protons). Expand around the peak and set the cursor anywhere under its integral by clicking with the left mouse button. Click Set int and type in the new integral value (e.g. for the acetate group, I would type 3).
• View your integral values: Type vp=12. This moves the spectrum and scale up by 12mm. Type dpir. This displays the integral values. If the values are overlapped, you will need to expand the region and retype dpir. Your spectrum is now integrated and you're ready to peak pick!

 

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, clickFlip.

 

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 Simple Proton Spectra:

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

• Add Text to your Spectrum: Type text('text here\\more text more'). The \\ opens a new line of text, which is similar to hitting Enter in Word. Your text will appear in the gray window below the spectrum (click Flip to view window). For example, I might type text('dh300\\V-500 CDCl3 1H NMR\\07-10-03'), which would look like (if printing using pltext(150,150)):
  dh300
  V-500 CDCl3 1H NMR
  07-10-03
• Print your Spectrum: Display the region you desire to print. To print an exact region, type sp=#p wp=#p, where the sp=#p is the value in ppm where it will begin the display and wp=# is the width in ppm of the desired region. For example, I want to print the region from 6.2 ppm to 8.2 ppm, so I type sp=6.2p wp=2.0p.
  • Type vsadj if you want the tallest peak to be scaled to fit the screen.
  • To print, see the Quick reference above for various commands; type, for example, pl pscale pltext ppf page. This will print the spectrum, scale, text, and peak frequencies.
  • NOTE: page must be typed at the end of each printing request in order to print the spectrum!
• When completed, be sure to exit VNMR and log-out properly. Click here to view log-off procedure.
  • To print stacked spectra: You will need to create an arrayed dataset, which will allow you to view and print all stacked spectra.
    • Load the spectra in exp1 and add them to an array:
      • type jexp1 - join experiment 1
      • type clradd - clear the add/sub buffer in exp5. This will erase anything in exp5.
      • click Main Menu => File and select the first desired spectrum and click Load.
      • type add - adds FID to add/sub buffer.
      • For adding all additional spectra, click File, select the desired spectrum, click Load, and type add('new').
    • Join exp5 and create array parameters:
      • type jexp5 - join experiment 5.
      • type gain='y' - turns off autogain, which is not allowed in arrayed experiments.
      • type d2=1,2,3... - sets arrayed variable. Use same number of variables as spectra.
      • type calcdim - calculates the array dimension.
      • type groupcopy('current','processed','acquisition') - updates parameters.
      • type ai - resets to absolute intensity mode.
      • type wft dssa - Fourier Transform all FIDs and display stacked spectra.
      • type svf('your filename') to save the arrayed spectra.
      • You may need to adjust the phasing. If phasing is incorrect, type ds(1) (this displays the first spectrum), or click Interactive. Type aph.
      • To adjust the scale of each spectrum: type ds(spectrum number) (where spectrum number is an integer. For the first spectrum, spectrum number is 1: ds(1); for the second spectrum, spectrum number is 2: ds(2); etc.). Adjust the scale as usual. To check, type dssa.
      • To print, use standard printing commands except replace pl with pl('all').
• To Print an Expanded Region or inset with your Spectrum:
  • Process your spectrum as you normally would (see Processing 1D Proton Data) and type pl pscale pir etc. but do not type page. The page command sends the job to the printer. You want to hold this job until you add your inset(s).
  • Put the cursors around the region for which you wish to print an expansion.
  • Type inset. The expanded view will appear on the screen. This view is now interactive and can be manipulated like usual. The full spectrum is no longer interactive.
    • Use the left mouse button to set the horizontal position.
    • Use the middle mouse button to set height.
    • Use the right mouse button to set size.
    • Use the vp command to set vertical position (e.g. type vp=40 to set the inset at 40 mm)
    • If you expand the inset and wish to reposition the new expansion, click sc wc and move as described before.
  • To print the inset: type pl pscale pir etc. If you would like another inset, repeat the process described above ensuring that you type pl pscale pir after each inset. When completed, typepage.

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• Acquire a 1D Carbon Spectrum:
  • Before beginning make sure you know how to prepare a sample, reserve NMR time, and log-in to a spectrometer.
  • Lock and shim according to standard procedure.
  • In the VNMR Main Menu screen, click on Setup =>C13,CDCl3 for deuterated chloroform. This selects the standard proton parameters. If you are not using CDCl3, click Nucleus,Solvent => C13, then choose your solvent. If your solvent is not on the list, click Other and type in your solvent (e.g. THF). If you get an error message, just select a solvent that has a chemical shift similar to your desired solvent. For a list of common NMR solvent chemical shifts, click here.
  • Once you have selected the solvent, type su.
  • Select the number of scans: The natural abundance of 13C is 1.108%, which means that roughly 1 in every 100 carbons will be NMR active. You will need more sample and scans than 1H spectra. Typent= 256. Note: nt should be a multiple of 4 in order to minimize noise. Since you are acquiring many scans, you may wish to set the block size to 4 or 8. To do this, type bs=4 or bs=8. With bs set to 4 scans, the resulting FID will be stored after ct=4 and you can Fourier transform (wft) or save these data [svf('filename')] at any time. This is good to check the evolution of signal to see if you have enough time to get good s/n.
  • Set your relaxation delay: Carbon T1s can be quite long, especially for carbonyls and quaternary carbons (these can be anywhere from a few seconds to hundreds of seconds!). Pulsing too frequently (i.e. too short relaxation delay) will saturate signals from carbons with long T1s, so it is therefore advisable to increase the relaxation delay for aromatic, alkenyl, or carbonyl containing compounds. This is set with d1. Setting d1 to 5 to 10 seconds should be sufficient. To do this, type d1=5 or 10.
  • Start the acquisition: Type ga. The instrument will automatically check the spinning, adjust the gain, acquire the spectrum with nt scans, and Fourier transform (wft) the result. When it's finished, you will hear a beep and see the resulting spectrum, which will generally not be correctly phased.
  • Phasing and Referencing is similar to the procedure with Proton: Click Here for Phasing and Referencing. Make sure that you reference to the carbon chemical shift (e.g. Chloroform-d appears as a triplet centered at 77ppm).
  • When completed, be sure to exit VNMR and log-out properly. Click here to view log-off procedure.

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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

• Run a DEPT Experiment:

  This is an arrayed experiment which will run 4 separate DEPT experiments: DEPT 45, 2 DEPT 90s with slightly different pulse widths, and a DEPT 135.

  • Acquire a quick 13C spectrum (Click Here for Procedure) and reference your solvent. Solvent peak is nulled in DEPT.
  • Type DEPT.
    • Type nt=64 or larger number if necessary.
    • Type go. A total of 4 FIDs, each having 64 scans, will be acquired.
    • After acquisition is complete, save your file [i.e. type svf('filename')]
• Process and Print DEPT Data:
  • Type wft: performs a weighted Fourier transform of all 4 FIDs.
  • Type ds(1) to display the first spectrum (this is the DEPT 45 spectrum; all peaks are positive) and phase it (for help with phasing, click here).
  • Type dssa to view all 4 spectra stacked vertically. You may want to scale the spectra to fit. To do this, type ds(#), where # is the number of the spectrum you wish to scale. Scale the selected spectrum as usual using the middle mouse button. Return to the stacked plot with dssa.
  • Type ds(1), click th and position the yellow threshold line below all the peak tops.
  • Type fp: this stores the peak frequencies in memory.
  • Type dll: displays the line list.
  • Type DEPTP: this is a macro that automatically processes and prints the DEPT data.
• Printing individual DEPT Spectra:

• Sometimes I have found it beneficial to print the individual DEPT spectra. With the help of the DEPT table above, it is rather straightforward to determine the carbon multiplicity. See the DEPT table above to see which spectrum gives which DEPT experiment. For example, from the second and third spectra (to view type ds(2) or ds(3)), which are DEPT 90 spectra, I will get only the methine carbons and from the fourth spectrum, I get the methylene carbons because they are the negative peaks.
• Type ds(#), where # is the number of the spectrum you wish to print. Manipulate and plot as you would a standard Carbon spectrum. To plot, type, for example, pl pscale ppf pltext page.
• When completed, be sure to exit VNMR and log-out properly. Click here to view log-off procedure.

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Determine ¹H-¹H connectivity (COSY):

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.

• Running a gCOSY Experiment:
  • Join experiment 1 by typing jexp1.
  • Type vttype=2 su to enable temperature control.
  • Type temp and slide the bar in the pop-up window to 25. This sets the temperature to 25 degrees Celsius. It is important to maintain a constant temperature while acquiring a gCOSY.
  • Shim well, acquire and process a 1D Proton spectrum (click Here for instructions).
    • Note the left-most and right-most peaks from your spectrum (for example, 8 and 2 ppm).
    • Type svf('filename') to save the spectrum.
  • Type jexp2: this joins experiment 2. If you get an error message, click Workspace => Create New.
  • Type mf(1,2). This moves the FID from exp1 to exp2.
  • Turn off the spin and adjust the lock level to 50% or higher using lock gain and lock power. Be sure not to saturate your lock signal with too high lock power. The lock power is too high if it has large fluctuations.
  • Type gCOSY: This loads the acquisition parameters.
  • Type setwindows: This is an in-house macro that allows you to easily set the sweep width in both dimensions. You will need to enter the following information:
    • "Enter the 1H left ppm limit:" Use a value 1 ppm greater than your left-most 1H peak. If your peak is 8 ppm, then type 9.
    • "Enter the 1H right ppm limit:" Use a value 1 ppm less than your right-most 1H peak. If your peak is 2 ppm, then type 1.
  • Type nt=#, where # is the number of scans you wish.
  • Type time and note the value. You can increase nt and check time again to fill your allotted instrument time.
  • Type go (please do not type ga).
• Data Manipulation:
  • Type setLP1 sinebell wft2d: This performs the 2-dimensional Fourier transform and the color map will be displayed. The color map is your 2-D spectrum with the levels displayed using different colors. Use the following table as a guide to color map navigation. Type d2d to display a contour map that matches the printout.

Interacting with the 2-D Color Map/Contour Map

To do the following...	You should...
Increase/Decrease the scale	Click on either vs+20% or vs-20% or type vs2d=vs2d*1.5 and click Redraw. The typed command increases the display by a factor of 1.5. You can use a larger number if you like (e.g.vs2d=vs2d*2, increases by a factor of 2.
Change the number of color levels	Use the middle mouse button to click on the color scale to the right of the color plot. Click on the smaller number to increase the number of colors displayed.
To expand on a region	Ensure that you are in the interactive mode; if not, click Main Menu=>Display=>Color Map. Click with the left mouse button on the left-most point of your desired region. Click with the right mouse button on the right-most point. Click on Expand.
To expand an exact region	Type sp=#p wp=#p (for the F2 dimension, usually vertical) and sp1=#p wp1=#p (for the F1 dimension, usually horizontal), where # are the numbers in ppm for the region of interest. sp designates the start of plot and wp is the width of the plot. You will need to click on Redraw to update the screen. For example, I want to expand the region between 1 and 4 ppm in F1 and between 2 and 4 ppm in F2, I would type sp=2p wp=2p sp1=1p wp1=3p, then I click Redrawto see the result.
To reference the 2-D spectrum	Expand the region of interest. Click Hproj(max) for the horizontal projection and Vproj(max)for the vertical projection. Place the cross-hair cursor on the diagonal position you wish to reference (the projections will help you to orient the cross-hair). Type rl(#p) rl1(#p), where # is the value in ppm you want to be the reference. rl sets the F2 dimension reference and rl1 sets the F1 dimension reference.
Redisplay the spectrum	Click on Redraw.
Display a projection of the 1D spectrum on the side of the 2-D plot	Click Proj, then click Hproj(max) for the horizontal projection or Vproj(max) for the vertical projection. Use the middle mouse to adjust the scale.
Display a trace of the 2-D plot	Click Trace and use the left mouse button to drag the cursor.
View the contour plot	Click Main Menu=>Display=>Contour
Increase number of levels on contour plot: Interactive plot	Type, for example, dconi('dpcon',15,1.2). The dpcon flag is for displaying the contours. The first number (15, in this case) is the number of contour lines (default is 4). The second number (1.2, in this case) is the relative spacing intensity (default is 2). You can input different numbers if you wish, but the second number must be greater than 1.
Increase number of levels on contour plot: Non-interactive plot	Type, for example, dpcon(15,1.2). The dpcon flag is for displaying the contours. The first number (15, in this case) is the number of contour lines (default is 4). The second number (1.2, in this case) is the relative spacing intensity (default is 2). You can input different numbers if you wish, but the second number must be greater than 1.

• Autoprinting your gCOSY with Projections generated from COSY:
  • Display the region of interest and click Autoplot: This plots your COSY with the projections generated from the 1-D data subsets. The indirectly detected dimension will have low resolution and thus, the projection for that dimension (usually F1) will have broad peaks. For better resolution projections, use the following procedure.
• Printing your gCOSY with 1-D Spectrum as Projections:

Open your COSY Spectrum. Click Main Menu=>Display=>Size=>Center.

• Join another experiment and retrieve the 1-D spectrum:
  • Type jexp1 or any other experiment number.
  • Load the 1-D spectrum; Fourier transform (wft), and phase (aph).
• Type jexp2 or join the experiment number where your COSY resides:
  • Click Display=>Contour and expand, scale, etc. the region of interest (refer to table for interacting with the color or contour map).
  • Type plgcosy and follow the directions on the screen: This is our in-house macro that prints your desired 2-D spectrum with high-resolution 1D plots on the sides.

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• LOGGING OFF OF INSTRUMENT SESSION:
  • After you are done, you must leave the instrument as you found it.
    
    I. In the VNMR window, type e. Eject your sample, remove it from the spinner, put back the reference sample in the spinner, and use the depth gauge to set the proper height.
    II. Place spinner with reference sample in magnet bore
    III. Type i. Insert the reference sample.
    IV. In the VNMR window type exit.
    V. After VNMR closes, right click on the background, and choose log out… at the bottom of the menu.
    VI. Click OK to completely exit the session.

Run a Homonuclear Decoupling (HOMODEC) Experiment:

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:

• Simple Acquisition of 31P and 19F NMR Spectra using Inova-300 (Ra: B-8 subbasement):
  • This instrument is equipped with an autoswitchable probe, which allows the user to select between 13C, 31P, 19F, and 1H by simply clicking Setup=>Nucleus,Solvent and choosing the appropriate nucleus. Note: H2 and N15 are not available using the Setup macro.
    • If you are unsure of the chemical shifts for your compound, do the following:
      • Type sw=100000. Acquire and phase the spectrum.
      • Place the cursors around the full region where your peaks fall (e.g. from 200ppm to -50ppm).
      • Type movesw. This will reset the spectral window to the cursor positions.
      • Acquire the spectrum.
      • Acquisition and processing are identical to simple proton acquisition.
• For the other instruments, probe tuning, the use of additional capacitor rods, and new acquisition parameters need to be setup. The VXR-500 (Anubis) can be used to acquire NMR spectra for 15N to 31P, 1H, and 19F. A probe is available for 107Ag to 15N. If you desire to run NMR on heteronuclei, please contact the NMR staff to arrange for training.