Exercises with Virtual Spectrometer


NOTE: Most commands in Nuts may be entered by using two letter commands or using the windows menus. Directions here are using the windows menu, but two letter commands are given in the menu. The two letter commands are based on the GE-CHARM software used for the QE-300. These commands are very similar to Bruker's. For more information and details about data processing with NUTS see the user's manual. User's Guides from Widener University, Brief Guide to Nuts and Detailed Guide to Nuts.

Create Ethanol Simulation File

  1. Load Nuts (Virtual NMR is an add-on part of NUTS)

  2. Create an NMR Simulation (Tools|NMR Simulation)

  3. Complete the Data Acquisition Parameters form (these values may be changed latter)
    1. Frequency (The spectrometer frequency, set to 300)
    2. Sweep Width (The spectral window, set to 4000)
    3. Offset Frequency (The simulation assumes quadrature detection so set OF = 1/2 SW)
    4. Number of Points (This is just for the display while creating the simulation file, 8192 is fine)

  4. Setup the Spin System (Edit|Add/Edit Simulation Data)
    1. Enter the number of spins (6)
    2. Enter the chemical shift for each nuclei
      1. -OH 5.0 ppm
      2. -CH2- 3.7 ppm
      3. CH3- 1.2 ppm
    3. Fill in the coupling constants (set all CH2 - CH3 coupling to 8 Hz.)
    4. Accept and Recalculate

  5. Create a Virtual Spectrometer File (File|Create Virtual Sample File)
    1. Concentration (1 mM)
    2. Sensitivity (10)
    3. 90 degree pulse width (10)
    4. Save File (filename)
    5. OK

  6. Save the simulation file (File|Save)

  7. Exit Simulator Routine <:ENTER>

Load Simulation File and Run Virtual Spectrometer

  1. Get the Virtual Sample File (vSpec|Get Sample)

  2. Set Parameters (vSpec|Parameters)
    1. Scans (1)
    2. Pulse Width (10)
    3. Recycle Delay (1)
    4. Receiver Gain (1)
    5. Sweep Width (4000)
    6. Offset Frequency (2000)
    7. Data Size (8192, must be a power of two, if not will change to closest value)
    8. Delay for 1st point (1 us)
    9. Note Acquisition time and Digital Resolution

  3. Acquire FID (vSpec|Go)

  4. Process FID
    1. Scale the FID to fit the screen (^F)
    2. Fourier Transform (Process|Transform|Fourier Transform)
    3. Phase Spectrum (Process|Phasing|AutoPhase)

  5. Zoom in and examine multiplets. Double click to get zoom cursor. Drag across region. Right click to expand.


Effect of Number of Data Points

  1. Change the simulation parameters to fewer data points and repeat (notice the sinc wiggles for small number of data points)

Effect of acquisition delay

  1. Reset the number of data points to 8192.

  2. In the Virtual Spectrometer Preferences set the acquisition delay to 100 us

  3. Run the simulation

  4. Fourier Transform Data and observe peaks (do not phase correct)

  5. Change the delay to 250 us and repeat

  6. Change the delay to 500 us and repeat

Effect of Gain

  1. Reset the acquisition delay to 1 us.

  2. In the Virtual Spectrometer Preferences, set the gain to 100.

  3. Run the simulation

  4. Notice the shape of the FID

  5. Fourier Transform and Phase Correct

  6. What happened?

Effect of Pulse Angle

  1. Reset Receiver Gain to the optimum setting.

  2. Run the simulation, Fourier Transform, and Phase Correct spectrum.

  3. Change the pulse width to 5 us (45 degrees since when the simulation file was defined, the 90 degree pulse was set for 10 us.), run the simulation, Fourier Transform and Phase Correct the spectrum using PS to set the same phase as the previous experiment. Do you notice any change in the spectrum?

  4. Change the pulse width to 1 us (9 degrees), run the simulation, Fourier Transform and Phase Correct the spectrum using PS to set the same phase as the previous experiment. Do you notice any change in the spectrum?

  5. Change the pulse width to 20 us (180 degrees), run the simulation, Fourier Transform and Phase Correct the spectrum using PS to set the same phase as the previous experiment. Do you notice any change in the spectrum?

  6. Change the pulse width to 30 us (270 degrees), run the simulation, Fourier Transform and Phase Correct the spectrum using PS to set the same phase as the previous experiment. Do you notice any change in the spectrum?

  7. Change the pulse width to 40 us (360 degrees), run the simulation, Fourier Transform and Phase Correct the spectrum using PS to set the same phase as the previous experiment. Do you notice any change in the spectrum?


Effect of Spectral Window

  1. Reset the pulse width to 10 us (90 degrees).

  2. Change the Sweep Width to 2000 Hz, run the simulation, notice the frequency of the tone, Fourier Transform and Phase Correct the spectrum using PS to set the same phase as the previous experiment.

  3. Take a close look at the spectrum. Where are the peaks located? What is the center of the spectral window? What is the low and high shift limits of the window?

  4. Move the spectral window to the right by changing the spectrometer offset to 1000 Hz in the spectrometer settings (vSpec|Parameters|Offset Frequency) and in the data acquisition settings (View|Spectral Parameters|Offset Frequency 1st dimension). Run the simulation, notice the frequency of the tone, Fourier Transform and Phase Correct the spectrum using PS to set the same phase as the previous experiment.

  5. Take a close look at the spectrum. Where are the peaks located? What is the center of the spectral window? What is the low and high shift limits of the window?


S/N Enhancement

  1. Change the EB Sensitivity for the simulation file to 1.0 (either by editing the file with notepad or by making the change in the NMR Simulation routine).

  2. Clear the old file by loading a new file. (File | New)

  3. Load the simulation file. (vSpec | Get Samples)

  4. Reset the parameters to Pulse Width, 10 us; Recycle Delay, 1 s; Receiver gain, 10; Sweep Width, 2000; Offset Frequency, 1000; Data Size 8192; Delay, 1 us.

  5. Run Simulation. Fourier Transform and Phase Correct the spectrum. Calculate the S/N (Zoom in on a peak then type SN. Check that the value is reasonable sometimes NUTS does not find the highest peak for the calculation.)

  6. Change the simulation for 4056 data points. Run the simulation, Fourier transform and phase correct the spectrum. Has the S/N improved? Why?

  7. Configure NUTS for dual display (AL) then (DD).

  8. Set the simulation for 10 scans. Run the simulation, Fourier transform and phase correct the spectrum. The new spectrum is on the bottom (Change the scale of the stored spectrum so they have the same peak intensity. Type (AM) and enter a value of 10. What has changed? Calculate the S/N. Has the S/N improved?

  9. Set the simulation for 1 scan. Run the simulation, set the line broadening to 1 (LB 1), use the exponential multiplication function (EM), Fourier transform and phase correct the spectrum. Calculate the S/N. If you scale the spectrum in the buffer by 0.37 they will have the same amplitude. Zoom in on a peak and observe any changes in the peak shape.

  10. Repeat the simulation. Change the Line broadening to 2. Exponential Multiply. Fourier Transform. Phase Same. Zoom in on a peak and observe changes in the shape.

  11. Work with several other Window functions. The help menu will provide useful information about what each is useful for and how to set the parameters.


For additional exercises, see the Virtual Spectrometer Tutorial. Available from the Acorn NMR Website at http://www.acornnmr.com.
This page is maintained by
Scott Van Bramer
Department of Chemistry
Widener University
Chester, PA 19013

Please send any comments, corrections, or suggestions to svanbram@science.widener.edu.

This page has been accessed 6025 times since 1/5 /96 .
Last Updated Monday, May 26, 1997 11:53:55.