Lecture: Software for NMR Concepts

This is an outline of a lecture given for NSF Faculty Enhancement Workshops at the University of Rhode Island and for NMR Concepts.A series of exercises designed to show features of each program is available. Topics are selected from the outline below for a particular audience. Additional information about this software is available from this site. If you have any comments or suggestions, please contact: svanbram@science.widener.edu


Introduction

  1. Where to get this file and more information: http://science.widener.edu/svb/nmr/nmr.html

  2. System Requirements: Most of the software discussed here will run on a 486 25 SX, but a 486 33 DX with 8 MB RAM is recommended as a minimal system. Because I use a PC, this listing does not include Macintosh applications. Some of the commercial applications are available for the Macintosh. Windows 95 versions are also available for some of the commercial applications.


Interpreted NMR Spectra


Software for demonstrating NMR Concepts

  1. NMR Spin System Simulator (SSS)
    1. Rotating frame and pulse
      1. Setup; 1 Spin;
      2. Setup; Parameters; observe 2 Hz
      3. Options; Animation; 1 ms
      4. 90° pulse on X
      5. Commands; Delay; 1 s
      6. Commands; Reset

    2. Relaxation effects
      1. Options; Relaxation
      2. 90° pulse on X
      3. Commands; Delay
      4. Commands; Reset
      5. Setup; Parameters; T1 = 1.0 sec, T2 = 0.1 sec
      6. 90° pulse on X
      7. Commands; Delay;
      8. Commands; Reset
      9. Setup; Parameters; Observe 0 Hz
      10. 90° pulse on X
      11. Commands; Delay; Reset

    3. T1 Inversion Recovery
      1. Options; Animation; Update 5 ms
      2. Setup; Parameters; Observe 2 Hz; T2 1 sec
      3. 180 ° pulse
      4. Commands; Delay; 0.1 sec
      5. 90 ° Pulse
      6. Commands; Delay; 1 sec;
      7. Commands; Reset
      8. Repeat with 0.69 and 1.0 sec inversion delay

    4. Homonuclear system
      1. Setup; AX Homonuclear
      2. Options; Animation; Update 10 ms
      3. Setup; Parameters; A = +1; X = -1; Coupling = 0
      4. 90 ° pulse
      5. Commands; Delay;
      6. Commands; Reset

    5. Spin Echo experiment
      1. 90 ° pulse
      2. Commands; Delay 0.15 sec;
      3. 180 ° pulse on Y
      4. Commands; Delay 0.15 sec;
      5. Repeat

    6. Homonuclear Coupling of Nuclei
      1. Setup; Parameters; Coupling constant 0.1
      2. 90 ° on X
      3. Commands; Delay 1 sec;

    7. Heteronuclear Decoupling
      1. Setup; AX Heteronuclear
      2. 90 ° on 1H X
      3. Delay 1/8J
      4. 180 ° on 13C X
      5. Delay 1/8J
      6. Delay 1/8J
      7. 180 ° on 13C Y
      8. Delay 1/8J
      9. Options; Animation 0.2 ms
      10. Commands; Delay 0.02 sec; continually pulse 180 ° 13C X
      11. Setup; Parameters; 1H 50 Hz
      12. 90 ° on 1H X
      13. Commands; Delay 0.02 sec; continually pulse 180 ° 13C X

  2. FTNMR Simulator
    1. Introduce
      1. 10 Hz, Intensity 1; T1 1, Done
      2. Noise 0; Flip Angle 90 L; Continue
      3. Show FID; All of it; Real
      4. Show FID; All of it; Imaginary
      5. Show FID; Show Vectors (note: mixing left and right hand rules).
      6. Show Points; Points Only; Fit cosine curve
      7. Cont; Don't Zero Fill; Do FT; New View; X-Range; 7 to 12 Hz
      8. Start Over; Same FID; Repeat with zero fill

    2. Apodization
      1. Start Over; Same Frequencies
      2. Add noise (0.5), 2048 data points,
      3. Continue; Do FT
      4. Start Over; Same FID
      5. Cont; Exp Smoothing; 1; Show FID; Do FT

    3. Averaging
      1. Start Over; Same Frequencies
      2. # Pulses 100; Continue; Do FT
      3. Start Over; Same FID; Continue;
      4. Exp Smoothing; Show FID; Do FT

    4. Phase
      1. Start Over; Complete Restart;
      2. Frequency 20 Hz
      3. 4096 points; noise 0; 1 pulse; Acquisition delay 0
      4. Show FID 0.8 sec; Show FID 0.08 sec
      5. Start Over; Same Frequency
      6. Acquisition delay 0.01
      7. Show FID 0.8 sec; Show Points; Fit cosine curve; Show vectors
      8. Continue; Do FT

    5. Multiple Spin System
      1. Start Over; Complete Restart
      2. 1 Hz; 2 Hz; 1024 points; T2 10 sec
      3. Show Frequencies; Show Vectors
      4. Continue; Do FT
      5. New View; X-Range; 0 Hz to 5 Hz

    6. Acquisition Parameters
      1. Start Over; Same Frequency
      2. 128 points
      3. Continue; Notice Acquisition Time; Do FT; New View; X-Range; 0 Hz to 5 Hz
      4. Start Over; Same Frequency
      5. Spectral Width 10
      6. Continue; Notice Acquisition Time; Do FT

    7. Simulate Spectrum
      1. Load 1-H spectrum of 1,2,3-trichlorobenzene
      2. Noise 0.5, 100 pulses,
      3. Show vectors
      4. zero fill, exp smooth, FT

  3. NMR-SIM

  4. Cool Edit
    1. Single Frequency: Generate Tone; 8000 Hz sample rate; 1000 Hz; 1 sec acquisition; Play; Frequency Analysis
    2. FID: Apply envelope to wave; play; FT
    3. Change Acquisition Time: File; New; Generate Tone; 0.1 sec acquisition; Apply Envelope; Play; Frequency Analysis
    4. Add harmonics to demonstrate sampling rate and spectral width
    5. Open SAMPLE.WAV to show sampling rate 8k, 16k, 32k. Play and zoom.
    6. Noisy FID: File; Open; S_N_test.WAV; Play; Frequency Analysis
    7. Apodize noisy FID by applying envelope; Play; Frequency Analysis.

  5. SAM (Shimming Ain't Magic)
    1. Start with Shimmed Signal and adjust each shim to show effect
    2. Randomize Shims and adjust

  6. Virtual Spectrometer
    1. Open Nuts
    2. Create Ethanol Spin System
      1. NS; Frequency, 300 MHz; Sweep Width, 4000 Hz; Offset, 2000 Hz
      2. Add Simulation Data (A)
      3. Number Spins 6
      4. Shifts
        1. OH 5.0 ppm
        2. CH2 3.7 ppm
        3. CH3 1.2 ppm
      5. Coupling (8 Hz)
      6. Accept and Calculate
    3. Create Virtual NMR File (V)
      1. Concentration 1 mM
      2. Sensitivity 10
      3. 90 Degree Pulse 10 us
      4. Save File
    4. Get Simulation (GS)
    5. Set Parameters (VP)
      1. Scans 1
      2. Pulse Width 10
      3. Reciever Gain 1
      4. Offset Frequency 2000
    6. Zero Go (ZG)
    7. Set Scale (^F)
    8. Fourier Transform (FT)
    9. Auto Phase (AP)
    10. Poor Resolution, Increse Data Size (8000)
    11. ZG, FT, AP, Zoom
    12. Still Not Optimum, Increase to 16000 and repeat
    13. Zoom in on Doublet and check S/N
    14. New FID, LB 0.2, EM, Process, check S/N

Software for Shift Prediction and Spectral Interpretation

  1. NMR Analyzer
    1. Simulate Proton NMR of ethanol (File, Auto)
      1. Number of Spins: 6
      2. Chemical Shifts
        1. OH 5.0 ppm
        2. CH2 3.7 ppm
        3. CH3 1.2 ppm
      3. Coupling Constants (8 Hz)
      4. Calculate
      5. Display Spectrum
      6. Change Spectrometer Frequency, Calculate, and Display

    2. Simulate 2-methyl-1-propanol (1st order spectrum since more than 7 spins)
      1. Shift Multiplicity J (Hz) H's
        3.4 doublet 8 2
        2.1 singlet 0 1
        1.7 heptuplet 8 1
        0.9 doublet 8 6

      2. Calculate
      3. Display Spectrum
      4. Change Spectrometer Frequency, Calculate, & Display

    3. Simulate Crotonaldehyde (Page 4-16 in lecture notes)
      1. Crotonaldeyhde Couplings
        Proton Shift Multiplicity a b c d
        a2.0 3 5.0 1.6
        b6.9 1 5.0 15.0 0.4
        c6.0 1 1.6 15.0 7.6
        d7.6 1 0.4 7.6

      2. Change Frequency

  2. ACD/CNMR and HNMR
    1. HNMR
      1. Draw Structure of Isobutanol
      2. Spectrum
      3. Integrate
      4. Selective Decoupling
      5. Change spectrometer frequency

    2. CNMR
      1. Draw Structure of Isobutanol
      2. Calculate 13-C Spectrum
      3. Turn proton decoupling on and off
      4. Change spectrometer frequency
      5. Spectral Editing
      6. Add Solvent

  3. C-13 NMR Module
    1. Draw Structure of Isobutanol
    2. Select and Calculate NMR
    3. Copy to Clipboard

  4. gNMR
    1. Paste Isobutanol Molecule from Clipboard, Include all C atoms (or import)
    2. Run initial Prediction
    3. View Spectrum
    4. Edit Proton Settings
      Nucleus Group Shift (ppm) Coupling
      1H # n   1 2 3 4 5
        1 3 0.9          
        2 1 2.1          
        3 2 3.4          
        4 1 1.8 8   8    
        5 3 0.9       8  

    5. Recalculate Spectrum
    6. Change Spectrometer Frequency (File, Options)
    7. Add C-13 in structure and preditct
    8. Edit C-13 Settings
      Nucleus Group Shift (ppm) Coupling
      13 C # n   1 2 3 4 5
        6 1 18          
        7 1 18          
        8 1 32          
        9 1 70          

    9. Change Spectrometer Frequency
      Nucleus Group Shift (ppm) Coupling
      13 C # n   1 2 3 4 5
        6 1 18 120        
        7 1 18         120
        8 1 32       120  
        9 1 70     120    

    10. Change Spectrometer Frequency (File, Options)

  5. SpecTool
    1. Data
    2. Tools
      1. Karplus Plot
      2. H Shift Prediction
      3. C Shift Prediction
    3. Ranges
    4. Spectra

  6. Hyper NMR
    1. Open Ethanol File
    2. Set View, rendering, numbers
    3. Setup shielding
      1. Quantum atoms (All)
      2. NMR Atoms (H's)
      3. Equivalent Atoms (4, 5, 6) and (7, 8)
    4. Setup Spectrum: Proton 300 MHz
    5. Compute and display spectrum
    6. Show Linewidth
    7. Label H 7 & 8, Compute and Display
    8. Change Label methyl C
    9. Compute and display spectrum
    10. Change Spectrometer Frequency

  7. WinDNMR


Software for NMR Data Processing

  1. MestRe-C
    1. File| Open| Isobutanol Proton FID
    2. Baseline Correct
    3. Fourier Transform
    4. Phase Correct
    5. Integrate

  2. NUTS
    1. Open Data File
      1. Demo Files from disk
      2. Pacific Lutheran University (H-1, C-13, APT, and DEPT)
      3. Widener University
    2. Background Correction [BC]
    3. Line Broadening [LB]
    4. Exponential Multiplication [EM]
    5. Fourier Transform [FT]
    6. Phase Correct [AP]
    7. Peak Pick [PP]
    8. Display Peak Data [CB]
    9. Integrate [AI] then [ID] to fine adjust
    10. Zoom (mouse, left and right buttons)
    11. More Information about Nuts (brief) (detailed)

  3. PCNMR 4 Windows

  4. Win NMR


Tutorial Software

  1. Proton NMR Basics

  2. Introduction to Spectroscopy

  3. Problem Solving in NMR Spectroscopy


Mathcad Files to Study FT and NMR

  1. The Fourier Transform with Mathcad.
    1. Introduction to the Fourier Transform. (*.mcd).
      1. Go Through Document
      2. Change Test Frequency to 2 Hz and Observe

    2. Lecture Version. Change Variables and observe FID and Spectrum.

  2. NMR Concepts with Mathcad
    1. Introduction to NMR (*mcd),
      1. Change nucleus b frequency to 8 Hz
      2. Observe FID (zoom in to first 10 seconds)
      3. Observe Spectrum (explain folding)
      4. Open Spectral Window, dwell time to 0.05 sec
      5. Observe FID (zoom in on first two seconds)
      6. Observe spectrum
      7. Reduce resolution, NA to 26
      8. Observe FID (Full View) and Spectrum

    2. Introduction to Quadrature detection (*mcd)

    3. Introduction to Phase Cycling (for quadrature detection) (*mcd)

    4. Introduction to Apodization for S/N and resolution enhancement. (*mcd)


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 27938 times since 1/5 /96 .
Last Updated Saturday, July 27, 1996