Exercises with NMR Spin System Simulator


Introduction

In this exercise you will use several different computer simulations to study the rotating frame model for NMR and then examine how the FID develops from this model. A strong understanding of this model will make it much easier to understand many other NMR experiments that we will be studying.

As you do this exercise, record your observations and comments. Take your time and think about what each step is showing. When you have completed the exercise, hand in your observations and comments.


Overview of the program, features available:

  1. Setup
    1. Parameters: This defines the spin system to observe
      1. Observe Frequency: This is the rotational frequency of the observed nuclei in the rotating frame.
      2. T1 Relaxation: This is relaxation along Bo.
      3. T2 Relaxation: This is relaxation in the XY plane.
    2. One Spin: A single nucleus. We will use this system for today's exercise.
    3. AX Homonuclear: Two nuclei of the same element, shows homonuclear (ie: H-H) coupling.
    4. AX Heteronuclear: Two nuclei of different elements, shows heteronuclear (ie: H-C) coupling.

  2. Commands
    1. Undo: go back one step.
    2. Reset: Resets the spin system to equilibrium starting point.
    3. Pulse: Applies a pulse of any Angle and Phase.
    4. Delay: Lets the spin system evolve for a set time interval.

  3. Options
    1. Relaxation: Toggles on/off T1 and T2 relaxation effects.
    2. Animation: Toggles on/off animation. This shows the evolution of the system during a delay. Changing the Update period controls the frequency of the frames. Suggested value is 2 ms on a 33DX computer. Shorter update periods make the animation go slower, longer update periods make the animation go faster.
    3. Labels: Toggles on/off the labels for the X, Y, and Z axes.


What is happening in the rotating frame?

Developing a model of the pulsed NMR experiment.

  1. Start the program and set defaults
    1. Switch to a one spin system (Setup, One Spin)
    2. Turn on Animation (Options, Animation, 2 ms)
    3. Label the Axes (Options, Labels)

  2. Apply a pulse and see what happens
    1. 90 degree pulse on X
    2. Observe for 1 second (Commands, Delay, 1 s)
    3. Describe What happened

  3. Make some changes to the observe frequency and see what happens
    1. Change the observe frequency to 5 Hz (Setup, Parameters, Observe frequency)
    2. 90 degree pulse on X
    3. Observe for 1 second (Commands, Delay, 1 s)
    4. Describe What happened, what is different
    5. Try some other observe frequencies (2 Hz, 1 Hz, -1 Hz) and describe what happens

  4. Change the pulse phase and see what happens
    1. Set the observe frequency to 5 Hz
    2. Apply a 90 degree pulse on Y
    3. Observe for 1 second
    4. Describe what happened, what is different
    5. Reset (Commands, Reset) and try pulses on -X and -Y
    6. Does this program use the left hand or right hand rule for applying pulses?
    7. Reset and try a 90 pulse with a 30 degree phase (Commands, Pulse)
    8. Describe what happens, is this what you expected?

  5. Change the pulse angle and see what happens
    1. Reset and apply a 45 degree pulse with a 0 degree phase (Commands, Pulse)
    2. Describe what happened, what is different, Look at the energy diagram and the magnitude of the magnetization vector (blue line) in the XY Plane. If only the magnetization in the XY plane is detected, what will happen to the size of the signal?
    3. Repeat with a 15 degree pulse angle.

  6. Introduction to Relaxation
    1. Reset
    2. Turn on Relaxation (Options, Relaxation)
    3. Apply a 90 degree pulse on X
    4. Observe for 1 second
    5. Has the net magnetization vector returned to equilibrium? Observe for additional time until it does. How long does this take?
    6. Describe what happened, notice the size of the net magnetization vector, the angle to the Z axis, and the magnitude of the magnetization in the XY plane.
    7. Change the observe frequency to 0 Hz, this will make it easier to see what happens, and repeat.
    8. Change T1 to 10 seconds and repeat (observe for 10 seconds or longer, you may want to change the animation settings to speed this up).
    9. Describe what changed for this experiment.
    10. Set T1 to 1 second and T2 to 1 second and repeat observations.
    11. Set T2 to 2 seconds. What happens? NOTE: actually the statement from the program is not correct, experimental systems have been found where T2 is longer than T1. Current understanding is that T2 can not be greater than 2*T1.


More Examples from Seminar

  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


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Scott Van Bramer
Department of Chemistry
Widener University
Chester, PA 19013

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

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Last Updated Monday, May 26, 1997 11:53:55.