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Department of Chemistry

University of Pittsburgh at Johnstown

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Energy Maps IV

Task: View the energy map of isoprene

Time: 6 minutes

In the last segment, we generated the energy map.  As you saw, it's two windows.  One is a map of the energy of the molecule as a result of changing the two angles we set. The other is a structure of the molecule; it changes as a function of the energy position selected on the map. You can see the relationship between the conformation of the sample and the corresponding energy.

At the end of the last lesson, we left two windows open.  Let's take a look.

  1. If you closed both windows previously, open them:
    1. Select File|Open and navigate to your working folder.
    2. Double-click on the isoprene.map folder.
    3. Select the arrow button in the Files of type box and choose Map(*.map) from the drop-down list.
    4. Select the energy.map  file.
  2. Two windows open:

    1. The left window is a three dimensional graph showing the relationship between the energy and the conformation of the molecule based on the search labels specified.
    2. The right window shows the lowest-energy conformation of the isoprene molecule. 
    3. There is a small spherical marker on the energy map in the left window.  It represents the energy corresponding to the structure in the right window. Click on another position on the energy map; the conformation will change.
    4. You'll notice a tool palette in each window; they function just as in the workspace.
    5. The rotate tool, , will rotate the map in the graph (left) window and the molecule in the right window.
  3. Change the conformation.
    1. In the graph window, choose the Select tool, .
    2. Click on a red-shaded portion of the graph. The conformation changes.
    3. Click on a different part of the map to see another conformation.
    4. Select the arrow button in the parameter bar at the bottom of the graph window and choose Energy from the drop-down menu bar. You may need to click the up or down arrow of the drop-down menu to bring Energy into view. 
    5. Select the arrow button in the parameter bar at the bottom of the structure window and choose DihedralAngle1. You may need to click the up or down arrow of the drop-down menu to bring DihedralAngle1 into view.
    6. Select the up arrow button of the parameter box in the structure window. Clicking on the button will change the value of the dihedral angle.  The marker on the energy map will move and the conformation will change in the structure window. See what happens when you click on the down arrow.
    7. Try the same thing with the bond angle: choose BondAngle1 from the drop-down list.  Click on the down and/or up arrow to see how the conformation changes.
  4. Animate the structure.
    1. Activate the conformation window by clicking anywhere in the window.
    2. Choose Edit|Annimate All Conformations.
    3. Select the forward arrow button, , to animate the structure through all the conformations sequentially.
    4. Select the stop button, , to halt the animation at any particular conformation.
    5. Select Done to close the Animate All Conformations dialog box.
  5. Find the lowest energy structure.
    1. From the Window menu select Window|New Conformational Analysis Window.
    2. Move the New Conformational Analysis Window to one side by clicking and dragging the title bar.
    3. Select the first item listed in the Conformational Analysis Window. The conformation in the structure window changes to the lowest energy.
    4. View the value of the energy, dihedral angle or bond angle, by selecting the corresponding option in the parameter bar of the Conformational Analysis Window.
  6. Analyze the lowest energy structure.
    1. Choose Options|Analysis Setting.
    2. Select the Show minima in the lowest []% of the range radio button
    3. In the text box next to % of the range type 1.
    4. Select Analyze. The box will close.
    5. The Conformational Analysis Window will show only the lowest energy.  Click on this value to display the lowest energy conformation in the structure window.
  7. Close the Conformational Analysis window.
  8. Chose File|Close to close both windows of the energy.map file.
  9. Warning!  Select No when asked if you want to save the changes to the energy.map file

Use the Geometry Label Wizard to generate search labels for a sequential search in the next lesson.