Energy Profile Tutorial

Tutorial for the Energy Profile Calculation

EXAMPLE: Since there may be more than one saddle point on the potential energy surface, it is prudent to verify that the saddle point found is connected to the energy minima associated with the reactants and products. Verification involves the calculation of an Energy Profile. In an Energy Profile calculation a bond length or bond angle in the activated complex is varied incrementally along the reaction coordinate and the resulting structure is optimized at each step. The bond length or angle varied in the calculation is usually the one that is changing in the normal mode of vibration associated with the imaginary frequency. Plots of the electronic energy versus the change in the bond length or angle are obtained in both the forward and reverse directions. By observing the models of the structures at each step along the plots, one can confirm that the activated complex leads to the products in the forward direction and to the reactants in the reverse direction.

Calculate an Energy Profile for the hydroboration of ethylene and verify that the activated complex found in Tutorial for the Construction of a Transition State Structure does form ethylborane in the forward direction and dissociates into borane and ethylene in the reverse direction.


PROCEDURE:

  1. To examine the reaction coordinate in the forward direction, open the ethylborane_ts_dft.spartan file in Spartan '10 and save it as ethylborane_ts_dft_ep_f.spartan in your (username) folder.



  2. Click on the "Model" in the tool bar and check "Labels" in the drop-down window to view the atom labels.



  3. Click the Constain Distance button on the top toolbar and then click on hydrogen atom H1 and carbon atom C1.



  4. Next, click the in the lower, right corner of the Spartan '10 window .



  5. Check the profile box in the lower left corner of the window by placing the cursor on the box and clicking the left mouse button. When the box is checked, the color of the flag will change to green.



  6. Also, two additional boxes will appear to the right of the properties symbol .



  7. We want to vary the C1-H1 bond length from 1.847 Å - the value in the activated complex - to 1.086 Å - the value in ethylborane - in eight steps. Highlight the number in the box to the right of the "to" , enter the value 1.083 and then press the "Enter" key on the keyboard. Next, highlight the number "10" in the box to the right of "Steps:" , enter the value 8 and press the "Enter" key on the keyboard.



  8. Finally, click the on the tool bar.



  9. Click "Setup" in the tool bar and select "Calculations" in the pop-up menu. When the "Calculations" window appears, choose "Energy Profile" at "Ground" state with "Density Functional," "B3LYP" and "6-31G* " in "Vacuum." Remove any checks from the boxes below and click the "OK" button.



  10. Select "Submit" from the "Setup" menu to initiate the "Energy Profile" calculation. The calculation begins with an optimization of the transition state geometry with C1-H1 distance fixed at 1.847 Å. The C1-H1 is decreased by 0.0951 Å, and the geometry of the new structure is optimized with the C1-H1 distances constrained at the new value. Again, the C1-H1 distance is reduced by 0.0951 Å, and the new structure is optimized. It takes approximately 15 minutes to optimize the geometries of the eight structures generated along the reaction coordinate. With the completion of the "Energy Profile" calculation, the program writes the output to a file with a .Prof.M0001 extension. In this example the file is ethylborane_ts_dft_ep_f.Prof.M0001.spartan .



  11. Close the ethylborane_ts_dft_ep_f.spartan file and open the ethylborane_ts_dft_ep_f.Prof.M0001.spartan file. Select "Spreadsheet from the "Display" pop-up menu.



  12. Click on the first box in the column to the right of the column labeled "Label." The box is highlighted when the color changes to blue. Next click the button on the toolbar at the bottom of the spreadsheet window . Select "E" in the "Add" window that appears and then click the button at the bottom of the "Add" window.



  13. The electronic energies (kJ/mol) for each structure are now listed in the second column of the spreadsheet.



  14. To enter the constrained C1-H1 distance for each structure in the spreadsheet click the Constain Distance button on the top toolbar.



  15. Next, click on the constraint marker between the C1 and H1 atoms.



  16. Finally, click on the properties symbol in the lower right hand corner of the Spartan'10 window.



  17. Click the to close the spreadsheet. Next, click the "Display" button on the Spartan'10 window and select "Plots."



  18. Click on the pull-down menu under "X Axis" in the "XY Plot" window and select "Constraint(Con1).



  19. Select "E(kJ/mol)" from the menu under "Y Axis" in the "XY Plot" window.



  20. Click the button at the lower right corner of the "Plots" window to create a plot of electronic energy versus the constrained C1-H1 distance.



  21. Click the button to advance along the reaction coordinate from the transition state to the eclipsed conformer of ethylborane and the button to advance in the reverse direction.



  22. At any one of the eight points on the reaction coordinate the bond distances, bond angles, and dihedral angles of the structure may be measured with , and .



  23. Build the eclipsed conformer of ethylborane in Spartan’10 and optimize the structure at B3YLP/6-31* level. Is there anything unusual about this optimized structure?



  24. Compare the bond lengths, bond angles, dihedral angles and energy of ethylborane with bond lengths and angles and energy of the structure at the minimum of the forward reaction coordinate to verify that the minimum structure is ethylborane.



  25. In the same manner the reverse reaction coordinate is investigated by repeating Steps 1 through 20. In this profile the C-B bond length is varied from 1.796 to 1.86Å.



  26. The minimum on the reverse side of the reaction is the H3B•C2H6 intermediate at the B3LYP/6-31G* level. The transition state structure closely resembles the H3B•C2H6 structure, and the transition state is said to occur early in the reaction coordinate.