Activation Complex Tutorial

Tutorial for the Construction of a Transition State Structure

EXAMPLE: Propose and build a model of the activated complex for the hydroboration of ethylene (eq 1). Use the B3LYP method and 6-31G* basis set to optimize of the "Transition State Geometry." Compute the frequencies and print the thermodynamic quantities.

Hydroboration is the addition of BH3 to an alkene, in this case ethylene (eq 1). One can imagine a number of possible pathways involving one or more elementary reactions. We will consider one of these pathways, the concerted cis-addition of borane to ethylene. In this elementary reaction a B-H bond in borane and the C-C bond in ethylene will lengthen as the two molecules approach each other to form the activated complex or transition state structure. The planarity around the boron and carbon atoms will be lost, and the distances between the boron and carbon atoms as well as the hydrogen and the other carbon atom are shorten to lengths that are longer than normal B-C and C-H bond distances. The Principle of Least Motion suggests that the most probable path in the concerted cis-addition reaction is the approach of the borane from above or below the plane of the ethylene molecule with a H-B-C-C dihedral angle of nearly zero degrees. Hence our initial guess of the transition state structure would look like the drawing below.



To which point group does the initial guess of the transition state structure belong?

PROCEDURE:

  1. Open Spartan '10 and build ethane. Click the button on the tool bar to ensure that the correct point group appears in the lower left corner of the Spartan '10 window.



  2. Convert the staggered conformation of ethane into the eclipsed conformation. Click on the button in the tool bar and then highlight the hydrogen,carbon, carbon and hydrogen atoms. The value of the H-C-C-H dihedral angle is displayed in the lower right-hand corner of the Spartan window. Just to the right of the value you will see the property symbol



  3. Highlight the value (60.00 °) in the box next to and type in 0.0°. Press the "Enter" key.



  4. Select "B" from the periodic table and the sp3 jack in the "model kit." Attach the BH3 unit to the carbon atom on the right.


  5. The B-H bond in the plane of the page must be inverted without loss of symmetry. Click on the button in the tool bar and then highlight the carbon atom on the left, the carbon on the right, the boron atom and the "B-H" hydrogen atom above the plane of page. The value of the C-C-B-H dihedral angle is displayed in the lower right-hand corner of the Spartan window. Just to the right of the value you will see the property symbol



  6. Highlight the value (61.32°) in the box next to and type in 0.0°. Press the "Enter" key. The symmetry of the structure remains Cs.



  7. There are too many hydrogen atoms. Either a hydrogen atom on the nitrogen atom or boron atom must be removed. To maintain Cs symmetry the hydrogen must be in the mirror plane. Click the delete button in the tool bar.



  8. Place the cursor over the hydrogen atom and click the left mouse button. I chose to delete the "B-H" hydrogen.



  9. A good starting estimate of the transition state distances between two second period atoms that are undergoing bond formation or bond dissociation is the equilibrium bond length plus 0.50 Å or the sum of the covalent radii plus 0.50 Å. Click on the button in the tool bar and then highlight the boron and carbon atoms. The distance between the boron and carbon atoms is displayed in the lower right-hand corner of the Spartan window. Just to the right of the value you will see the property symbol .



  10. Highlight the B1-C1 bond distance (1.578 Å) in the box next to and type in 2.1 Å (sum of the covalent radii + 0.5 Å).



  11. Press the "Enter" key to set the distance between the boron and carbon atoms at 2.1 Å.



  12. In the same manner click on the button in the tool bar and then highlight the hydrogen and carbon atoms. Next highlight the value (1.094 Å) of the H-C bond distance in the box near the symbol and type in 1.5 Å. Press the "Enter" key to set the H-C distance.



  13. To decrease the distance between the hydrogen and boron atoms we will reduce the H-C-C and C-C-B bond angles. Click on the button in the tool bar and then highlight the boron and two carbon atoms.



  14. Highlight the value of the C-C-B bond angle (110.57°) in the box next to symbol and type in 85.0°. Press the "Enter" key to set the C-C-B angle.



  15. Finally, click on the button in the tool bar and then highlight the hydrogen and two carbon atoms. Next highlight the value of the H-C-C bond angle (110.57°) in the box next to symbol and type in 90.0°. Press the "Enter" key to set the H-C-C angle. The H-B distance is now 1.455 Å which is a reasonable estimate of the bond forming distance in the transition state. This structure is our initial guess of the transition state structure with Cs symmetry. Select "save as" from "File" pull-down menu and enter the file name "ethylborane_ts_dft_guess.spartan." Click the "Save" button in the "Save As" window to save the guess structure.



  16. Click "Setup" in the tool bar and select "Calculations" in the pop-up menu. When the "Calculations" window appears, choose "Transition State Geometry" at "Ground" state with "Density Functional," "B3LYP" and "6-31G* " in "Vacuum." Check Compute: "IR" and Print: "Thermodynamics." Optimization of a transition state geometry often requires a significantly larger number of iterations than the optimization of the equilibrium geometry. Hence, we will set the maximum number of iterations at 200 by entering “GEOMETRYCYCLE=200" in the space to the right of “Options:” in the “Calculations” window. Press the "Enter" key.



  17. Click the "OK" button to close the "Calculations" window and select "save as" from "File" pull-down menu. Enter the file name "ethylborane_ts_dft".spartan" and click the "Save" button in the "Save As" window.



  18. Select "Submit" from the "Setup" menu to initiate the calculation.



  19. When the smaller "Spartan '10" window appears, click the "OK" button.



  20. The energy state of the activated complex should be located at a first-order saddle point on the potential energy surface i.e. a point which is a maximum in one direction and a minimum in all other directions. The structure associated with the first-order saddle point will exhibit one imaginary frequency and the normal mode of vibration associated with this frequency should emulate the motion of the atoms along the reacation coordinate.




  21. To confirm that the energy state of our structure is located at a first-order saddle point, click on "Display" in the tool bar and select "Spectra" from the pop-up menu. The "Spectra" window which appears contains the frequencies of the normal modes of vibration for the structure. The imaginary frequencies have an "i" in front of the number and appear at the beginning of the list. Are there any imaginary frequencies?



  22. To determine if the motion of the atoms in the normal mode of vibration associated with the imaginary frequency is consistent with the formation of products in the forward direction and reactants in the reverse direction, click the box next to the imaginary frequency in the "Spectra" window and observe the animation. Does the structure appear to move toward the product in one direction and reactants in the other direction. To slow the frequency of the animation, change the number in the box labeled "Steps" to 35. Place the cursor (arrow) on the structure and click the left button on the mouse. Click the checked box to stop the animation.