EXAMPLE: Propose and build a model of the activated complex for the hydroboration of ethylene (eq 1). Use MNDO as a low-level method for the optimization of the "Transition State Geometry" followed by a high-level optimization with the Hartree-Fock method and the 6-31G* basis set. Compute the frequencies and print the thermodynamic quantities and vibrational modes to the output file.

PROCEDURE:

1. Open PC Spartan Pro and build ethylene.
   
   



2. Rotate the model 90° about the C-C bond. Select "B" from the periodic table and the sp² jack in the "model kit." Hold down the Insert button on the keyboard , place the cursor above the ethylene molecule, and click the left mouse button.
   
   



3. To rotate the model of BH₃, hold down the Control button on the keyboard , press the left mouse button, and move the mouse. Hold down the Control button on the keyboard , press the right mouse button, and move the mouse to translate the BH₃.
   
   



4. One procedure used to build an activated complex is the Reaction. This procedure utilizes the linear synchronous transit method and is activated by clicking button in the tool bar. Bonding or nonbonding electron pairs in the reactants are "pushed" to form new bonds or break old bonds in much the same way that you illustrate reaction mechanisms in organic chemistry.
   
   
   General Procedure:
   
   1. To break a bond between two atoms and form a new bond between two bonded atoms, click on the bond that is to be broken - be sure the bond is highlighted (changes color) and then click on the bond between the atoms where the new bond is to be formed.
   
   
   
   2. To break a bond between two atoms and form a new bond between two nonbonded atoms, click on the bond that is to be broken - be sure the bond is highlighted. Press the Shift key on the keyboard and HOLD, click on the atom common to the old and new bonds, and then click on the new atom.
   
   
   
   3. To create a bond between two atoms, click on the atom with a lone pair of electrons - be sure the atom is highlighted. Press the Shift key on the keyboard and HOLD, click on the highlighted atom a second time, and then click on the new atom.
   
   
   
   
   
   
5. As an initial guess for the activated complex, consider a structure in which a new bond between a hydrogen atom in the borane and a carbon atom in ethylene and a new bond between the boron atom in borane and the second carbon atom in ethylene are just beginning to form.
   
   



6. To form a bond between a hydrogen atom in the borane and a carbon atom in ethylene, click on the hydrogen atom to highlight it, press the Shift key on the keyboard and HOLD, click the highlighted hydrogen atom again, and then click on the carbon atom.
   
   



7. To form a bond between the boron atom in the borane and the second carbon atom in ethylene, click on the carbon atom to highlight it, press the Shift key on the keyboard and HOLD, click the highlighted carbon atom again, and then click on the boron atom.
   
   



8. Click the button in the lower left corner of the PC Spartan Pro window to obtain a rough approximation of the activated complex. The geometry of this structure is the starting geometry for the optimization calculation.
   
   



9. To optimize the geometry of the activated complex, click on the "Setup" in the tool bar and select "Calculations" from the pop-up menu. Pick "Transiton State Geometry," Semi-Empirical, and MNDO. Check the boxes next to "Frequencies" and "Vibrations Modes."
   
   



10. Click the "OK" button to close the "Setup Calculations" window and select "Submit" from the "Setup" menu. When the "Save As" window appears, create the "Hydro_ts.spartan" file in your "Spartan" folder on the Z drive for the results of the calculation. Each time the "PCPro" window appears, click the "OK" button.
    
    



11. To perform the high-level optimization , click on the "Setup" in the tool bar and select "Calculations" from the pop-up menu. Pick "Transiton State Geometry," the Hartree-Fock method, and the 6-31G(*) basis set. Be sure the boxes next to "Frequencies" and "Vibrations Modes" are checked. Click the "OK" button to close the "Setup Calculations" window and select "Submit" from the "Setup" menu. Each time the "PCPro" window appears, click the "OK" button.
    
    



12. 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.
    
    
    



13. 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 "Vibrations" from the pop-up menu. The "Vibrations List" 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?
    
    



14. 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 "Vibrations List" 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 and press the "Enter" key on the keyboard. Click the box a second time to stop the animation.