Molecular Orbitals on Borane Tutorial

Tutorial for Molecular Orbitals on Borane

EXAMPLE: Use Spartan '10 to build BH3. Select the semi-empirical method AM1 and optimize the geometry. Print the molecular orbital coefficients, orbital energies, and electrostatic and atomic charges to the output file. Construct graphical representations of the molecular orbitals and map the electostatic potential on an isodensity surface for the molecule.


PROCEDURE:


Build a Model
Geometry Optimization
Output File
Isosurface Display of MO
Electrostatic Potential Map

Construction of a Molecular Model

  1. Double click on the Spartan '10 icon, , and then click "File" in the upper left corner of the Spartan '10 window.



  2. Select "New" from the pop-up menu.



  3. Click the "Inorganic" tab in the "model kit" located on the right .



  4. Select "B" from the periodic table.



  5. Select the sp2 jack in the "model kit."



  6. Place the cursor in the center of the window and click the left button on the mouse.



  7. Hold the left button on the mouse down and move the cursor horizontally to rotate the model around the z-axis.



  8. Hold the "Shift" button on the keyboard down and press the right button on the mouse. Move the cursor vertically to increase (up) or decrease (down) the size of the model. To center the model in the window, place the cursor on the model, hold the right button on the mouse down, and move the model to the center of the window.



  9. For other functions associated with the mouse and for help with the software click "Help" in the top, right corner of the window and then click the "General Operation Features" in the "Spartan '10 Help" window to observe topics for which help is available.



  10. Select "H" from the periodic table and click the button in the "Model Kit." Place the cursor at the end of the a stick representing a sp2 hybrid orbital on the boron atom and click the left button on the mouse to attach a hydrogen atom to the boron atom.



  11. Attach hydrogen atoms to the remaining sp2 hybrid orbitals (sticks) on the boron atom in the same manner.



  12. Finally, click the button to initiate a molecular mechanics program. Bond angles and lengths are varied until a minimum in the molecular-mechanics potential energy is obtained. The molecular geometry found at the minimum is used as the starting geometry for the optimization calculations. The point group to which the molecule belongs is indicated in the lower left corner of the window.






Determination of the Molecular Geometry Associated with a Minimum on the Potential Energy Surface

  1. Click "Setup" in the tool bar.



  2. Select "Calculations" in the pop-up menu. When the "Setup Calculations" window appears, click on the first pull-down menu in the "Calculate:" row and select "Equilibrium Geometry."



  3. Select "Semi-Empirical" from the second pull-down menu as the method or level of calculation.



  4. Pick "AM1" as the type of semi-empirical method from the third pull-down menu in the row labeled "Calculate:."



  5. Since the molecular geometry (atomic coordinates) obtained from the molecular mechanics minimization will be used as the starting geometry for the optimization calculation, select "Current" from the pull-down menu in the row labeled "Start from:." BH3 is a neutral molecule and the spin multiplicity of the ground electronic state is 1. Select "Neutral" in the box labeled "Total Charge" and pick "Singlet" in the "Multiplicity" box. These settings are the default values for "Total Charge" and "Multiplicity."



  6. Since we intend to determine the atomic charges that best fit the electrostatic potential , check the "Charges & Bond Orders" box in the "Print:" row. We will want a list of the the molecular orbitals and orbital energies. Check the "Orbitals & Energies" box in the "Print:" row . When the "Symmetry" box is checked (the default setting), the molecular symmetry of the starting geometry is used in the calculation.



  7. Click the "OK" button to remove the "Step-up Calculations" window. Again, click "Setup" in the tool bar at the top of Spartan '10 window.



  8. Select "Submit" in the pop-up menu, or click the "Submit" button at the bottom of "Calculations" window. A "Save As" window will appear since we have yet to create a folder in which to store the results of the calculations. Create a "Spartan" folder in your (username) folder and save your compuational work in this folder.



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



  10. When the optimization is completed, the Spartan '10 window will reappear. Again, click the "OK" button.





Output File

  1. Click "Display" in the tool bar at the top of Spartan '10 window and select "Output" from the pop-up menu. Enlarge the "Output" window. The output includes the type of calculation ( Geometry Optimization), the method of calculation (AM1), and the point group (D3h) to which the model belongs.



  2. The energy (kJ/mol) of the optimized structure is displayed just below the number of cycles required for convergence.



  3. A table of molecular orbital energies and coefficients appears next. Each column in the table contains the energy of a MO in units of Hartree and electron volts. Just below the energy is the the Mulliken symbol for the irreducible representation to which the molecular orbital belongs. The coefficients cji for the molecular orbital are listed beneath the symmetry label. ci is a basis set function such as a valence AO. For example, molecular orbital #1, , has an energy of -O.79988 Hartree or -21.76581 eV.



  4. The atomic charges and bond orders are found at the end of the output file.





Construction of an Isosurface for a Molecular Orbital

  1. Click "Setup" in the tool bar at the top of Spartan '10 window and then select "Surfaces" from the pop-up menu.



  2. Click "HOMO" in the drop-down window.



  3. Select "HOMO," the highest occupied molecular orbital.



  4. Click the box to the left of "HOMO" in the "Surface" window.



  5. Click the button to close the "Surfaces" window.



  6. The isosurface for the highest occupied molecular orbital (one of the e' MOs) appears in the "Solid" style.



  7. Place the cursor on the isosurface and then click the left mouse button. Next, click "Display" in the tool bar at the top of window and select "Properties" from the drop-down menu.



  8. A "Surface Properties" window will appear.



  9. To select a different style, click on the "Style:" box and highlight "mesh" in the pull-down menu.



  10. Click the button to close the "Surface Properties" window.



  11. Place the cursor on the isosurface. Press and hold the left mouse button and then move the cursor up or down to rotate the isosurface on the x-axis and left or right to rotate the isosurface around the y-axis. Other mouse functions for orienting the isosurface in the window are available.



  12. To remove the isosurface from the window, click "Display" in the tool bar at the top of Spartan '10 window and select "Surfaces" from the pop-up menu. Click the checked box next to "HOMO."





Map of Electrostatic Potential on an Isodensity Surface

  1. Click "Setup" in the tool bar at the top of Spartan '10 window and then select "Surfaces" from the pop-up menu. Click the button at the bottom of the "Surfaces" window and select "More Surfaces..." in the drop-down menu.



  2. In the "Add Surfures" pop-up menu select density in "Surface" pull-down menu. click the "Property:" pull-down menu in the "Add Surface" window and select "potential."



  3. Next, select "potential" in the "Property:" pull-down menu.



  4. Click the button in the "Add Surface" window.



  5. Click the box to the left of "Electrostatic Potential Map" in the "Surface" window.



  6. Click the button to close the "Surfaces" window.



  7. Place the cursor on the isodensity surface. Press and hold the left mouse button and then move the cursor up or down to rotate the isodensity surface on the x-axis. Other mouse functions for orienting the isodensity surface in the window are available.



  8. Place the cursor on the isodensity surface and click the left mouse button. Next, click "Display" in the tool bar at the top of Spartan '10 window and select "Properties" from the pop-up menu. A "Surface Properties" window will appear. In the top left corner of the window you will find the maximum negative (-25.389 kJ/mol) and positive (142.707 kJ/mol) electostatic potentials. These values are represented on the isodensity surface with the colors red and blue. The electron density at any point on the isodensity surface is 0.002 electrons/bohr3. 1 bohr = 0.52917725 Å



  9. To remove the isosurface from the window, click "Display" in the tool bar at the top of Spartan '10 window and select "Surfaces" from the pop-up menu. Click the checked box next to "Electrostatic Potential Map."



  10. Click the button to close the "Surfaces" window.