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Administrator To save the iterations as a movie, click Record Each Iteration. The following illustration shows the distances between atom pairs at the completion of the docking computation. The distances in the Actual cell are close to the distances in the Optimal cell. iteration values Note that while the docking computation proceeds, one molecule remains stationary and the second molecule moves. To stop the docking computation before it reaches it’s preset RMS values, click Stop Calculation on the Calculation toolbar. Both docking and recording are stopped. The Status bar displays the values describing each iteration of the docking computation. The following illustration shows the docked polymer molecules. Your results may not exactly match those described here. The relative position of the two fragments or molecules at the start of the docking computation can affect your results. For more accurate results, lower the minimum RMS gradient. Tutorial 8: Viewing Molecular Surfaces Frontier molecular orbital theory says that the highest occupied molecular orbitals (HOMO) and lowest unoccupied molecular orbitals (LUMO) are the most important MOs affecting a molecule’s reactivity. This tutorial examines the reactivity of double bonds by looking at the simplest molecule containing a double bond, ethene. Create an ethene model: 1. From the File menu, choose New. 2. Draw a double bond in the ChemDraw panel. A molecule of ethene appears. Before you can view the molecular orbital surface, you must calculate it. 44 •Chem3D Tutorials <strong>CambridgeSoft</strong> Tutorial 8: Viewing Molecular Surfaces
3. From the Calculations menu, point to Extended Huckel and select Calculate Surfaces. To view the Highest Occupied Molecular Orbital (HOMO): 4. From the Surfaces menu, point to Choose Surface, and select Molecular Orbital. 5. From the Surfaces menu, point to Molecular Orbital to see the HOMO/LUMO options. Select HOMO (N=6). The pi bonding orbital surface appears. To view the Lowest Unoccupied Molecular Orbital (LUMO): 1. From the Surfaces menu, point to Molecular Orbital to see the HOMO/LUMO options. Select LUMO (N=7). The pi antibonding orbital surface appears. NOTE: You may need to rotate the molecule to view the orbitals. These are only two of twelve different orbitals available. The other ten orbitals represent various interactions of sigma orbitals. Only the pi orbitals are involved in the HOMO and the LUMO. Because the HOMO and LUMO control the reactivity of a molecule, you can conclude that it is the pi bonding interactions of ethene that control its reactivity. This is a specific case of a more general rule: pi bonds are more reactive than sigma bonds. Tutorial 9: Mapping Properties onto Surfaces NOTE: This example is designed to demonstrate Gaussian minimization. You can also do it using CS MOPAC or Extended Hückel calculations. <strong>ChemOffice</strong> 2005/Chem3D Chem3D Tutorials • 45 Tutorial 9: Mapping Properties onto Surfaces
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