Unformatted text preview: Molecular Modeling CHEM 1310HP
Written by Dr. Sherrill and Matt Kennedy Fall 2009 **Note: Bring your laptops to lab with you. This is a dry lab. The WebMO login page is http://vergil.chemistry.gatech.edu/~webmo/cgi-bin/login.cgi Brief explanation of drawing in WebMO: The WebMO interface is fairly intuitive. Here are a few notes on drawing molecules. Once you log in, select "New Job" from the menu bar, and then select "Create New Job". This should take you to the drawing screen. There are instructions at the bottom of the window. Clicking on the screen adds an atom, dragging adds a bond, and clicking and dragging adds an atom and a bond. Typing a letter changes the atom type. You can also click on the small Periodic Table icon on the left (just below the icon that looks like H2O) to bring up a periodic table from which you can select an element. Draw the non-hydrogen atoms. You can add the hydrogen atoms automatically by going to the "Clean Up" menu and selecting "Add Hydrogens." You can draw double or triple bonds by dragging bonds between atoms more than once. Part I: Shapes of molecules. For each molecule, draw the molecule and optimize its geometry by using mechanics/optimize: (a) (b) (c) (d) H2 O BH3 NH3 PH3. For each molecule, after it's optimized, draw a sketch of the 3D shape of the molecule, and write down the HXH bond angle, where X is the central atom.
Part II: Bond lengths Bond lengths of C-C single, double, and triple bonds. Draw each of the following molecules, and for each, optimize the geometry using mechanics/optimize: ethane (H3C-CH3), ethylene (H2C=CH2), and acetylene (HC---CH, triple bond). Write down the C-C bond length for each molecule. Part III: Draw the molecular orbitals of N2. 1. Draw an N2 molecule. Make sure it has a triple bond. 2. Clean up the bond length by clicking clean-up, then select mechanics/optimize. 3. Click the right-arrow at the bottom of the builder window to submit the job; select the QChem engine if it isn't already selected. 4. On the "Configure Q-Chem Job Options" screen, change the calculation type from "Molecular Energy" to "Molecular Orbitals." Leave the other options the same. Click the right arrow button at the bottom of the screen to submit the computation. 5. The Job Manager window will open, showing your job running or waiting in the queue. Once the status is complete, you can view the results. These jobs will stay around in your account, so if something goes wrong, you should be able to close your browser, re-open it, log in again, and still find the jobs here in the job manager. 6. Click the magnifying-glass icon next to the job you just ran to see the results. 7. Find the list of molecular orbitals at the bottom of the page. It will list the first 10 by default. That's enough, we only want the first 7. Click on the magnifying-glass icon next to one of the MO's listed at the bottom of the page. This will open the "MO Viewer" tab above. Once this opens, try to stay inside the MO viewer tab to avoid a bug in the software that happens when switching between MO Viewer and other tabs. 8. In the MO viewer, you should see one of the MO's displayed, and also a list of MO's in a table to the left. You can view each of the first seven (7) orbitals by clicking on the first seven rows of this table. As you click a different row, that MO should then be shown in the viewer window. Try to avoid clicking on the row corresponding to the orbital you're already viewing (this is another bug). 9. Sketch each of the first 7 orbitals on a piece of paper for turning in as part of your report. Be sure to color-code the orbitals (i.e., if the orbitals have two different colors, make sure your drawing reflects this by using, for example, light and dark shading). *WRITE DOWN THE
ENERGIES OF EACH MO ALONG WITH YOUR SKETCH*. The energies are given in the table on the left-hand side of the MO Viewer, and they are in atomic units (Hartrees). 10. You will probably need to rotate the orbitals so you can see them properly. Try to rotate each orbital so that the N-N bond is lying horizontal. You might want to right-click in the viewing window and select opacity/transparent so you can see where the nuclei are. You might be looking at the molecule end-on and have to rotate it so you can see both nuclei. You can rotate the molecule by holding down the left mouse button while dragging the mouse around. 11. Once you have all the orbitals, look at the table of MO's in the MO Viewer, and find the box labeled "Electrostatic Potential" just below it (use this box instead of the one at the very bottom of the page). Click this box to bring up the Electrostatic Potential. This will show a color coded map of the electrostatic potential, where red indicates negative charge, and blue indicates positive charge. Rotate the electrostatic potential around a little (by moving the mouse while the left mouse button is held down) to see what it looks like. Draw a rough sketch on paper (again, oriented so that the N-N bond is horizontal and in the plane of the paper) and note where the blue and red regions are.
Post Lab Report and Questions (60 points)
Lab Notes/Observations as described in the procedure (15 points) Part I 1. Identify the VSPER shape for each of the molecules considered in this part (H2O, BH3, NH3, PH3). (8 points) 2. BH3 and NH3 have different shapes. Why is this? (4 points) 3. NH3 and H2O have the same VSEPR shape, but significantly different bond angles. Which one has the smaller bond angle, and why is it smaller? (4 points) Part II. List ethane, ethylene, and acetylene in order of decreasing C-C bond length. Why are they in this order? (9 points) Part III. 1. Compare the shapes and energies of MO's 1 and 3. Both of these MO's are made up mainly by adding the s orbitals on the two nitrogens (orbital 1 by adding two 1s orbitals, orbital 3 by adding two 2s orbitals). Based on the relative size of MO's 1 and 3, explain why you would expect orbital 1 to have a lower energy. (10 points) 2. Out of the first 7 orbitals, which ones (if any) are degenerate? If you identified any degenerate orbitals, how are their shapes related? (10 points) 3. For each of the 7 orbitals, identify their diatomic MO label (e.g., sigma 1s, sigma 1s*, sigma 2s, sigma 2s*, pi 2p, pi 2p*, sigma 2p, sigma 2p*, etc.) (10 points)
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