Name: ___________________________ Chemistry Period: ________ Date: _______ Computational Chemistry Lab “Start-of-Class Question”: 1. Draw the Lewis Diagram for the molecule HCOOH (The C is bonded to 2 “O”s and 1 “H”.) What is the molecular geometry around the Carbon? What is the molecular geometry around the central Oxygen? Part A: Molecular Geometry 1. On a computer log in to: molview.org 2. Hit the trash can button to clear the default molecule. You can build your own molecules on the left side and then click 2D → 3D to see the 3-dimensional structure on the left. Scroll in and out using the mouse to zoom in/out on your molecules. 3. Click the C and place a Carbon atom on the left side of the screen in the “build space.” 4. Click the F and add 4 Fluorine atoms bonded to the Carbon atom that you already have. To create a bond: start by clicking on the Carbon and dragging the Fluorine to where you want it on the screen. (Yes, the C might disappear - it is actually still there but sometimes in structures we leave out “C”s as a shorthand way to write things. 5. Click broom button to “clean” the molecule, minimizing the energy. This puts the molecule in the correct geometry. 6. Click 2D → 3D and examine the 3D structure that’s created. Describe the molecular geometry (linear, trigonal planar, bent, trigonal pyramidal, tetrahedral) and record your answer Date Table #1. 7. Under the Jmol tab, select Distance. Click on two atoms to measure the distance in nanometers between them - this is the bond length. 8. Measure all the different bond lengths in the molecule and record your values in Data Table #1. 9. Under the Jmol table, select Clean. T his clears all the lines that you just drew. 10. Under the Jmol tab, select Angle. Click on one atom, click on a second atom, and the double click on a third atom to measure the bond angle between them. 11. Measure all the different bond angles in the molecule and record your values in Data Table #1. 12. Hit the Trashcan to delete the molecule and then build the other molecules listed in Data Table #1 and record the information for each of them following steps 5 - 12. 13. Answer analysis questions #1-4 DATA TABLE #1: Molecule Geometry Bond Lengths Bond Angles CF4 PH3 H2O C2H6 C2H4 C2H2 NaCl Part B: Polarities 14. Clear any molecules that you currently have in molview. 15. Build CH3Cl. 16. Click broom b utton to “clean” the molecule, minimizing the energy. This puts the molecule in the correct geometry. 17. Under the Jmol tab click Bond Dipoles. This places arrows on the bonds to show you what the direction electrons are pulled in if the bond is polar. In the Bond Polarity box in Data Table #2 record which bonds are polar and the direction of electron pull. 18. Clean the structure under Jmol. And select Overall Dipole. This gives you an overall direction of electron pull in the structure (aka molecular polarity). If no arrow is present then that means there is either no electron pull OR the electron pull is in opposite directions and therefore the molecule has a net pull of ZERO. Record this information in the box in Date Table 2. 19. Under the Jmol tab select MEP Surface. Y ou two options, opaque and lucent, chose whichever one you like better. This shows you the electron cloud around the molecule and the amount of electron density around the atoms. Record information about this cloud in Data Table 2 (red is negative, blue is positive, yellow is neutral, and describing whether it is symmetrical or asymmetrical. 20. Repeat Steps 14 - 19 for the other compounds in Data Table #2. 21. Answer Analysis Questions #5 - 8. DATA TABLE #2 Molecule CH3F CF4 HCl NH3 Bond Polarities Molecular Polarity Electron Cloud/Electron Densities C2H6 CO2 H2O C2H2 CH3OH NaCl C2H4 Part C: The Benzene Molecule 22. With molview draw the structure for C6H6. (You might want to draw it on paper first.) 23. Then add one more bond using the bond button on the left menu bar. Use this bond to connect the last Carbon on the left to the Carbon all the way on the right. Yes this will look really weird right now. 24. Click 2D → 3D to see this molecule 3 dimensionally. 25. Find the geometry around each Carbon atom, each bond length, and each bond angle. Record all this in Data Table #3. 26. Answer Analysis Question #9 - 11 27. Using molview create your own molecule. They can be as crazy and huge as you want. The crazier the better. Create a 3D representation and then answer question #12 DATA TABLE #3 Molecule Geometry Bond Lengths Bond Angles C6H6 (Benzene) Analysis Questions: 1. What do you notice about the number of unbonded electron pairs on the central atom and the bond angles in a molecule? 2. Thinking about repulsion and attraction of particles, which do you think causes more repulsion, unbonded electron pairs or bonds? What does this do to bond angles? 3. Which bonds tend to be longer (double bonds, single bonds, or triple bonds)? Which bonds tend to be shorter? Compare the molecule C2H6 to the molecule C2H2 and C2H4 to figure this out. 4. How does the molecular symmetry affect the overall dipole of the molecule? 5. How do the bond dipoles affect the overall dipole of the molecule? 6. What do you think the term “dipole” actually means? 7. How can the MEP Surface view be used to describe the electron density around a molecule? 8. During the first part of lab you investigated which kinds of bonds were longer/shorter. Do the bond lengths for benzene (C6H6) correspond to what you thought they should be? 9. Watch the video that on the Google Classroom assignment, then describe what resonance means and it means if a structure has multiple resonance forms? 10. After watching the video, why do you think the bond lengths on benzene were different from what you expected? 11. Investigate the molecular geometry around each of the central atoms in your benzene molecule as well as the bond polarity and molecular polarity for benzene.
