• Document: Chem 106: Computational Handout 7 Molecular Properties
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Chem 106: Computational Handout 7 Molecular Properties Objectives: rendering nice pictures, molecular orbitals, electrostatic potentials, point charges In This Exercise: we will learn how to render nice pictures of molecular structures. We will also learn how to make pictures of molecular orbitals (MOs) and electrostatic potentials (ESPs). We can also use the MOs and ESPs to determine atomic charges. Setup: Install CYLview (http://www.cylview.org/Download.html), a program for rendering molecular structures in three dimensions. There are different versions for Mac and PC. If you are using a Mac, you will need to have X11 (XQuartz) installed. You can download a DMG installer at https://www.xquartz.org/. It is quite possible you already have this program installed, so I would suggest trying to run CYLview on its own first. Files: The calculations in this exercise are relatively easy, but you will need the checkpoint files that are generated when the jobs are run. These files are provided in the repository in the population/chk/ folder. Run Calculations: Locate the Diels–Alder transition states for: - butadiene + ethylene - butadiene + acrolein (endo) - butadiene + acrolein (endo) + BF3 (bound trans) Use B3LYP-D3BJ/6-31G* in the gas phase and save checkpoints: %chk=g09.chk %nprocshared=4 %mem=3GB #p b3lyp/6-31g* empiricaldispersion=gd3bj opt freq=noraman pop=(chelpg,npa) Also, locate the isolated ground states: acrolein_BF3_isolated.gjf acrolein_isolated.gjf butadiene_acrolein_ts.gjf butadiene_ethylene_ts.gjf butadiene_isolated.gjf ethylene_isolated.gjf You can use the same trick as in Exercise 5: freeze the structures and look for the imaginary frequency instead of doing a bond scan. CYLview: We will now render a three-dimensional picture of one of the transition states. 1. Open CYLview. Click on the DIR button and switch to the directory containing butadiene_ethylene_ts.out. (If you are using a mouse, it is possible the scroll wheel will not work properly.) Click DIR again and select the filename. 2. Click on the INTER button to add atom dotted bonds between the appropriate atoms. 3. Click on the Style button and select Houkmol. (You can also choose your own style.) 4. In the bottom right of the window, click on Set Focal Point and then click on an atom. The “camera” will place this atom in focus. The focal scale can be displayed by selecting “Show Focus scale on screen.” You can adjust the focal depth in picture by selecting between Weak and Strong. “Focus follow selected atom” will maintain your choice if you rotate the molecule. 5. Similarly, you can gray out atoms that are in the back by selecting “Set Fog Depth.” 6. Click on Preview (also in the bottom right) to render the image on screen. 7. To generate a PNG file in the current directory (which will automatically have the same name), click on Generate. Click on the Config button in the upper right to choose the size of this image. By default, the “generated” image will be twice the size of the image on screen. 8. Click on the Atoms button and click on Hide C–H. This option is useful for structures that have a lot of hydrogens. Render this image as well. If you need to display a particular C–H, then you will need to determine the atom number of the hydrogen, select it from the list, and click on Reset. Reset All will display every atom again. Make a Movie: Three-dimensional structures with a lot of atoms in them can be hard to understand, particularly in presentations. One strategy that can be helpful is making a movie. 1. Click on Poses in the upper right. Orient the molecule as you would like for the start of the movie. Click on “Add.” This creates a pose called “default.” 2. Click on 640x480. This will be the resolution of your movie. I don’t recommend making it any bigger because this task is very computationally intensive. 3. Click on Anim in the upper right. Click on Start pose and select “default.” 4. Under Rotation Animation Options, click + until the Angle span is 360. Select a duration of 5 s and press Add. This will give you a linear rotation of 360 degrees that takes 5 seconds. 5. Click on Play Animation to get a preview. You may want to adjust the fog/focusing for the movie. 6. Click on Render animation to make an MPG file. This process could take a while, particularly if your computer is slow. Unfortunately, it can also make CYLview crash. Plotting Molecular Orbitals: In this section, we will learn how to make pictures of the HOMO and LUMO. 1. We will need a “formatted checkpoint file,” which is the human-readable version of the .chk file. On Odyssey, locate the checkpoint for isolated butadiene: [ekwan@rclogin04 chk]$ formchk butadiene_isolated.chk Read checkpoint file butadiene_isolated.chk Write formatted file butadiene_isolated.fchk FChkPn: Coordinates translated and rotated. FChkPn: Coordinates match /B/ after translation and rotatio

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