Computational Chemistry at GVSU

In this exercise we will observe several properties of formaldehyde computed using AM1. It is very feasible to use ab initio methods on formaldehyde, but we use AM1 here since it is very fast and we only have an hour.

1. Build formaldehyde and clean it. At the yellow tool bar below the top menu, change "NO LABEL" to "CHARGES". Under "Geometry:Measurements", measure the carbonyl bond length.
   
   
2. Using AM1, select the task "Geometry Opt. & Frequency". Set the File Prefix to formaldehyde. Run the calculation.

   Draw formaldehyde at right -->,

   labelling the atoms with their charges,

   and the carbonyl length.

 

Q: Are the charges what you would expect?

 

 

3. Electron Density: Choose Analyze->: Density. Select "High" resolution. Click on "Calculate Total Charge Density". Choose Analyze->: Surfaces, and set the transparency to 70%.

Choose Analyze->: Slices, and click on "Create New Slice". Click on "Create Slice Plot in Graph Window"

Q: Which atom has the greatest electron density?

Delete the slice.

4. Electrostatic property map: We will now calculate the electrostatic potential, which is the potential that a positive point charge would experience at each location in a grid. Choose Analyze->: Potential and click on "Calculate electrostatic potential". Then choose Analyze->: Property Maps. Find the file formaldehyde_Potential.mbk and "Load" it. Click on Add Property, and the electron density contour will be shaded with the electrostatic potential at its surface.

Q: Which color is a negative electrostatic potential? Which is a positive potential?

 

5. Site for Nucleophilic Attack: Next we'll map the LUMO onto the electron density contour. When a nucleophile first approaches an electron-poor atom, its HOMO will "dock" with the LUMO of the electrophile, since this is the orbital most available for accepting electrons. Hence it is often instructive to map the LUMO onto the electron density contour to localize the point of nucleophilic attack. To do this, select the following:

Analyze->: Orbitals: LUMO (click on calculate) (this computes the LUMO)

Analyze->: Density, (click on calculate) (This regenerates the electron density surface)

Analyze->: Property Maps

Find formaldehyde_AlphaLUMO.mbk, and Load it. Then click on Add Property.

Q: Which atom is the electrophile?

6. Which of the molecules below has the longest C=O bond? Divvy up the molecules amongst yourselves to test your hypotheses (at least at the AM1 level). Choose a molecule, build it and do an AM1 geometry optimization calculation. Measure the carbonyl length and the charges. Using data from others, find these values for all molecules below. NOTE: for formamide, you will need to let AM1 know how to deal with the amide linkage. Next to "AM1", choose "MORE..." and then, at the very bottom, change the "MM correction for CONH Linkage" to "USE".