Assignment CompChem6: Applications II

Use WebMO to complete the following exercises. You are encouraged to comment on the additional results provided by WebMO in your answers, if appropriate.

1. Bond orders of allyl radical (exercise 8.6).

Build the planar allyl radical C₃H₅ and perform a Geometry Optimization at the Hartree-Fock 3‑21G level. Note that allyl has an odd number of electrons and is therefore a doublet.

View the output and run a New Job Using This Geometry. Run a Calculation = “AIM=BondOrders” job at the same level of theory. Be patient since AIM jobs take a relatively long time!

Starting with the same geometry, run a GAMESS Geometry Optimization job at the UHF (Unrestricted Hartree-Fock) 3‑21G of this doublet molecule. Also, starting with the same geometry, run a MOPAC Geometry Optimization job at the PM3 level of theory.

Construct a table with columns for AIM, GAMESS, and MOPAC and rows for each unique bond order and a row for calculation time. Comment on your table.

2. Heat of formation for CO₂ via an isodesmic reaction (example 8.6).

Build and perform Optimize + Vib Freq calculations on carbon dioxide (CO₂), formaldehyde (H₂CO), and methane (CH₄) at the HF/6-31G(d) level. Tabulate the energy (0 K) and enthalpy (298 K) for each.

Use these results to calculate D_rxnH for

CO₂ + CH₄ ® 2 H₂CO

Explain why this reaction is an isodesmic reaction. Explain what kind of computational results can be expected for such reactions.

Combine your D_rxnH result with the experimental heats of formation for methane and formaldehyde to predict the heat of formation for carbon dioxide. Compare your predicted heat of formation with the experimental value. Experimental heats of formation may be obtained from the NIST Chemistry Webbook (http://webbook.nist.gov/chemistry).

3. IRC calculations to verify H₂CO ® H₂ + CO transition state (pp. 173-176 and example 8.3)

Compute the H₂CO ® H₂ + CO transition state by building the following planar structure:

Double check your geometry before proceeding.

Perform a Transition State Optimization of the structure at the HF/3-21G level. View the Results, and then run a new Vibrational Frequencies job with the same geometry and theory. Report the value of any negative frequencies. Note the energy and H‑H bond length.

Perform a forward IRC calculation by running a Calculation = “IRC=(CalcFC,Forward)” job using the transition state geometry and same theory. View the result and note the energy and H‑H bond length. Use this geometry as the starting point for a Geometry Optimization calculation at the same theory. Note the final energy and the H‑H bond length.

Perform a reverse IRC calculation by running a Calculation = “IRC=(CalcFC,Reverse)” job using the transition state geometry and same theory. View the result and note the energy and H‑H bond length. Use this geometry as the starting point for a Geometry Optimization calculation at the same theory. Note the final energy and the H‑H bond length.

If either Geometry Optimization calculation job fails, view the Raw Output file and determine why the job failed. Report the line(s) in the output file that indicates the reason for failure. Attempt the Geometry Optimization again, but preview the input file and use “Opt=(MaxCycle=100)” instead of the “Opt” keyword.

Report all numerical values for energy and H‑H bond length in a table. Also, include a sketch of the Potential Energy Surface for the H₂CO ® H₂ + CO reaction coordinate, along with pictures of the reactant, transition state, and products.

4. WebMO version is rapidly gaining popular acceptance in the chemistry community. We are interested in any final suggestions you might have for WebMO, particularly involving its usability, View Results report, and user interface, to make it even more user-friendly and useful.