Assignment CompChem5: Applications I
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. Electrophilic attack of nitrobenzene using partial charge analysis (pp. 165-167 and exercise 8.4).
The observed isomeric product distribution of electrophilic attack on nitrobenzene was explained using electron density maps of the reaction intermediate in ECESM. Another method for predicting the product distribution is to analyze the partial charges on the otho, meta, and para carbons of nitrobenzene reactant.
Build nitrobenzene such that the nitro group lies in the molecular plane and has equal NO bond lengths. Pre-optimize this structure at the PM3 level with the additional keyword “NoSymmetry”. [The NoSymmetry keyword prevents Gaussian from terminating if the symmetry changes during optimization, since the WebMO Z-matrix variables do not enforce the symmetry of the molecule.] Perform an Optimize Geometry calculation of nitrobenzene at the HF/3-21G level also using the additional keyword “NoSymmetry”. When the job has completed, use the New Job Using This Geometry button to perform a Single Point calculation at same level of theory with the additional keyword “Pop=NPA”. [The Pop=NPA or Pop=NBO keywords request that Gaussian perform a Natural Bonding Orbital analysis of the molecule, in which electrons are assigned to “organic chemistry” orbitals as core electron pairs, single bonds, double bonds, lone pairs, etc.] Finally, use the New Job Using This Geometry button to perform a Single Point calculation at same level of theory with the additional keyword “Pop=CHelpG”. [The CHelpG keyword requests that Gaussian calculate an electrostatic potential-derived potential in which atoms are assigned partial charges to match the electrostatic potential at the van derWaals surface.]
Construct a table with columns for isomer (ortho, meta, para), Mulliken partial charge, NBO partial charge, ChelpG partial charge, and nitration product distribution percentage. Use these results to explain the preferred site of electrophilic attack by NO2+.
Intuitively explain the computed partial charges by drawing several resonance structures for nitobenzene.
Note: It is the practice of researchers who publish charge distribution analyses to run their jobs at the MP2/6-31(G) level and use the “Density=MP2” keyword to perform the population analysis with the MP2 computed density.
2. CH bond dissociation using a rigid PES scan (pp. 171-172 and exercise 8.2).
Build CH and clean up only its geometry. Perform a Scan calculation by specifying Calculation as “Other(Scan)” at the MP2/6-311+G(p,d) level. Note that CH has an odd number of electrons and is therefore a doublet. Check the Preview Input box and edit the bond length variable line so that it looks something like
B1 0.5 20 0.1
which instructs Gaussian to start the B1 coordinate at 0.5 Å and increment it 20 times by 0.1 Å each time.
Use the Summary of the Potential Surface Scan near the end of the raw output to tabulate both the SCF and MP2 energy as a function of bond length. Use Excel to plot both of these functions in the same figure. Comment on the difference between these plots. Calculate the CH bond dissociation energy in kcal/mol by taking th difference between the minimum and separated energies. Compare your result to experimental values from a general or organic chemistry textbook.
3. Vinyl alcohol isomerization reaction coordinate using a relaxed PES scan (p. 171).
Either recall or recalculate the vinyl alcohol transition state in which the H‑O‑C‑C dihedral angle is approximately 90 degrees. Perform a Transition State Optimization calcualtion at the PM3 level. Run a new Vibrational Frequencies job using the same geometry and theory. State why or why not you believe this conformation to be a transition state.
Run a new job using the same geometry. However, while in the Build Molecule window, display the index of each atom and note the index of the alcohol H. Run a Geometry Optimization calculation using the same level of theory, and check the Preview Input File box. Edit the “Opt” keyword so that it reads “Opt=Z-Matrix”. Also, change the line that defines the alcohol H dihedral angle and might look something like
D2 0.0 S 18 10.0
This instructs Gaussian to start this coordinate at 0 degrees and increment it 18 times by 10 degrees each time. At each step, the Opt keyword instructs Gaussian to optimize all other coordinates.
Use the Summary of Optimized Potential Surface Scan near the end of the raw output to tabulate the PM3 energy in both Hartree and in kcal/mol as a function of dihedral angle. Use Excel to plot the kcal/mol values. From your plot, determine the forward and reverse barrier heights. Why is the barrier not symmetric?
Note: Relaxed potential energy surfaces scans are also available with the Opt=AddRedundant keyword, but the specification of scanned coordinates then goes in the redundant coordinate section of the input file, not in the Z-matrix specification section. See the Opt keyword in the Gaussian User’s Reference manual for details.
4. How could WebMO be improved to assist you with your calculations? Please be as imaginative and thorough as possible with your suggestions and constructive criticism!!