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Chemistry 304
Computational Project
Goals of the project.
Practical:
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Learn to apply a variety of computational methods to a particular problem.
Compare the molecular mechanics, semi-empirical, and Hartree-Fock approaches
to a particular problem.
Wider:
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Read the literature with a critical eye.
Search the internet for issues related to an assigned problem. This includes
electronic search of journals available through Hekman Library.
Read:
a. “Elusive Carbocation Isolated as a Solid”, Chemical and Engineering News,
April 29, 2002, page 30.
b. “The Stable Pentamethylcyclopentadienyl Cation”, by Joseph B. Lambert,
Lijun Lin, and Vitaly Rassolov, Angewandte Chemie, International Edition,
2002, Vol. 41, pp. 1429-1431.
Background
Complete Chapter 3 of Spartan ’02 Windows. Omit pages 31-33.
Answer questions:
Answer the questions on the reverse side of this sheet after you have read the above two
articles.
Second Wednesday:
Turn in the cover page of an article from the primary chemical literature. This article
should make use of molecular mechanics, quantum mechanics, or molecular dynamics in
some field related to physical chemistry for the biological sciences, or advanced organic
chemistry (synthesis).
Final Report:
A separate handout will be provided to you later in the course module. That handout will
detail more of what is expected in your formal written report for this part of the course.
For now it is important for you to keep a laboratory notebook, and electronic versions of
pertinent computational studies, so that you can refer back to them at a later time.
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Chemistry 304
Computational Chemistry
Name: ____________________________________
Issues related to reading the two papers.
1. What is so surprising about the reported synthesis of C5Me5+? That is, why was an
article written in C&EN about this paper?
2. How is the reported geometric structure of this cation different from what was
expected?
3. Was the electronic structure expected to be a triplet (two unpaired spins) or a singlet
(all spins paired)?
4. How did the authors explain the difference between the expected and the observed
geometric and electronic structure?
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Chemistry 304
Computational Chemistry Project
Computational work related to the C5Me5+ project.
Keep a record of your work in your laboratory notebook. Make sufficient notes to
yourself that you will be able to write a formal report about this laboratory exercise when
you are finished.
1. Begin your work by completing a series of calculations on the model C5H5+. Computational
chemists often use model compounds to explore the electronic structure of more complicated
molecules. Hence we begin by replacing the methyl group in C5Me5+ by an H atom.
a. Simple Hückel Molecular Orbital, SHMO (http://www.chem.ucalgary.ca/SHMO).
SHMO divides the electrons into σ and π type. Only the π-type are considered in SHMO.
 How many π electrons does the cation have?
 Does SHMO predict the cation to be a singlet or a triplet? (Singlet means no unpaired
electrons, triplet means two unpaired electrons.)
 Is the HOMO degenerate? (Degenerate means that two orbitals have the same energy.)
 Sketch a “picture” from above, of the three occupied π molecular orbitals.
 Sketch an energy level diagram of the five π molecular orbitals.
 Is it possible to switch to a singlet state using the SHMO method?
 Is it possible to consider a non-planar ring in the SHMO method?
The remainder of the work on this project should be done using Spartan ’02 or Spartan ‘04. Save
all your work into a desktop folder called Spartan. I suggest you save files for each part, labeled
something like MMFF, AM1, and HF. All theoretical studies should be done with the option
“Equilibrium Geometry”. (You will also want to turn on the switch labeled “Orbitals &
Energies”.) In each case sketch the structure in your notebook and indicate clearly the C–C bond
lengths.
b. Molecular Mechanics, Force Field MMFF, remember to specify cation and triplet
 In the case of molecular mechanics, it is important to specify the “correct” atom types
for each atom, in the build module. You can see the importance of this by specifying
aromatic carbon atoms for all five atoms in one calculation. (Usage note: In Build
Mode, connect five carbon atoms together in a ring that show a partial double bond
valence. To connect the last two to build the ring, use the “Make Bond” palette icon.)
Complete this calculation. Record bond lengths and a heat of formation, or steric
energy.
 What geometric structure does molecular mechanics predict?
 Can you make a plot of the HOMO from a molecular mechanics calculation? Why or
why not?
 As mentioned in class, atom types are important in molecular mechanics. To see the
effect of atom types, you should change one of the five carbon atoms to an sp3 C
atom. (There is more than one way to do this.) You will get different results
depending upon the atom types you choose. Make a notation in your notebook,
showing the different results you obtain from these two different runs.
c. Semi-Empirical, AM1, remember to specify cation and triplet
 What geometric structure does AM1 predict?
 Are the upper occupied orbitals degenerate? How do you know?
d. Hartree-Fock (HF), 3-21G*, remember to specify cation and triplet
 What geometric structure does HF predict?
 Are the upper occupied orbitals degenerate? How do you know?
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Can you make a plot of the HOMO from a HF calculation? Why or why not?
Plot both the HOMO and HOMO-1. How do these compare to the SHMO result?
Are they describing the same basic electronic structure? Explain.
2. Now repeat all of the above using the full cation, C5Me5+, with Spartan ’02. I suggest you save
files for each part, labeled something like MMFFMe, AM1Me, and HFMe. All theoretical studies
should be done with the option “Equilibrium Geometry”. In each case sketch the structure in your
notebook and indicate the C–C bond lengths for the ring part of the structure. In addition, there is
one torsional angle that Lambert et al. refer to. You should record the computed value of that
torsional angle for use in your report later.
a. Molecular Mechanics, Force Field MMFF, remember to specify cation and triplet
 What geometric structure does molecular mechanics predict?
b. Semi-Empirical, AM1, remember to specify cation and triplet
 What geometric structure does AM1 predict?
c. Hartree-Fock (HF), 3-21G*, remember to specify cation and triplet
 What geometric structure does HF predict?
 Plot both the HOMO and HOMO-1. How do these compare to the SHMO result and
to the result for the model cation C5H5+? Are they describing the same basic
electronic structure? Explain.
3. Now we turn to consideration of the singlet state of the cation. Consider the model cation
again, C5H5+. Complete Hartree-Fock calculations on the singlet state of the cation. All theoretical
studies should be done with the option “Equilibrium Geometry”. (Do not turn on the “Orbitals &
Energies” switch here.)
Hint: Note that you should start from a clean file to do this work. You will not be able to
converge the molecule if you start from the symmetric (D5h) structure. I will explain this in class.
Start from a molecule that has one C–C bond considerably longer than the others. This will
happen naturally if you build the molecule and do not do a molecular mechanics minimization.
a. Hartree-Fock (HF), 3-21G*, remember to specify cation and singlet
 What geometric structure does HF predict for this singlet state?
 Plot the LUMO, HOMO, and HOMO-1. How do these compare to the SHMO result
and to the result for the model cation C5H5+? Are they describing the same basic
electronic structure? Explain.
 Did the molecule optimize to a symmetric structure, that is, with all C–C bond
lengths identical? Sketch the molecule in your notebook, label all the C atoms, and
show the bond distances.
 Now overlay a sketch of the HOMO with the bond distance sketch in your notebook.
Do the observed bond distances make sense to you? Explain.
4. Now look back on all the work you have done. Analyze the theoretical work as it compares to
the experimental work.
 Obviously the triplet work does not agree with the experimental, since the reported
experimental molecule was a singlet. Please state this in your report.
 Does your singlet theoretical work correlate well with the experimental? Carefully
compare bond lengths and planarity in answering this question.
 Point out any differences between experiment and theory, paying particular attention to
bond lengths and planarity.