Chemistry 4560/5560 Molecular Modeling
Spring 2017
Name:……………….………………………
Class Worksheet 7
1. Run a potential energy surface scan for hydrogen molecule (H2) at
i) restricted
ii) unrestricted
HF/6-31G(d) level. Scan the bond length from 0.4 to 3.5 Angstrom every 0.1 Angstrom (30
steps).*
a) Plot the energy as a function of the bond length (e.g. using Excel or Matlab). Are the surfaces
different or are they the same? Briefly(!) describe the differences.
…………………………………………………………………………………………….
…………………………………………………………………………………………….
……………………………………………………………………………………………..
b) Now try this with specifying that the initial guess for the UHF calculation has to be mixed at
each optimization step: Guess=(Mix,Always)
Plot the energy as a function of the bond length. Which surface looks correct? Focus in particular
on the behavior at long distances.
RHF
correct
incorrect
UHF
correct
incorrect
2. Calculate molecular orbitals for the H2 molecule, using both restricted and unrestricted HF
levels for
i) equilibrium bond distance
ii) the longest (3.7 A) bond distance
a) compare the  and eigenvalues (orbital energies):
R = equilibrium
RHF
UHF
 occupied eigenvalues:
 virtual eigenvalues:
 occupied eigenvalues:**
 virtual eigenvalues: **
* If your job crashes because atoms are too close, deal with it.
**In case  eigenvalues turn out to be missing, explain why. Hint: drawing the electron configuration may help.
1
Chemistry 4560/5560 Molecular Modeling
Spring 2017
R = 3.5 Angstrom
RHF
UHF
 occupied eigenvalues:
 virtual eigenvalues:
 occupied eigenvalues:**
 virtual eigenvalues:**
b) plot the molecular orbitals in Gabedit and compare. Based on what you see, you should be
able to explain the observation above. Draw the electron configuration of the two H atoms (H2
molecule at the long bond distance) for the:
RHF calculation
UHF calculation
What species did the H2 molecule dissociate into with
RHF calculation: ………………….
UHF calculation: ………………………………
2. Run an RHF/6-31G(d) calculation on a singlet ozone O3. (Use the experimental geometry:
O-O bond lengths=1.272 A, O-O-O bond angle=116.8°.).
a) test the stability of the calculation. What is the stability report:
………………………………………………………………………………………….
b) Optimize the wavefunction (Stable=Opt). Report the total SCF energy and the two highest
occupied orbitals and two lowest occupied orbital eigenvalues for both spins:
Energy: E = ……………………………… [
]
HOMO-1
HOMO
 eigenvalues:
 eigenvalues:
2
LUMO
LUMO+1
Chemistry 4560/5560 Molecular Modeling
Spring 2017
3. Repeat problem 2 but now using unrestricted calculation:
a) test the stability of the calculation. What is the stability report:
………………………………………………………………………………………….
b) Optimize the wavefunction (Stable=Opt). Report the total SCF energy and the two highest
occupied orbitals and two lowest occupied orbital eigenvalues for both spins:
Energy: E = ……………………………… [
]
HOMO-1
HOMO
LUMO
LUMO+1
 eigenvalues:
 eigenvalues:
4. Repeat problem 2. again using again unrestricted calculation, but also using Guess=Mix on
top of it
a) test the stability of the calculation. What is the stability report:
………………………………………………………………………………………….
b) Optimize the wavefunction (Stable=Opt). Report the total SCF energy and the two highest
occupied orbitals and two lowest occupied orbital eigenvalues for both spins:
Energy: E = ……………………………… [
]
HOMO-1
HOMO
LUMO
LUMO+1
 eigenvalues:
 eigenvalues:
Which approach gave the correct result (without any wavefunction instability)?
…………………………………………………………………………………………………….
5. Calculate molecular orbitals for ozone at RHF/6-31G(d) and UHF/6-31G(d) level (use
Guess=Mix for the latter). Plot the orbitals in Gabedit and compare. Briefly (!) describe the
differences: …………………………………………………………………………………………
………………………………………………………………………………………………………
………………………………………………………………………………………………………
………………………………………………………………………………………………………
3
Chemistry 4560/5560 Molecular Modeling
Spring 2017
6. The isomers of butane are N-butane and isobutene.
a) Compute the isomerization energy (at 0 K) of N-butane  isobutene at AM1, PM3, PM6 and
HF/6-31G(d) levels and compare to the experimental value of -1.64 kcal.mol-1. Remember that the
energy in the thermodynamic sense includes ZPE and thermal corrections.
E (kcal.mol-1)
Method
AM1
PM3
PM6
HF/6-31G(d)
Experiment
-1.64
b) Compare the CPU time required for optimizations and frequency calculations for both
molecules (together) by each method
Method
CPU time (s) per step
Optimization
AM1
PM3
PM6
HF/6-31G(d)
4
CPU time (s)
Frequency calculation