Molecular
Orbital
Calculations
for
Chlorine,
Ethane and Benzaldehyde
By Nick Newcomer and Mathew Kumbier
Introduction
The reactivity of a molecule is directly related to
the
molecule’s electronic structure. By knowing the most probable locations
of the
electrons and their energies, it is possible to predict properties
about the
molecule such as molecular dipole moment, polarizability, vibrational
frequencies, probability of absorption of visible light, and tendency
to donate
electrons.1 These types of calculations were originally done
by hand
and took lots and lots of time. As technology advanced and as computers
advanced, systems were created to decrease computation time and hand
errors.
One such computation system uses the programs Jmol, GAMESSQ, and MOPAC.
This
website specifically shows the results of use of these programs for diatomic
chlorine, ethane,
and
benzaldehyde.
The Calculations
All three molecules were first built in the program
wxMacMolPlt using the premade prototype molecules whenever possible.
The
molecules were then saved as .cml files. These .cml files were each
opened in
Jmol where a mechanics optimization was preformed and the files were
saved as
.xyz files. From here, wxMacMolPlt was once again used to generate AM1
and PM3
geometry optimization input files (.inp files) for the program GAMESSQ
to
calculate with the three basis sets (3-21G, 6-31G, and DZV). After the
calculation was completed, the resulting .log files were opened in
TextEditor
in order to note the dipole moment of each molecule and the .inp file
of the
largest basis set (DZV) was used to calculate the vibrational
frequencies. Next,
for diatomic chlorine, a potential energy surface versus bond length
was
calculated in GAMESSQ and then graphed with all three basis sets in
IgorPro
while a calculation for UV-Vis transition energy calculations were
being run on
the best geometric optimization of benzaldehyde. After the calculations
for the
UV-Vis data was completed, the .log file was examined and the
transition from
ground state data was noted.1
As a whole, the use of computers and their
computational
techniques are invaluable. What may have taken weeks for a group of
highly
trained chemists to calculate, took a relatively short amount of time
by pairs
of undergraduate level chemistry majors. These methods save numerous
amounts of
resources including time and money (not to mention paper). The
calculations built upon themselves, so the later and more difficult
calculations were dependent on the somewhat simpler earlier
calculations.
References
1.Molecular
Orbital Calculations;
Mihalick, J., Gutow, J.,; Chemistry 371 Lab Manual Spring 2011;
University of
Wisconsin Oshkosh: Oshkosh, WI, 2011.
2. webbook.nist.gov/chemistry
3. cccbdb.nist.gov entries
for benzaldehyde, chlorine, and ethane geometries and dipoles.
4. Mac
Jmol, version 2010; Jmol Development Team (accessed March 10,
2011)
5. GAMESSQ,
version
1.2; Ekstrand, Jason, Iowa State University, 2008; (accessed
March 10, 2011)
6. wxMacMolPlt,
version
7.4.2; Bode, B. M., Gordon, M.S., Jmol Graphics and Modeling,
1998; (accessed March 10, 2011)