The molecular structure of molecules determines a
great deal of its activity. When predicting reactivity of
molecules, having the most optimized structure increases the
prediction's accuracy. Characteristics such as vibrational
frequencies, polarizability, dipole moment, electron donation and
absorption probabilities can be predicted.
The molecular orbitals in molecules can be described
using wave functions. For a molecule with greater than one
electron, solving for exact values is not possible. Operators can
operate upon the wavefunction to extract useful information such as
energy and position.
The three compounds being experimented upon are;
Bromobenzene, Hydrogen Cyanide and Nitrogen1.
This experiment utilized the self-consistent field
(SCF) theory for calculations. SCF is where an electron i is selected
and its wavefunction
Ψi is normalized. Then the electric
field produced by the other electrons is used to optimize
until its energy is at a minimum because the variational principle
states that any approximation of the energy of a wavefunction will be
an overestimate. Then
is replaced into the pool of
ψ's and the process is repeated for each electron in the molecule. That
process is repeated until the molecule's energy has been optimized to a
The optimization process was started with AM1 and
PM3 because they were
low level optimization, these were used to complete 321-G, which was
used for 631-G, which was used for DZV optimization. This ordered
successively improved the results while minimizing overall calculation
time, since results from the previous level were used as a basis2.
The molecules are constructed using the program;
wxMacMolPlt. The structures from this program were opened in Jmol
and a mechanics optimization was performed. These files were
saved as .xyz. WxMacMolPlt was again used to generate AM1 and PM3
geometry optimization input files (.inp) from the optimized .xyz
files. GammesQ software was used to compute the results.
The results were checked by opening the .log file
and looking for a notification that the program "exited
gracefully." This was an indicator that the calculations were
completely successfully. These steps were repeated for Nitrogen,
Hydrogen Cyanide and Bromobenzene. Bromobenzene calculations were
started first because of the increased time they required. Jmol
was used to see if the molecular orbitals calculations appeared logical
compared with existing knowledge of pi and sigma bonds.
Geometry optimization was completed in order,
starting with the AM1 and PM3 then going to 321-G, 631-G and finally
Double Zeta Valence (DZV). wxMacMolPlt ws used to generate a
vibrational frequency input file (.inp) which was computed using
GamessQ. Dipole moments were extracted from the .log files by
opening them in a text editing program and searching "debye" which were
the units. The potential energy surface and bond length were
plotted against each other for Hydrogen Cyanide, and optimized using
321-G, 631-G and DZV. The values were extracted using Jmol and a
Follow these links to view optimization and interactive molecular
Alternate research shows the bond angles in bromobenzene to be
120degrees between C-C-H3.
This is slightly higher than the values recorded in
this work of 119.4 degrees.
This same research shows bond lengths of 1.081angstrom.
This is again slightly higher than the 1.07 angstrom
recorded in this work.
Conclusion: Computational results
are useful when data is difficult or impossible to obtain
experimentally and a prediction is difficult to produce by doing
calculations by hand. Additionally, computational results are cheaper
to generate; all one needs is a computer, a power socket, and time.
Computational calculations don't require a single reagent, so they are
also safer. On the other hand, spectroscopic data can sometimes be more
descriptive, accurate, or useful than computational results.
Gutow, Jonathan. "Chemistry 371 Lab Manual Spring 2011." (2011): 11-18.
Atkins, Peter, and Julio De Paula. Physical Chemistry. 9thth
ed. New York: W. H. Freeman and Company, 2010. Print.
3. Peebles, Sean, and Rebecca Peebles. "Determination of heavy
atom structure of bromobenzene by rotational spectroscopy." Journal
Structure 657.1-3 Sept. (2003): 107-16. Web. 7 Mar. 2011.
4. Benzene, bromo-. National Institute of Standards and Technology,
2008. Web. 14 Feb. 2011.