Quantum
Calculations on Lithium Monoxide, Ethylene, and Chlorobenzene
by Demetria Dickinson and J. Wyatt Seagren
Introduction
Classical mechanics prove to be very accurate at describing things
larger than molecules. Unfortunately, these theories break down
at the molecular level. Thus, quantum mechanics was born, and can
now be used to calculate structures and properties of molecules much
more accurately. This allows for calculation of vibration
frequencies, bond lengths, bond angles, and more. However, until
recently only highly educated and dedicated physical chemists or
chemical physicists could do these calculations, due to their extreme
complexity. Now, with the advent of computers, programs are
available to do these calculations for people. In this web page
will be models and calculations for optimized geometry, bond lengths,
angles, levels of theory, vibrational frequencies, and bond stretching
for the molecules LiO, C2H4, and C6H5Cl.
Experimental
The following molecules were made with the UWO Quantum Server on an
Apple computer: LiO, C2H4, and C6H5Cl. MOPAC, a
semi-empirical method, uses empirical data to estimate the values of
two electron overlap integrals, needed for calculating Hamiltonians,
was used to calculate the optimized geometry. The Hamiltonians
AM1 and PM3 were used. If the calculation didn't work, a search
was made for the word “fail” in the raw output file to check what might
have gone wrong. Once the optimized geometries were finished for
AM1 and PM3, the raw output was copied and pasted into
TextEditor. The files were saved as “.log”, then opened in
MacMolPlt, where the geometry was optimized if the AM1 or PM3 had
failed. The input files were then set up for GAMESS. The
file was checked for the word "fail" to make sure the optimization was
complete. Once the geometry was optimized, MacMolPlt was used to
write files for optimizing the geometry at the following levels of
theory, 321-G, 631-G, 6311-G, and DZV(Double Zeta Valence), however
6311-G proved to be unreliable. The files were ran in GAMESS, and
could be qeued up to run one after the other to increase
convenience. The lowest level, 321-G was ran first, with 631-G
following, and DZV following that, using the previous configuration as
the starting point for the calculations, also making sure to set
Initial Guess to Huckel when not using the same level of theory.
To finish, the file was written as a ".inp" file. Once again, the
file was checked for "fail" because the energy plot might not obviously
show it. Once this was all complete, the bond lengths, angles,
HOMO, and LUMO orbitals could be viewed in MacMolPlt. To find the
dipole moments, it was necessary to open the file in TextEditor and
search for "/D/". The vibrational frequencies of the molecules
were calculated using the highest level of theory file for each
molecule in MacMolPlt, except for LiO, and the file was written as
".inp" with the run type set to Hessian and in Hess. Options Numeric
Method was chosen. The files were ran in GAMESS, afterward in
MacMolPlt the vibrational frequencies were available to look at.
Also, the log files were opened in Jmol to build models of
bond lengths, bond angles, and HOMO orbitals, for the purposes of this
web page. Jmol was also used for the skeleton of this web
page. Kompozer was used to edit the web page.
Conclusion
As outlined in this web page, the computer software programs
GAMESS,
MacMolPlt, and Jmol allowed us to accurately calculate values and
models
for the molecules LiO, C2H4, and C6H5Cl. For vibrational
frequencies, the calculations are a bit off from the experimental, but
for the other calculations the software gives a pretty good
approximation, although generally for non-degree values the calculation
gives a higher estimate than the experimental.
References:
(1) Mihalick, J.; Gutow, J. Quantum Calculations I.
Oshkosh, WI, 2009.
(2) Gutow, J. Molecular Orbitals/ Quantum Calculation
Experiment 2. Oshkosh, WI, 2009.
(3)
Computational
Chemistry Comparison and Benchmark DataBase,
(c) 2002, U.S. Secretary of Commerce.
Accessed 3/30/10.
(4)
National Institute of Standards and
Technology Chemistry WebBook, (c)
2008, U.S. Secretary of Commerce.
Accessed 3/17/10.
Based on template by A. Herráez as modified by J. Gutow