Molecular Orbital Calculations of Hypoclorite, Formaldehyde, and Anline
Andres Michalkiewicz and Alexis Vandehey
Abstract: Various
properties, including optimized geometry, highest occupied moleular
orbitals, lowest unoccupied molecular orbitals, bond lengths,
electrostatic potential, dipole moments, vibrational frequencies, and
partial atomic charges, were calculated for three molecules,
hypochlorite, formaldehyde, and aniline, using various levels of
molecular orbital theory on a computer software program. These
levels of theory included AM1, PM3, 6-21G, 6-31G, and DZV, the latter of
the three being of the ab initio level of theory, generally accepted as
the best level of theory for quantum calculations. The DZV level
of theory was used for most of our calculations as this is the one that
yielded our best results overall.
Introduction: Different properties of the electronic structures of molecules, such as
vibrational frequencies, dipole moments, bond lengths, electrostatic potential,
and partial atomic charges, help to determine its molecular reactivity.
This web page explores the geometric optimizations of three molecules,
hypochlorite, formaldehyde, and aniline, assuming that the lowest energy
potential would be the most stable. With advances in technology over the
years we were able to use computer software to calculate large integrals of the
Hamiltonian operator and normalization constants for these molecules with relative ease
at different levels of theory.
Two general types of theory were used to analyze each
molecule and integrate out its optimized geometry. AM1 and PM3 were two
levels of theory used as they use empirical data to get values for two electron
overlap integrals needed for calculating the expectation value of the
Hamiltonian operator. Ab initio, however, is generally accepted as the
best level of theory as this takes into account all the integrals that need to
be calculated. The difference between the ab initio and the standard
AM1/PM3 theories are the size of the basis sets, number of trial wavefunctions,
used to determine the energy. These methods in order of increasing basis
set size are 3-21G, 6-21G, 6-31G, and DZV.
In this experiment the programs wxMacMolPlt and
GamessQ were used in tandem to calculate the molecular orbitals of the three
molecules Hypochlorite, Formaldehyde, and Aniline. To perform all the
necessary calculations, the first step was to get the optimized geometry of
each molecule at each level of theory. This was done using the Avogadro
software program on the lab computer. As the initial geometries were still
somewhat rudimentary for some of the levels of theory (namely AM1 and PM3)
further analysis to refine them was done in wxMacMolPlt where an .inp file was
created and saved to a folder for easy access. Each molecules corresponding
.inp file at each level of theory was then run using the GamessQ software. The
AM1.log file, which was the initial file that was started with, obtained from
GamessQ was then used to generate a 6-21G.inp file, which in turn was used to
generate a 6-31G.inp file followed by a DZV.inp file, these three all of the ab
initio level of theory. Jmol, modeling software, was then used to
visualize various aspects of these molecule for each level of theory as well as
to display some physical constants for each molecule that were calculated by
the Gamess program.
Conclusion:
Computional results can be useful in some areas. When finding the bond length between two atoms the computational results were decent when comparing to the NIST values of aniline. However, for hypoclorite the computated bond lengths in Jmol were not similar to the NIST value of bond length, The bond angles were also found in jmol on aniline. The angles computed were alike the literature values, meaning that computional results may be benefical on some molecules when calculating bond angles. The different levels of theory potrary decent optimized geometries. In some cases the dipole moments computed were significant, as thhey were close to the literature value. For example, anilines dipole moment for DZV on the experimental date was found to be 1.53, which is the same as the NIST value. Yet, formaldehydes DZV dipole moment was 3.2 and the literature value was 2.3. That compuation was not very accurate then. The computations of jmol and macmolplt seem to work better for the bigger molecules than the smaller ones.
It
was valuable to look at the different levels of theory because they
were not always the same. Although, it was thought that DZV would be the
most accurate level, because it was the highest in energy, that was not
the case for every molecule on certain computations.
References:
1. Mihalick, J.; Gutow, J.; Quantum Calculations; University of
Wisconsin-Oshkosh: Oshkosh, WI, 2014; p 1-12.
2. Chang, Raymond; Thoman, John W. Physical Chemistry for the Chemical Sciences, 1st ed.;
University Science Books: Canada, 2014.
3. Listing of experimental data for ClO- (chlorine monoxide anion) 2015, http://cccbdb.nist.gov/exp2.asp accessed
4. Listing of experimental data for H2CO (Formaldehyde) 2015, http://cccbdb.nist.gov/exp2.asp
5. Listing of experimental data for C6H5NH2 (aniline) 2015, http://cccbdb.nist.gov/exp2.asp