Abstract Avagadro,
MacMolPlt, and GamessQ were programs used in this experiment to a
structural picture of the assigned molecules (F2, H2CS,
and benzoic acid) and outlines of electron orbitals.Information was also collected regarding
dipole moments, charge separation, UV absorption, and many other quantum
mechanical measurements under different levels of theory – AM1, PM3, 6-21G,
6-31G, and DZV (double zeta valence- deemed best).Molecular renderings and various
translational, vibrational, rotational, and electronic energy phenomena were
calculated using these sophisticated programs and presented in this site for the
assigned molecules – F2, H2CS, and benzoic acid.
Introduction
Quantum mechanics is a powerful tool for gaining insight into
particular forces that govern molecular interactions and atomic
relationships. The immensely complex calculations made in these
computer programs would take a team of chemists months to decipher,
allowing one to make assertions about molecular phenomena with
confidence. Wavefunctions for electrons are represented in these
visual aids by colorful, bulbous molecular orbitals. This enables
an onlooker the ability to visualize what these calculations are
outlining. The wavefunctions created using different levels of
theory provide a variety of perspectives on the particular behavior on
an atomic scale. The larger the data set, more factors taken into
account offer a clearer the picture of what is happening in molecules.
Each of the aforementioned chemical
computer programs played a unique role in the determination of the
characteristics of each of the assigned molecules.Much of the information gained from
utilization of these programs was compared to literature values, gathered
before lab time, to test its accuracy.Avagadro is a molecule
building/assembling program.It
contained many familiar functions commonly seen in chemistry programs of this
ilk.It was used to create the assigned
molecules, by piecing together the atoms, to obtain an idea of the structure
and to get a platform with which to start measurements.MacMolPlt
was then used to generate AM1 & PM3 geometry optimization input files
(.inp) under optimized geometry.It can
be used to check molecular charge, bond angle and length, and molecular orbital
information.MacMolPlt held all of the files created and used in the
website.Finally, GamessQ performed all of the number-crunching functions.It took the information gleaned from the
other two programs to perform all of the complex energy calculations. Experimental Avagadro
was introduced and students became familiarized with its tools and
functions.The three respective assigned
molecules were drawn using this program and saved under a filename.Molecules were optimized geometrically. Molecules could then be put into animation,
enabling one to see how molecules might rotate in space. Students were allowed to amuse themselves by
viewing the different molecular orbital outlines displayed around each of these
molecules.After setting up geometry
optimization, input files were made for each molecule under the program MacMolPlt and GamessQ.Vibrational
frequencies were calculated and dipole moments were improved by taking extra
measurements into account (adding diffuse functions).Potential energy versus bond length for each
molecule was calculated using MacMolPlt
and GamessQ.An additional energy calculation was made
under this program for the molecules – UV-vis transition energy.Input files were saved under five different
levels of theory, but further calculations were executed only under the DZV level of theory. Conclusion
There are many obvious advantages
to using computer software to execute quantum mechanical calculations over
doing them by hand.One that comes to
mind throughout the experiment is that these computations are endlessly
complicated, and some of the ones made in the building of this website would
take an intelligent, seasoned chemist about a lifetime.Another advantage is that error is minimized
for the most part, insofar as the level of complexity or factors the programmer
is willing to take into account while building these programs.Bond length and bond angle data output was
very near values referenced in prelab.It is very probable that vibrational and transition energy data calculated
in this experiment are very close approximations to actual value, based on the
proximity each value was to each other in the different levels of theory.This experiment did offer an idea of the
utility of computers in this area, and knowledge of how computer programs would
operate in the real world if one of these transition energies was needed. References
1. Listing of experimental data for F2 (fluorine diatomic)2015, http://cccbdb.nist.gov/exp2.asp?casno=7782414
2. Fluorine. 2016, https://en.wikipedia.org/wiki/Fluorine
3. Listing of experimental data for H2CS (Thioformaldehyde) 2015, http://cccbdb.nist.gov/exp2.asp?casno=865361
4. Calculated electric dipole moments for H2CS (Thioformaldehyde). 2015, http://cccbdb.nist.gov/dipole2.asp
5. Listing of experimental data for C6H5COOH (Benzoic Acid) 2015, http://cccbdb.nist.gov/exp2.asp?casno=65850
6. Mihalick, J; Gutow, J. Quantum Calculations. 2015 p 1-12
Molecular Information for Benzoic Acid is shown below. Information for
the other molecules can be found through the following links: Fluoride Thioformaldehyde
Jmol0 will appear here.
Benzoic acid highest occupied molecular orbital- orbital 61.
HOMO of benzoic acid. Its 61st orbital shell, containing the electrons of highest energy.
Jmol1 will appear here.
Depiction of the lowest unoccupied orbital shell of benzoic acid.
Layout of the lowest energy orbital pattern for benzoic acid that is unoccupied by electrons.
Jmol2 will appear here.
Electron charge distribution of benzoic acid
This picture demonstrates the asymmetry of charges involved in benzoic acid. Cooler colors depict more electronegativity.
Bond length comparison between literature and experimental values for benzoic acid. Bond Literature Value (Angsr) Experimental Value (Angst)
O=C
1.22
1.22
O-C 1.36
1.36
C-C
1.48
1.40
C-C(arom.) 1.39
1.39
O-H
0.95
0.96
C-H
1.09
1.07 Bond Angle Literature (Deg) Experimental (Deg)_______
C-C=C
119.9
120.6
C-O-H
85.0
85.0
C-C-H
121.2
119.5
UV-Vis calculations were
done using the DZV level of theory and were found to be 6.00eV
,6.11eV,6.15eV, 7.92eV, 8.18eV, 8.85eV, 9.24eV, 9.30eV, 9.75eV, and
9.78eV.
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