Quantum Calculations Kathy Senn and Sean Gretzinger
Abstract: Molecular orbital theory is used to determine certain values
for molecules. Using calculations based on the basis sets AM1, PM3,
3-21G, 6-21G, 6-31G, and DZV, properties of molecules can be found and
compared to experimental values. This was done on hydrogen bromide
(HBr), methanol (CH3OH) and o-dichlorobenzene (C6H4Cl2). DZV gave the
best results for some properties, and different values compared to
experimental for other properties. None of the basis sets were exactly
correct at all properties calculated.
Introduction/Experimental: Quantum mechanics can be used to model molecules and calculate
many of their properties. The calculation methods include
semi-empirical ones such as AM1 and PM3, which base part of their
calculations on experimentally-determined values. Another method
is ab initio, which calculates everything from scratch with no
experimentally-determined values included. These basis sets
include 3-21G, 6-21G, 6-31G, and DZV (double zeta valence).
With increased processing capacity, it has become faster and easier to
do quantum mechanics calculations using a computer program.
The geometry and properties of the molecules hydrogen bromide/
hydrobromic acid (HBr), methanol (CH3OH), and o-dichlorobenzene
(C6H4Cl2) were calculated using different basis sets. First, all
three molecules were drawn in Avogadro.7 Using wxMacMolPlt8, AM1 and PM3
input files were created. The input files were used to run geometry
optimization calculations in GAMESS9, using GamessQ10 to submit them. The
results were
used as the starting points for geometry optimizations using the
higher-level basis sets. HBr
was optimized using 3-21G, 6-31G, and DZV. Methanol and
o-dichlorobenzene were optimized using 6-21G, which was used as the
starting
point for 6-31G, which was used as the starting point for DZV.
After the geometry optimizations were done, the following was calculated
for each molecule: bond lengths and angles, HOMO and LUMO orbitals,
electrostatic potential maps, partial atomic charges, the best dipole
moment, and vibrations. Additionally, for o-dichlorobenzene, predicted
UV-Vis peaks were calculated. All of these calculations were done using
GAMESS and visualized using Jmol11.
Access to the results of the calculations for each molecule: hydrogen bromide, methanol, o-dichlorobenzene
Conclusion: These calculations were useful in some areas and not helpful
in others. For the best optimized geometry, DZV, the bond lengths and
angles were helpful. All values were very close to the experimental. It
also was very useful in being able to visualize the HOMO and LUMO
orbitals along with the electrostatic potential maps.
Some parts of the calculations were not as useful as they deviated from
the experimental values. UV-Vis predictions on o-dichlorobenzene were
way lower than the experimental value. Also, the vibrational wavenumbers
were not close in most instances. There were more calculated vibrations
than peaks on the IR spectrum.
In most cases, some theories worked better than others. For the dipole
moment, the semi-empirical levels of theory gave the closest in all
three molecules. The only way to get DZV close to the dipole was by
putting in different values for diffuse orbitals. This process was long
and tedious and not an efficient use of time.
The size of the basis set did not always matter. The values from the
largest basis set, DZV, were not always closest to the experimental
values. Also. without the experimental values, it would be difficult to
determine if the calculated vales were correct.
References: 1. NIST. http://cccbdb.nist.gov/ (Accessed February 23, 2016).
2. Chang, R.; Thoman, J.W., Jr. Physical Chemistry for the Chemical Sciences; University Science Books:
Canada, 2014.
3. National Institute of Advanced Industrial Science and Technology. Spectral Database forOrganic Compounds SDBS. http://sdbs.db.aist.go.jp/sdbs/cgi-bin/direct_frame_top.cgi (Accessed March 1, 2016).
4. Gutow, J.; Mihalik, J. Quantum Calculations. Chemistry 371 Physical
Chemistry II; University of Wisconsin Oshkosh, Oshkosh, WI, 1998,
revised 2016, 1-12.
5. Bakiler, M.; Maslov, I.V.; Akyuz, S. J. of Mol. Struct., 1999,475, 83-88.
6. Sigma Aldrich. 1,2-dichlorobenzene. http://www.sigmaaldrich.com/catalog/product/sigald/270598?lang=en®ion=US (Accessed March 4, 2016).
7. Avogadro. http://avogadro.cc/wiki/Main_Page. (Access February 23, 2016).
8. Bode, B.M. and Gordon, M.N. J. Mol. Graphics Mod., 16, 133-138 (1998).
9. GAMESS. http://www.msg.ameslab.gov/GAMESS/ (Accessed February 23, 2016).
10. GAMESSQ. http://www.msg.chem.iastate.edu/GAMESS/GamessQ/ (Access February 23, 2016).
11. The Jmol developement team. http://www.jmol.org, (Access February 23, 2016).