Successful molecular orbital calculations for O₂, OCS, and m-xylene were completed. It was found that out of the 6-21G, 6-31G, and DZV basis sets, DZV yielded the most accurate energy prediction for each of the molecules since the geometry optimizations using the DZV basis set yielded the lowest energies for systems. The software used successfully calculated geometries, vibrational frequencies, electronic transitions frequencies, dipole moments, and many other properties, and many calculations were compared to literature values.

Reactivity of molecules can be determined by electronic structure. Ab initio quantum chemistry methods, which are computational methods based on quantum chemistry, were used to calculate information about three different molecules O₂, OCS, and m--xylene. These basis sets are built from the linear combination of atomic orbitals. Three different basis sets were used to calculate the optimized geometry of these molecules. In increasing size of the basis set there are 6-21G, 6-31G, and DZV. The larger the basis set is the more accurate the predictions tend to be. The molecule is modified in these calculations until the geometries and bond lengths have the lowest potential energy. The more accurate the calculated geometry is the better the predicted electronic structure will be. Therefore, a better optimized geometry will have more accurate predictions such as molecular dipole moment, polarizability, vibrational frequency, probability of absorption of visible light, and if reactions will occur. Molecular orbitals may be characterized by wavefunctions for electrons. The variational principle allows approximate true wavefunctions with linear combinations of trial wavefunctions to be made. Trial wavefunctions are not eigenfunctions of the Hamiltonian, however, thus the expectation value of the energy must be calculated. The "basis set" wavefunctions that are used to form the trial wavefunction is normalized, but the total wavefunction must be normalized, putting additional constraints on coefficient values.  In this experiment the Avogodro² program was used to built structures for each of the molecules. Molecular mechanics optimizations were then completed on the structures and saved as .xyz files. The wxMacMolPlt³ software  used the .xyz files to generate AM1 and PM3 geometry optimizations (.inp) files for the Gamess⁴ computation package. If calculations worked molecules they were saved as .log files. These .log files could then be used in Jmol⁵ to observe structure and make calculations. The ab initio molecular calculations were carried out using Gamess and the Gaussian type basis sets: 6-21G, 6-31G, and DZV.

 References
1. J. Mihalick, J. Gutow. Molecular Orbital (MO) Calculations, UW Oshkosh 2013.
2. Avogodra software. http://sourceforge.net/projects/avogadro/ (accessed February 13, 2014).
3. Bode, B. M. and Gordon, M. S. J. Mol. Graphics Mod., 16, 133-138(1998).
4. M.W. Schmidt, K. K. Baldridge, J. A. Boatz, S.T. Elbert, M.S. Gordon, J.H. Jensen, S. Koseki, N. Matsunaga, K.A. Nguyen, S.J. Su, T.L. Windus, M. Dupuis, J.A. Montgomery J. Comput. Chem. 14, 1347-1363(1993).
5. The Jmol Development Team. http://www.jmol.org, accessed February 2014.

Using directory /Users/student/Desktop/jmolpp/Intropage for all molecules
  adding JmolPopIn.js
  ...jmolApplet0
      ...adding O2_picture.png
copying and unzipping jsmol.zip directory into /Users/student/Desktop/jmolpp/Intropage for all molecules
      ...copying
file:/Users/student/Desktop/PeterPresley/02_DVZ_geo_opt_UHF.log
         to
/Users/student/Desktop/jmolpp/Intropage for all molecules/02_DVZ_geo_opt_UHF.log
      ...adding O2_picture.spt
  ...jmolApplet1
      ...adding ocs_picture.png
copying and unzipping jsmol.zip directory into /Users/student/Desktop/jmolpp/Intropage for all molecules
      ...copying
file:/Users/student/Desktop/PeterPresley/ocs_DVZ_geo_opt.log
         to
/Users/student/Desktop/jmolpp/Intropage for all molecules/ocs_DVZ_geo_opt.log
      ...adding ocs_picture.spt
  ...jmolApplet2
      ...adding m-xylene_picture.png
copying and unzipping jsmol.zip directory into /Users/student/Desktop/jmolpp/Intropage for all molecules
      ...copying
file:/Users/student/Desktop/PeterPresley/mxylene_DZV_geo_opt-3.log
         to
      ...compressing large data file to
/Users/student/Desktop/jmolpp/Intropage for all molecules/mxylene_DZV_geo_opt-3.log.gz
/Users/student/Desktop/jmolpp/Intropage for all molecules/mxylene_DZV_geo_opt-3.log.gz
      ...adding m-xylene_picture.spt