Quantum Calculations



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