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.    

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