The reactivity of a molecule is determined by its electronic structure, and thus predictions of properties such as the vibrational frequencies, molecular dipole moments, and polarizability can be made.  These calculations were performed by physical chemists and chemical physicists.  However, now electronic structure calculations by computers with software packages can be made by non specialists.  They use the computer analysis to improve geometry and energy calculations, thus predicting if reactions will work.   This saves money, time, and materials.  Furthermore, the programs show three dimensional models of the molecule demonstrating the molecular orbitals.  However, computer output needs to be analyzed not just taken as being accurate.  A person needs to be skeptical and compare the regularity of data from the different levels of theory.  MOPAC uses empirical data and estimates the values for two electron overlap integrals.  AM1 and PM3 are the Hamiltonians used.  The best level of theory is ab initio.  AM1, PM3, and ab initio theories can be used to calculate the optimized geometry, HOMO orbitals, dipole moments, and vibrational frequencies of hydrogen chloride, methanol, and aniline molecules.¹  Furthermore, the potential energy surface versus bond length for each level of theory for hydrogen chloride was generated to show that the bigger the basis set the better the geometry.  A UV-Vis spectrum for aniline was used as a comparison for calculations of the transitions energies of the two highest levels of theory for aniline.²

The UWO Quantum Server was used on an Apple computer to construct the following molecules:  hydrogen chloride, methanol, and aniline.  MOPAC’s Hamiltonians, AM1 and PM3, were used to calculate the optimized geometry.  If the calculation failed, the raw output file was searched for the word “failure” to see what occurred.  Once all the optimized geometries were completed for AM1 and PM3, the results were transferred to a specifically named computer file by copying the raw output and pasting the text into TextEditor.  The files were made to plain text and saved as “.log” which was then opened in MacMolPlt.  MacMolPlt was used to optimize the geometry if the AM1 or PM3 failed previously and the input files were set up for GAMESS.  The file was checked in Console and “failure” searched to see if its optimization was complete.  Once the molecule was optimized, MacMolPlt was used to write files to optimize the geometry of the molecules at 321-G, 631-G, and 6311-G levels of theory.  For HCl instead of 6311-G, DZV or double zeta valance was used for the basis.  The files were queued and run using GTK-GAMESS.  The lowest level was run first, from either the AM1 or PM3 file, and used as the input for the next level of theory calculation.  For example, 321-G was used for the starting point for 631-G.  Then that file, 631-G, was used for the highest level of theory, 6311-G or DZV.  Once completed, the files were yet again checked for failure by opening the file in Console, because just looking at the energy plots could be deceiving about the completion of the optimization.  Once all the levels of theory were complete, they could be used to view the bond lengths, bond angles, and HOMO orbitals in MacMolPlt.  The dipole moments were found by opening the file in TextEditor and searching for the last occurrence of “/D/”.  For the calculation of the vibrational frequencies of HCl, CH₃OH, and aniline, MacMolPlt was used along with the highest level of theory, DZV and 6311-G.  The categories for the vibrational calculation in MacMolPlt were selected and the file written.  TextEditor was again used to view the file to get the vibrational frequency for HCl.¹  For methanol and aniline, the files of the molecules were opened in Jmol to show the frequencies that corresponded to the peaks in the IR spectrum.  Also, for HCl, CH₃OH, and aniline the log files were opened with Jmol to create the models of bond lengths, bond angles, and HOMO orbitals, for this webpage.  The Jmol files were saved and then opened in Kompozer to generate the template for the webpage.  For each ab initio level of theory result for HCl, a potential energy surface versus bond length input file was generated using MacMolPlt, run in GAMESS, and graphed in IGOR.  Using the best level of theory for aniline, 6311-G, an input file was written for the UV-Vis transition calculation.  It was then run in GAMESS; once completed the ".log" file was opened in TextEditor and searched for “CIS TRANSITION DIPOLE MOMENTS”.  Looking at the oscillator strength, the transitions were recorded.²

To view the results for the models and calculations of Hydrogen Chloride, Methanol, and Aniline click on molcules below.

References:
(1)  Mihalick, J.; Gutow, J. Quantum Calculations I.  Oshkosh, WI, 2009.
(2)  Gutow, J.  Molecular Orbitals/ Quantum Calculation Experiment 2.  Oshkosh, WI, 2009.