Molecular Orbital Calculations for Chlorine, Ethane and Benzaldehyde

By Nick Newcomer and Mathew Kumbier


    The reactivity of a molecule is directly related to the molecule’s electronic structure. By knowing the most probable locations of the electrons and their energies, it is possible to predict properties about the molecule such as molecular dipole moment, polarizability, vibrational frequencies, probability of absorption of visible light, and tendency to donate electrons.1 These types of calculations were originally done by hand and took lots and lots of time. As technology advanced and as computers advanced, systems were created to decrease computation time and hand errors. One such computation system uses the programs Jmol, GAMESSQ, and MOPAC. This website specifically shows the results of use of these programs for diatomic chlorine, ethane, and benzaldehyde.

The Calculations

    All three molecules were first built in the program wxMacMolPlt using the premade prototype molecules whenever possible. The molecules were then saved as .cml files. These .cml files were each opened in Jmol where a mechanics optimization was preformed and the files were saved as .xyz files. From here, wxMacMolPlt was once again used to generate AM1 and PM3 geometry optimization input files (.inp files) for the program GAMESSQ to calculate with the three basis sets (3-21G, 6-31G, and DZV). After the calculation was completed, the resulting .log files were opened in TextEditor in order to note the dipole moment of each molecule and the .inp file of the largest basis set (DZV) was used to calculate the vibrational frequencies. Next, for diatomic chlorine, a potential energy surface versus bond length was calculated in GAMESSQ and then graphed with all three basis sets in IgorPro while a calculation for UV-Vis transition energy calculations were being run on the best geometric optimization of benzaldehyde. After the calculations for the UV-Vis data was completed, the .log file was examined and the transition from ground state data was noted.1

Chlorine                    Ethane                    Benzaldehyde


    As a whole, the use of computers and their computational techniques are invaluable. What may have taken weeks for a group of highly trained chemists to calculate, took a relatively short amount of time by pairs of undergraduate level chemistry majors. These methods save numerous amounts of resources including time and money (not to mention paper). The calculations built upon themselves, so the later and more difficult calculations were dependent on the somewhat simpler earlier calculations.


       1.     Molecular Orbital Calculations; Mihalick, J., Gutow, J.,; Chemistry 371 Lab Manual Spring 2011; University of Wisconsin Oshkosh: Oshkosh, WI, 2011.
      3. entries for benzaldehyde, chlorine, and ethane geometries and dipoles.
      4. Mac Jmol, version 2010; Jmol Development Team (accessed March 10, 2011)
      5. GAMESSQ, version 1.2; Ekstrand, Jason, Iowa State University, 2008; (accessed March 10, 2011)
      6. wxMacMolPlt, version 7.4.2; Bode, B. M., Gordon, M.S., Jmol Graphics and Modeling, 1998; (accessed March 10, 2011)