Much of the reactivity of a molecule is determined by it's electronic structure. Properties like the molecular dipole moment, polarizabilty, vibrational frequencies, probablity of absorption of visible light, and tendency to donate electrons in a reaction can be deduced from a description of the probable positions and energies of electrons within a molecule. Complicated calculations using multiple wavefunctions to help determine the properties of these electrons were calculated by physical chemists and chemical physicists using pencil and paper. With the help of computers and software packages, these calculations can be made by non-specialists. These programs help to predict whether reactions will work, which saves money, time, and materials. Some programs can generate three dimensional models of the molecule and their orbitals. The best level of theory is ab initio. MOPAC, JMOL, and GAMESS software can be used together to determine the HOMO and LUMO orbitals, dipole moments, vibrational frequencies, and other properties of Br₂, BH₃, and m-Xylene.

The WxMacMolPlt was used to build the molecules Br₂, BH₃, and m-xylene. These files were saved as .cml files and then opened in the software package Jmol. Molecular mechanics was used by Jmol to obtain an initial guess as to the geometry of the molecules by treating them as collections of classical harmonic oscillators. The program looks for whichever arrangement of atoms generates the least amount of stress. The new coordinates were saved as .xyz files. WxMacMolPlt was then used to open the .xyz files in order to optimize the geometry quantum mechanically. Since exact eigenvalues and eigenfunctions cannot be found for multiple atom molecules, estimates are made based on empirical results.¹ MOPAC, a semi-empirical method, used AM1 and PM3 hamiltonians to make input files “.inp” to be computated in the GAMESS software package. GamessQ was used to submit these to the GAMESS package. The .log files were checked to ensure that they converged gracefully before moving on to the next step. Once the lowest level of computation was complete (6-21G) and checked, it was used to generate the next highest level of theory and so on. UV-vis and vibrational frequency calculations were done along with the geometry optimization using WxMacMolPlt. Once all of the levels of theory were completed, they were used to check bond angles and lengths, dipole moments, expected LUMO and HOMO orbitals, and so on, all of which has been compiled into 3 separate web pages that are available for viewing by clicking on the corresponding molecules below.

To view the results for the models and calculations of Br₂, BH₃, and m-Xylene click on molcules below.

References:
(1)  Mihalick, J.; Gutow, J. Chem 371 Molecular Orbital Calculaitons.  Oshkosh, WI, 2012.