Molecular Orbital Calculations of KO, H2O and Phenol
Performed by: Heather Barkholtz and Alyssa Dreger
March 9, 2011


    The location of of electrons and the value of their energies allow the prediction and base of calculations of molecular dipole moment, polarizability, vibrational frequencies, probability of absoption of visible light and the tendency to donate electrons for each reaction.1 Jmol. GAMESS and Molecular Mechanics were used in this experiment to detetmine and calculate these various values. Molecular mechanics bases calculations upon classical instead of quantum mechanics by treating molecules as harmonic oscillators. Force constants of different types of molecules are derived from vibrational and rotational spectroscopy.1 Molecular mechanics is primarily used for predicting molecular geometry and qualitative information about relative energies of different molecular conformations.1
    GAMESS is a program which has several different systems which allow it to perform various calculations on one molecular system. MOPAC is one system which is semi-empirical. It uses this data to provide an estimate of the electron overlap integrals to determine the values of <H>.1 The Hamiltonian <H> is “an operator that carries out a mathematical function on the function (ψ).”2 Most commonly used in this environment, this operation is the second derivative of ψ which is then added to the product of V(x). This has a significant impact on quantum mechanics in that it corresponds to the total energy of the system (the sum of the potential and kinetic energies). MOPAC principally performs four different calculations; MNDO (moderate neglect of differential overlap), MNDO/3, AM1 and PM3. “The parameterization is derived from experimentally determined enthalpies of formation, ground state geometries, dipole moments and ionization potentials.”1 AM1 and PM3 are principally the calculations run in this experiment performed on all molecular systems.
    The other type of calculations performed through the GamessQ is done with ab initio. Ab initio calculates all integrals, yet approximations still reside due to the result of a finite basis set and a self consistent field model. Ab inito is good software for calculating geometries, vibrational frequencies, electronic transition frequencies, dipole moments and other various functions. MINI is the lowest level of calculation performed in ab initio which gives quick approximate results. The next level is 6-21G Gaussian basis set. 6-31G, DZV and TVZ (double and triple zeta valence) are the increasing levels subsequently.1 Calculations were performed on KO (M.W. 55.0977 g/mol, linear geometry), H2O (M.W. 18.0153 g/mol, bent geometry, dipole moment at 1.85 D, and vibrational frequencies at 3656.65, 1594.59, and 3755.79Å) and phenol (C6HOH, M.W. 94.1112 g/mol, dipole moment at 1.7 D and vibrational frequencies at 36800-1300 and 1300-650Å)3 respectively. Because KO is a diatomic molecule, rarely exists and therefore has no bond, only MINI and TZV were performed on KO. The more typical calculations, 6-21G, 6-31G and DZV were performed on the aromatic and polyatomic compounds H2O and phenol. Calculations were performed by building a molecule, molecular mechanics, MOPAC and then ab initio.


The assigned molecules were first designed in wxMacMolPlt and attached with a file name of .cml. Once created these files were opened in Jmol and mechanically optimized and saved as a .xyz file. From these files, an AM1 and a PM3 geometry optimization were done and saved as an input (.inp) file using the MOPAC input builder and queuing the run through GAMESS. Once the optimization had successfully run the log file was saved and opened in wxMacMolPlt to ensure the molecular optimization has run in as few steps as possible. Using the results from the AM1 and the PM3 runs, the higher order calculations, TZV for KO, and 6-21G, 6-31G and DZV for H2O and phenol, were performed using the same technique used for prior calculations. Multiple runs were necessary for all molecules to ensure the lowest energy level possible.1 The results were then saved as log files again, and an energy plot was made for the KO using Igor Pro. The dipole moment was then extracted from the log files using Text Editor. Geometry optimization was performed a second time on the smallest polar molecule using diffuse functions. Once completed, a potential energy surface versus bond length plot was made for KO. This was done using ab initio for 6-21G, 6-31G and DZV for both water and phenol. Finally using GamesQ .inp files were created for UV-Vis spectra of both water and phenol. Potential energy plot were then created using IgorPro and molecular vibrations of each molecule were compared using Jmol.1





    There are various situations in which computational results can be useful and others in which it is too time consuming and not useful. In times for the need of extremely accurate data or in situations in which multiple calculations are needed to be done efficientl, computational results and mechanics are useful. Instances in which a simple or few calculations need to be done computational data would not be useful because it would be quicker to perform the calculations manually. Computational data is also quite useful when experiments are diffcult to perform or the results from an experiment are inaccurate. Computational data is quite reliable and therefore in situations in which future experiments or further data depends on existing data, computational data would be more useful than manual or experimental data. Computational results are useful in determining ground state geometries, relative energies and enthalpies however are not useful for UV-Vis and dipole moment calculations.


1.     Gutow, J. Chemistry 371 Lab Manual; University of Wisconsin-Oshkosh Spring 2011,    p 14-18.
2.     Atkins, P.; DePaula, J. Physical Chemistry; 9 ed.; W.H.  Freemany and Company: New York, 2010, p 267.
3.     NIST Chemistry WebBook 2008, accessed Mar. 6    2011.