Quantum Calculations on Lithium Monoxide, Ethylene, and Chlorobenzene

by Demetria Dickinson and J. Wyatt Seagren

Introduction

Classical mechanics prove to be very accurate at describing things larger than molecules.  Unfortunately, these theories break down at the molecular level.  Thus, quantum mechanics was born, and can now be used to calculate structures and properties of molecules much more accurately.  This allows for calculation of vibration frequencies, bond lengths, bond angles, and more.  However, until recently only highly educated and dedicated physical chemists or chemical physicists could do these calculations, due to their extreme complexity.  Now, with the advent of computers, programs are available to do these calculations for people.  In this web page will be models and calculations for optimized geometry, bond lengths, angles, levels of theory, vibrational frequencies, and bond stretching for the molecules LiO, C2H4, and C6H5Cl.
      

Experimental

The following molecules were made with the UWO Quantum Server on an Apple computer:  LiO, C2H4, and C6H5Cl.  MOPAC, a semi-empirical method, uses empirical data to estimate the values of two electron overlap integrals, needed for calculating Hamiltonians, was used to calculate the optimized geometry.  The Hamiltonians AM1 and PM3 were used.  If the calculation didn't work, a search was made for the word “fail” in the raw output file to check what might have gone wrong.  Once the optimized geometries were finished for AM1 and PM3,  the raw output was copied and pasted into TextEditor.  The files were saved as “.log”, then opened in MacMolPlt, where the geometry was optimized if the AM1 or PM3 had failed.  The input files were then set up for GAMESS.  The file was checked for the word "fail" to make sure the optimization was complete.  Once the geometry was optimized, MacMolPlt was used to write files for optimizing the geometry at the following levels of theory, 321-G, 631-G, 6311-G, and DZV(Double Zeta Valence), however 6311-G proved to be unreliable.  The files were ran in GAMESS, and could be qeued up to run one after the other to increase convenience.  The lowest level, 321-G was ran first, with 631-G following, and DZV following that, using the previous configuration as the starting point for the calculations, also making sure to set Initial Guess to Huckel when not using the same level of theory.  To finish, the file was written as a ".inp" file.  Once again, the file was checked for "fail" because the energy plot might not obviously show it.  Once this was all complete, the bond lengths, angles, HOMO, and LUMO orbitals could be viewed in MacMolPlt.  To find the dipole moments, it was necessary to open the file in TextEditor and search for "/D/".  The vibrational frequencies of the molecules were calculated using the highest level of theory file for each molecule in MacMolPlt, except for LiO, and the file was written as ".inp" with the run type set to Hessian and in Hess. Options Numeric Method was chosen.  The files were ran in GAMESS, afterward in MacMolPlt the vibrational frequencies were available to look at.  Also, the log files were opened in Jmol to build models of bond lengths, bond angles, and HOMO orbitals, for the purposes of this web page.  Jmol was also used for the skeleton of this web page.  Kompozer was used to edit the web page. 



 
 
 LiO Optimum Geometry
Click here to go to a page with the results and discussion of the calculations for LiO. The page contains the following:
  • a display of the highest occupied molecular orbital (HOMO)
  • data for the potential energy of bond stretching
  • vibrational frequency data
  • dipole moments and partial charges
 
 Click here to go to a page with the results and discussion of the calculations for C2H4. The page contains the following:
                  • a display of the highest occupied molecular orbital (HOMO)
                  • animations of the modes in the vibrational spectrum
 

C6H5Cl Optimum Geometry
Click here to go to a page with the results and discussion of the calculations for C6H5Cl. The page contains the following:
  • a display of the highest occupied molecular orbital (HOMO)
  • animations of the modes in the vibrational spectrum
  • UV-Vis transition calculations
 
Conclusion

As outlined in this web page, the computer software programs GAMESS, MacMolPlt, and Jmol allowed us to accurately calculate values and models for the molecules LiO, C2H4, and C6H5Cl.  For vibrational frequencies, the calculations are a bit off from the experimental, but for the other calculations the software gives a pretty good approximation, although generally for non-degree values the calculation gives a higher estimate than the experimental. 

References:
(1)  Mihalick, J.; Gutow, J. Quantum Calculations I.  Oshkosh, WI, 2009.
(2)  Gutow, J.  Molecular Orbitals/ Quantum Calculation Experiment 2.  Oshkosh, WI, 2009.
(3)  Computational Chemistry Comparison and Benchmark DataBase, (c) 2002, U.S. Secretary of Commerce.             Accessed 3/30/10.
(4)  National Institute of Standards and Technology Chemistry WebBook, (c) 2008, U.S. Secretary of Commerce.         Accessed 3/17/10.




Based on template by A. Herráez as modified by J. Gutow
Page skeleton and JavaScript generated by export to web function using Jmol 11.8.20 2010-02-28 19:28 on Mar 17, 2010.