Quantum Computations
By: Charles Ullman and Luis Padilla
Abstract:
A computer and the programs GAMESS, GamessQ, Avogadro, MacMolPlt, and
Jmol were used to calculated the lowest energy geometry for the
molecules F2-, FHF-, O3 and [1,1'-diethyl-2,2'-carbocyanine]
+.
The molecules' geometry were then used to calculate their bond lengths,
vibrational frequencies, partial atomic charges, electrostatic
potentials, dipole moments, HOMO, LUMO and UV absorption peaks. All of
the results can be seen in the links below.
Introduction:
It is possible to build a molecule through pure theoretical
calculations; molecules are built from scratch using computers and
computer programs. The calculations are too difficult and time consuming
for humans to complete them in a feasible amount of time. In this
experiment, a computer and the programs GAMESS, GamessQ, Avogadro,
MacMolPlt, and Jmol are relied on. GAMESS is a program that does the
mathmatical processing. GamessQ is the user interface that can store and
cue calculations. GamessQ sends the information to GAMESS and gets the
product in return. Avogadro is a program that can be used to build
molecules. MacMolPlt is a program that can generate input files for
GAMESS to complete. Jmol is a program that can be used to create
molecules and view molecules. A JavaScript extension for Jmol is used to
create html pages. The theoretical calculations completed by GAMESS
stem from Quantum Mechanics (QM). One of the theories taken from QM is
the Hartree-Fock Self Consistent Field (HF-SCF). The HF-SCF is a method
that makes the computer calculate certain geometries of the molecule
ensuring that the final product is the lowest energy possible for the
molecule. It starts by picking an electron and calculating its effective
potential energy. Then the lowest energy of the electron is chosen. If
the lowest energy for the electron is not met, the process will restart
until the electron's energy is the lowest. The computer then checks if
the energy of the entire molecule is the lowest. If the energy of the
entire molecule is not the lowest, the calculation will repeat until the
energy of the molecule is the lowest. The programs and theories
mentioned above are applied to the molecules, F2-, FHF-, O3 and
[1,1'-diethyl-2,2'-carbocyanine]
+.
Experimental:
Avogadro was used to create the basic molecular geometry for all of the
molecules. The molecular mechanics geometry optimization mode, MMF94,
was used to roughly estimate the best geometry for the molecule. The
geometry of the molecules were all saved as a .xyz extension. The .xyz
files were then sent to MacMolPlt to create .inp files. Using the input
builder, basis was set to 6-31G, run type was set to optimization, SCF
type was set to RHF if molecules had paired electrons or UHF if
molecules had unpaired electrons, multiplicity was set accordingly to
each molecule, Exe type was set to normal run, molecule charge was set
accordingly to each molecule, Coord. Type was set to Unique cartesian,
initial guess was set to Huckle, and number of steps was set accordingly
to each molecule to create an .inp file. The .inp file was sent to
GamessQ and GamessQ sent it to GAMESS to be completed. Once the file was
completed, GamessQ exported a .log file of the molecule. The .log file
was opened in MacMolPlt and an .inp file was created except with the
basis set to Dunning cc-pVDZ. The .inp file was sent through GamessQ and
a .log file returned. The .log file was opened in MacMolPlt and an .inp
file was created except with the basis set to Dunning cc-pVTZ. The .inp
file was sent through GamessQ and a .log file returned. Now that all of
the molecular geometries were completed for each molecule, the HOMO and
LUMO of each molecule were created by Jmol. The .log of the CCT
calculations were opened on Jmol and by right clicking the molecule and
selecting surfaces-molecular orbitals, the HOMO and LUMO orbitals could
be selected. The .log CCT
calculations were opened on Jmol and by right clicking the molecule and
selecting Surfaces-Molecular Electrostatic Potential, the molecules
electrostatic potentials were displayed. The partial atomic charges were
displayed by typing, "$Label %P$" in the console of Jmol. For each of
the geometry optimizations, the bond lengths were assigned to each bond
by opening the console command on Jmol and typing, "$measure
allconnected(*)(*)$". For the molecule F2-, Jmol did not
understand that the Fluorines were still bonded to each other. To
measure the distance between them, the fluorine atom was double left
clicked and a line appeared. The line was dragged to other fluorine
atom, automatically displaying the length. The bond angles were
displayed by typing, "$measure allconnected(*)(*)(*)$" in the console of
Jmol. The vibrational frequencies were calculated, by opening the CCT
.log files and changing the Run Type to Hessian and the Hess. Options
was set to Numeric Method. The file was written as a .inp and sent to
GamessQ, which returned a .log file. The .log file was opened on Jmol
and by right clicking the molecule, the vibrations were turned on. For
the energy plots for F2-, the basis sets .log were opened on MacMolPlt
and the Run Type was set to Energy Surface and Initial Guess was set to
Huckle. The file was saved as .inp and sent to GamessQ, which returned a
.log. The .log energy files were opened on Jupyter and the energy plots
for F2- were calculated using the imports matplotlib.pyplot, k3d and
GamessUSReader. For the UV-Visible transition energies, the CCT .log
file for the aromatic compound was opened using text editor and the
commands, "$CONTRL CITYP=CIS$END" and "$CIS NSTATE=10 $END" were entered
below the $SYSTEM line.
Links to Molecules of Interest:
1,1'-diethyl-2,2'-carbocyanine(+)
FHF-
Ozone
F2-
Based on a template by A. Herráez and J. Gutow