The Caffery, Dobosh, and Richardson Hyperchem tutorial was used to perform a variety of tasks such as the visualization of MO formation, the execution of scripts, log files and macros to gain information about the system.  Walsh diagrams were constructed for water and beryllium hydride using scripts available in Hyperchem.  Images were also captured to display the images generated by Hyperchem displaying the "action" of MO formation.  Images were also captured  of various molecules and their MO's.

Introduction

The purpose of this lab was to become familiar with molecular geometry and molecular properties resulting from the molecular geometry.  A series of five experiments were performed.  Each experiment introduced a new Hyperchem tool.

Experiment 17: Exploring the Formation of Molecular Orbitals - 1
The purpose o this experiment was to gain an understanding of the theoretical treatment of chemical bond formation.  Scripts  allowed graphs to be made of energy changes as atoms move closer together.  The method used for this simulation was MNDO.  This method uses an approximation of Neglect of Differential Overlap (NDO).  NDO reduces the number of calculations.  MNDO uses the valence electrons in each atom of the molecule in calculating the attractive forces of electrons to the nuclei and electron-electron repulsion.  Scripts instructing Hyperchem to perform the animation were executed on H2 Sigma H2* Sigma, O2 Pi and O2* Pi MO formation.  Hyperchem's "compute orbital" was used to create an isosurface of H2 and orbital plots of the density.

Experiment 18:  Exploring the Formation of Molecular Orbitals - 2
The purpose of  this experiment was to use a HyperChem log file to obtain information about the chemistry of a system.  The
log files give information on 9 levels, 9 yielding the most information and 1 being the least informative.

Experiment 19:  Molecular Orbitals: Ethene and Formaldehyde
The purpose of this experiment was to perform molecular orbital calculations via the Extended Huckel method.  This was performed on ethene and various twisted forms of ethene, and carbene, and formaldehyde.

Experiment 20:  Walsh Diagrams for H2X Molecules
The purpose of this experiment was to use the information provided by the HyperChem log file and to use a macro to create Walsh diagrams for water and beryllium hydride.

Experiment 21:  Jahn-Teller Effect
The Jahn-Teller distortion occurs when two ligands that are trans to each other move either closer to or farther away from the metal than the other four molecules in an octahedral transition metal complex.  The purpose of this experiment was to examine the changes of the binding energy in the complex as the symmetry changes from O_h to D4h by elongation and compression of the z-axis.

Experimental Method
The experimental method was similar to the one described in : Caffery, Dobosh, and Richardson Laboratory Exercises using
Hyperchem, experiments 17, 18, 19, 20, 21.  The molecules constructed were saved as *.ent* files then renamed *.pdb* to be published on the WWW.  Other images were captured and saved as .jpg or.gif files to be published on the WWW.

Results

Experiment 17: Exploring the Formation of Molecular Orbitals - 1
Images captured from this experiment can be viewed at the MO image site for this lab.
The following  HOMO and LUMO energies were obtained:
Table1

	Oxygen	Hydrogen
HOMO	7.732218 eV	-18.313272 eV
LUMO	24.706390 eV	7.349720 eV

The bond length of the Hydrogen molecule was 0.25 Angstroms.

The plot of each energy (core, electronic, total, and binding) versus distance on a graph.  The data for this graph was obtained from the log file.
Table 2

Figure 1

Experiment 18:  Exploring the Formation of Molecular Orbitals - 2
Below is an image captured which displays the charges of the atoms in an HF molecule.
Figure 2

Equations for five orbitals in HF were written from a portion of a log file:
Table 4

Equation	Energy (eV)	Symmetry
Y1 = 0.920Y(Fs) - 0.136Y(Fpy) +0.365Y(Hs)	-43.16	1 sigma
Y2 = -0.30924Y(F2s) - 0.82549Y(Fpy) +0.47217Y(H1s)	-17.77429	2 sigma
Y3 = -1.00000Y(Fpx)	-14.82447	1 pi
Y4 = 1.00000Y(Fpz)	-14.82447	1 pi
Y5 = 0.23737Y(F2s) - 0.54779Y(Fpy) - 0.80223Y(H1s)	5.27487	3 sigma

Experiment 19:  Molecular Orbitals: Ethene and Formaldehyde
Below are CHIME molecules of ethene and formaldehyde.  Images of the carbene energy levels can be viewed at the MO image site for this laboratory.
Figure 3

Figure 4

Experiment 20:  Walsh Diagrams for H2X Molecules
The Walsh diagrams and spreadsheet for this lab are shown below.
Table 5

Figure 5

Table 6

Figure 6

Experiment 21:  Jahn-Teller Effect
Below is the data table displaying the energy change as the axis is changed for MnF63^- and NiF63^-.
Table 7

Axial Lengths (A)	MnF63- Energy (kcal/mol)	NiF63- Energy (kcal/mol)
1.50	450.6927	-104.7308
1.55	380.4525	-135.9877
1.60	324.3291	-158.3309
1.65	278.477	-172.919911
1.70	238.09	-178.522
1.75	225.3371	-183.2738
1.80	182.7260	-188.4922
1.85	162.333911	-186.5733
1.90	145.0823	-185.5086
1.95	124.7359	-185.0451
2.00	111.365	-182.8782
2.05	103.8073	-79.20835
2.10	83.260	-174.4423
2.15	75.7346	-168.922163
2.20	72.7886	-162.895310
2.25	74.37419	-81.9790
2.30	80.7136	-151.9503
2.35	96.9307	-154.4541
2.40	137.7856	-146.483457
2.45	137.3261	-81.11731
2.50	215.226	-80.858055

Discussion
Experiment 17: Exploring the Formation of Molecular Orbitals - 1
    The results of this experiment displayed in Table 2 and Figure 1 show significant changes in the electronic energy and core energy as the bond distance decreases.  As the bond distances decreases, it is observed that the core energy increases.  This has a direct correlation with the MNDO calculation.  As bond distance decreases, the core electrons begin to play a small but observable role in the binding.  Thus, the inverse is also true.  As bond distance increases the core energy becomes less active and an increase in valence binding is observed.  As the bond distance decreases the repulsion between nuclei and inner electrons of one atom for the nuclei and inner electrons of other atoms in the molecule increases.  This also accounts for an increase in the core energy as bond distance decreases.  Figures 7 - 11 at the MO image site show the images captured as the bond distances decreased.  The Hydrogen LUMO can also be viewed here.  This orbital appears to posses a node between the two atoms.  Therefore it is an antibonding orbital.

Experiment 18:  Exploring the Formation of Molecular Orbitals - 2
    Table four displays the weight of the molecular orbitals that are participating in the HF molecule.  Since molecular orbitals are linear combinations of atomic orbitals, the information provided by Hyperchem gives an approach to describe which orbitals are interacting and a molecular orbital diagram could then be produced.  Other information such s the charge distribution in a molecule are also related to the wave coefficients.  Since the wavefunctions are normalized, the sum of the squares of their coefficients is 1.  The charge density on a particular atom from all of the molecular orbitals is the sum of the squares of the coefficients of the occupied orbitals centered on that atom times the number of electrons in the molecular orbital.  In this case all of the molecular orbitals are doubly occupied and the charge distribution is observed in  figure 2 above.

Experiment 19:  Molecular Orbitals: Ethene and Formaldehyde
    The orbitals for this experiment can be viewed at the MO image site, figures 13-17. These figures are of the molecular orbitals of the carbene fragment and can be displayed as follows.  The third orbital is essentially a py orbital pointing along the absent C=C bond, which sill be formed in ethene.  The fourth orbital is the non-bonded pz orbital that will form the pi orbital of ethene.  The fifth orbital is the anti-bonding combination of the second orbital, and the sixth orbital is the anti-bonding combination of the lowest energy orbital.

Experiment 20:  Walsh Diagrams for H2X Molecules
    The wavefunction coefficients produced by Hyperchem show that as the angle decreases from 180, with respect to the 1A1 orbital, the H1s and H2s orbitals do not play a very large role in the binding.  The formation of the 1A1 orbital is highly governed by the O 1S orbital at 160 degrees. Where at 180 degrees the H1s and 2s orbitals are participating.  In water the electronic energy at 90 degrees suggest that it is more stable than either the 105 or 180 angles. In beryllium hydride, the most stable angle, according to electronic energy is 180.  It is suggested here that the electronic energy alone is not necessarily a good measure of relative stability for strained systems.  Both electronic and nuclear energies must be considered when predicting the lowest energy conformation in strained molecules.

Experiment 21:  Jahn-Teller Effect
    For the two metal complexes studied, it is seen how the binding energy of the complex changes as the complex  goes from a pure Oh to D4h symmetry  as the bond is elongated or compressed.  The data in Table 7 shows that elongation is favorable in the Mn complex while compression is more energetically favorable in the Ni complex.