Download A COMPUTATIONAL STUDY OF CRYSTAL VIOLET

Computational Study of Crystal Violet Hydroxylation
Revised: 2/18/15
A COMPUTATIONAL STUDY OF
CRYSTAL VIOLET HYDROXYLATION
REPORT INSTRUCTIONS
All Spartan and Excel files for this experiment must be attached in the ELN. Create a
computational study page in the this week’s folder. No formal lab report sections are needed and
this assignment is due with the postlab work for the wet lab portion of the experiment.
INTRODUCTION
Spartan will be used to visualize the changes in molecular structure as the reaction proceeds from
reactants to product. Energies, orbitals, and charges will be found to create a reaction
coordinate diagram (a representation of reaction progress). The energies found will be for
reactants, products, and the transition state. A transition state (‡) is the highest energy
arrangement of atoms formed as the reaction proceeds from reactants to products. The energy
required to reach the transition energy is called the activation energy (Ea). The magnitude and
sign of the energy difference between the reactants and products is responsible for the
spontaneity of the reaction (i.e., the value and sign of ΔG).
H3C
N
CH3
H3C
N
CH3
-OH
C+
H3C
N
CH3
CH3
N
H3C
CH3
H3C
OH
N
CH3
N
CH3
Computational Study of Crystal Violet Hydroxylation
Revised: 2/18/15
PROCEDURES
Crystal Violet (CV+)
1. Build the crystal violet (CV+) cation as shown above:
a) In the Inorganic menu, choose the trigonal planar geometry and C, then click on the
screen. This is the center carbon atom.
b) Add all 3 rings by clicking on Rings (choose Benzene if not displayed) in the builder
menu. Click on the 3 bonds of the central carbon, adding a benzene ring to each.
c) Go to the Inorganic menu and choose N and then the trigonal planar geometry. Add
one nitrogen atom to each benzene ring directly across from the center carbon atom.
Switch to the Organic menu to add the -CH3 groups to the nitrogen atoms. Minimize
the structure to add hydrogen atoms.
d) In order to get the most correct molecular geometry for the CV+, the calculation must
start with the 3 benzene rings in the same plane (in other words, with CV+ flat). Go to
the Geometry menu and choose Measure Dihedral. Click on the 4 atoms in the order
indicated to measure Dihedral Angle A. Once all 4 atoms are covered with a gray mask,
enter "0" in the field in the bottom right corner of the screen and hit Enter. Repeat this
process for Angles B and C.
2. Go to the Geometry menu and choose Define plane. Click on the 3 carbon atoms around the
central carbon atom. A triangle should appear with the central carbon in the middle.
3. In the Surfaces menu, add HOMO and LUMO.
In the Calculation menu choose
Equilibrium Geometry and Semi-Empirical. (Remember to change the charge to cation.)
(Do NOT click the Minimize (
) button again, it will undo the work done in 1d.) If an
error message appears stating that the calculation ran out of optimization cycles, resubmit
the calculation. The resulting structure looks like a propeller with the dihedral angles above
having values around 20°.
4. In the Surfaces window, individually click on the box next to LUMO and then HOMO to
Computational Study of Crystal Violet Hydroxylation
Revised: 2/18/15
display each plot separately. Rotate these images to observe their appearance from all sides
then paste these images into a table (Table I). (Note: Images should all be arranged in the
same orientation.)
5. In the Model menu, click on Space Filling. Rotate this image also and then paste it into the
table in the same orientation as the images above.
Hydroxide and Hydroxylated Crystal Violet
6. Calculate OH (Note the charge!) and CVOH for the Equilibrium Geometry, using the
−
Semi-Empirical method. (For CVOH: Do NOT start with CV+, just build with a tetrahedral
C for the central carbon (do NOT measure dihedral angles or set planes). Arrange the
molecule so that the OH group is pointing at you.)
7. Paste the HOMO, LUMO, and space filling images in Table I. Animation of the Reaction
8. Open the CV+ file created previously and save it under a different name. Open the Surfaces
window and delete any surfaces present. Add a bent oxygen atom close (but not attached to)
the CV+’s central carbon (do not attach it to any part of CV+). Do this by clicking on (
selecting the bent oxygen atom (
(
),
), then double click or hold down the Insert key. Delete
) the open valence (yellow stick) on the oxygen that points toward the CV+ (leaving
one open valence to turn into a hydrogen atom). Do not minimize this arrangement (if you
do so by accident, go to the Edit menu and select Undo).
9. Select Transition State under the Build menu. Click on the oxygen and, while holding down
the Shift key, click again on the oxygen and then on the central carbon of CV+. Double click
on either atom. A blue arrow will appear pointing from the oxygen to the carbon. Click
at the bottom right of the screen. An estimation of the transition state (‡) will appear. Ignore
the “No Match” that appears in the bottom right corner – it is a notification that the complex
created does not appear in Spartan’s database.
10. Select Measure Distance under the Geometry menu. Click on the oxygen and then the
central carbon. Replace the current bond in the box at the bottom right of the screen with
3.40 (3.40 Å) and press Enter.
At this distance, CV+ and -OH are still two separate
reactants.
11. From the Geometry menu select Constrain Distance. Click on the oxygen and then the
Computational Study of Crystal Violet Hydroxylation
Revised: 2/18/15
central carbon, and then, in the bottom right corner of the screen, click on
changes to
so that it
. Go to the Display menu and choose Properties. Click on the pink marker on
the pink line that just appeared between the two atoms, this should open up the Constraint
Menu. Click on the box next to Profile. Change the value in the box on the left to 1.40 (1.40
Å), leave the middle box set to 3.40 (3.40 Å), change the Steps to 20. Hit enter and then
close the window.
12. Go to the Setup menu and choose Calculations.
Select Energy Profile and Semi-
Empirical. Change the Total Charge to Neutral. (Leave the Unpaired Electrons set at 0.)
Make sure Global Calculations (lower left of the Calculation window) is checked, then
Submit the calculation. This calculation can take up to 5 minutes to complete. When the
calculation is complete as message will appear stating “Your job created a new document.
Would you like to open it?”. Click Yes.
13. Go to the Setup menu and open the Surfaces window.
Add HOMO, LUMO, and
Electrostatic Potential Map surfaces. If the Pending is not replaced by Completed in the
Surfaces window, go to the Setup menu and choose Submit.
14. Create a plot showing the affect of distance between the oxygen and the central carbon (the
constrained distance) on the complex's over all energy (E) and the partial charge on the
oxygen atom:
a. Go to the Geometry menu, choose Constrain Distance. Click on the pink marker on the
HO-C bond, and then click on
in the bottom right hand corner of the screen to add
the distances to the Spreadsheet. Click on
(this removes the Constrain Distance
selection).
b. Go to the Display menu and open the Spreadsheet window. (Label and Constraint
columns should be visible.) Click on Add... select E and the click Apply and then OK.
Energy values will appear for each distance in the spreadsheet window. Close the
Spreadsheet window.
c. Go to the Display menu and open the Plots window.
Click
and then choose
Constraint for the X Axis and E (kJ/mol) for the Y Axis. Click Add and the plot will
appear. Arrange the complex so change in the HO-C bond can clearly be seen.
Computational Study of Crystal Violet Hydroxylation
Revised: 2/18/15
15. On the plot just created, begin by clicking on the plot point at the longest constraint distance
(when CV+ and –OH are separate species) and then start clicking on the plot points for
shorter and shorter distances (until at the shortest distance CVOH is present). (You can also
use the
buttons beneath the molecule.) Observe how the benzene rings are twisting as
the HO-C bond shortens.
In the Model menu, click on Space Filling and repeat the
investigation of how the constraint distance affects the CV-OH complex. What orientation
does the –OH take as it approaches CV+? Is the transition state closest to the reactants and
products?
16. In the Model menu, click on Ball and Spoke. Go to the Display menu and open the Surfaces
window. Click on the box next to the Electrostatic Potential Map. Double click on the
density potential surface to change the Style (field in the lower right corner of the screen) to
Transparent. Again, repeat the investigation of how the constraint distance affects the CVOH complex.
Note: (1) Bonds are smoothly broken and formed during the course of a reaction. (2) Relate
the migration of charge during the reaction as indicated by the colors on the Electrostatic
Potential Map – red indicates electron rich areas, blue indicates electron poor areas. Pay
special attention to the appearance of the surface at the shortest and longest distance.
17. Create another table (Table II) recording the distance (Constraint) and energy (E) for the
reactants (longest distance (i.e. constraint)), transition state (‡, highest energy), and product
(lowest energy). (You will need to open the Spreadsheet window to find this data).
18. Click on the box next to HOMO and click through the points on the plot to discover how the
HO-C distance changes the HOMO and LUMO appearances. Pay special attention at the
distances for the reactants and the transition states.
Which orbital on the CV+ and which
orbital on the –OH would provide an in phase overlap that would lead to bonding?
Answer the questions on Sapling.