Dr. Xie, 32-335
Computational Chemistry Lab Module: Study of Conjugated Systems
Introduction
In this experiment, we will use CAChe software package to model the geometry and
stability of conjugated vs. isolated and cumulated dienes. We will also study molecular orbitals
of an allyl cation, as well as dienes and dienophiles in Diels-Alder reactions.
Refer to Wade’s Chapter 15 for chemical theory related to conjugated system. Refer to
the following web pages or any other internet references for introduction to computational
theory:
http://www.ccl.net/cca/documents/dyoung/topics-orig/compchem.html
http://www.chem.ox.ac.uk/course/cache/
The following step-by-step procedure is provided for you to follow in the lab.
Experimental Procedure
Part 1: Study of Geometry and Stability of Conjugated, Isolated, and Cumulated Dienes
In this part, you will study three molecules by building their structures, optimize them, and
obtain their energy (heat of formation). The steps will be repeated for: 1,3-pentadiene, 1,4pentadiene, and 1,2-pentadiene.
1. Run the CAChe program by clicking “Start”, “Programs”, “CAChe”, then “Workspace”.
2. The CAChe program should run and the window will look like:
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Note in the task bar both “CAChe” and “CalcMgr” are running. DO NOT close “CalcMgr”
while CAChe is running since CAChe needs the calculation manager to function properly
when computing energy or optimizing structures.
3. We will now build the 1,3-pentadiene molecule first. To do this, click on the icon on the left:
Notice the default properties (element, hybridization, charge, and bond order) in the
following picture:
Click in empty space to place a carbon (sp3) there. To draw a bond, click at the middle of the
first carbon atom and drag to a new location with the mouse button held down. A carbon-carbon
bond has just been made. Continue to make new bonds until a five carbon skeleton has been
built. Note the atom highlighted is selected, and those grayed out are not. This is important
since any further operations (such as change to a different element, hybridization, charges, bond
order) will only affect the selected atoms or bonds. For our purpose, we need to make some
changes so as to produce the first molecule--1,3-pentadiene. To do so, switch to the selection
tool by clicking on this icon:
Then click on the bonds you want to change to a double bond (holding down a shift key allows
for multiple selection). The bonds selected become highlighted. Change them from single to
double bonds using the tool bar. Next, select the 4 double bonded carbons and change them to
sp2 hybridization (from the default sp3). After making other necessary changes, click in an
empty space to select the entire molecule. You should see 1,3-pentadiene on the screen, though
the molecule may not look pretty and hydrogens on each carbon are probably missing.
4. Now that the entire molecule is highlighted, beautify the molecule (add hydrogens, clean up
the bond angles, etc.) by clicking on the menu “Beautify” “Comprehensive”. We now have a
1,3-pentadiene molecule on the screen.
Some additional useful operations are explained here:
The magnifying glass allows for enlargement or shrinking of a molecule. The hand tool
allows for movement of a structure, and the curved arrow allows for rotation of a molecule.
Take a moment to try them out and get familiar with the way these tools work.
5. Save the molecule by clicking “File” “Save “ and give it a name (I suggest you use the name
of the molecule followed by your initial).
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6. Click on “Experiment”, “New”, and click on the “Start” button. Note how the program start
to optimize the structure (# of cycles shown) and the energy of the molecule is decreasing
(approaching its lowest value, or “true” value). Once the optimization is completed, record
the heat of formation in your lab notebook and fill in the value in the table below. (you will
need all information from these calculations to complete your lab report.) Close the
experiment status window and the experiment window.
7. The optimized molecule is now shown on the screen. Examine the geometry of the molecule
by rotating it. (Which atoms must lie in the same plane?) Measure all carbon-carbon bond
length in 1,3-pentadiene by selecting only two adjacent carbons (hold shift key down) and
clicking “Adjust”, “Atom Distance”. Record all bond length in your lab notebook and
directly on the structure.
8. Repeat steps 3-7 for 1,4-pentadiene and 1,2-pentadiene (note the carbon with two double
bonds on it should be changed to sp hybridization), each time saving them as separate files.
When examining the geometry of 1,2-pentadiene, pay attention to the relative position of the
atoms attached to #1 and #3 carbon (both with one double bond). Are they in one plane or in
two planes that are perpendicular to each other?
9. Are the relative energy trend (not absolute values) for the three compounds in consistent
with the values from the textbook?
Table 1: (include this table in your lab report in “Results and Discussion” section)
Structure
Calculated
Energy
(kcal/mol)
Energy from Heat
of Hydrogenation
(Wade p640)
Comments (geometry)
H2C C CH CH2 CH3
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Part 2: In this part of the lab, we will build the structure of an ally cation
1. Open a new window (“File”, “New”) and build an allyl cation. Note all three carbons are sp2
hybridized and one terminal carbon has a positive charge. Make all necessary changes and
beautify it with “Beautify” “Comprehensive”.
2. Save the molecule. Run a new experiment to calculate HOMO and LUMO of this allyl
cation. To do this, click “Experiment”, “New”, and then change the “Property” field to
“HOMO & LUMO”. Click “Start” button.
3. At the end of the calculation, close the experiment status window and the experiment
window. The optimized structure is shown on the screen.
4. Display the MO’s by clicking “View” “Show Surfaces”, and choosing one MO at a time
(HOMO has a lower # than LUMO). Rotate it so that you are looking at the molecule from
the side. Draw a picture of HOMO and LUMO for allyl cation in the following table. (pay
attention to the size of lobes of the new MO’s) Note the use of color is arbitrary and within
the same MO, one color is used for positive and the other negative sign of a wave function
(e.g. blue in HOMO can be assigned +, then green in the same MO is -) (red in LUMO is +
then gold is -, vice versa). Compare these results to those orbitals shown in 15-8 of Wade’s
textbook (under the topic of “MO’s of allylic system”).
Table 2:
Molecule
HOMO
LUMO
Calculated
From Wade Textbook,
Chapter 15 (for comparison)
5. Measure each adjacent carbon-carbon bond length and place the values directly on the
structure shown in Table 2. Are these results surprising? How could you explain them?
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Part 3: In this part of the lab, we will study the Diels-Alder reactions between a diene and a
dienophile and their HOMO-LUMO interaction
1. Build a molecule of ethylene (dienophile part of Diels-Alder reaction). Calculate its HOMO
& LUMO (follow the procedure in Part 2). Draw these MO’s in Table 3, and write down
their energy values (in electron volts, or eV). Again when drawing MO’s, different colors
represent opposite signs of a wave function.
2. Repeat the same calculation for 1,3-butadiene (diene) and place the results into the same
table.
3. The Diels-Alder reaction takes place when HOMO of the diene interact with LUMO of the
dienophile, or HOMO of dienophile with LUMO of the diene. Given the results from steps 1
and 2, can these orbitals (HOMO of one molecule and LUMO of the other) interact
constructively (same sign of orbitals interact) or destructively (opposite signs of orbitals
interact)?
4. The rate of a D-A reaction can be accelerated by lowering the energy gap between HOMO of
one molecule and LUMO of the other. This may be done by adding electron-withdrawing
groups to a dienophile and electron-donating groups to a diene. Repeat the calculations done
in steps 1 and 2 with the following molecules:
N
C
C
N (as dienophile, like ethylene above), and 2,3-dimethyl-1,3-butadiene
Note a CN (both C and N sp hybridized) group is an electron-withdrawing group while the
methyl groups in 2,3-dimthyl-1,3-butadiene are electron-donating. Record the energy value in
Table 3 of next page.
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Table 3
Molecule
H
H
HOMO picture and energy
(A) H
H
LUMO picture and energy
(B)
N
C
C
(C)
N
(D)
Based on the energy values shown above, which orbital interaction between C and D is more
important, HOMO of C with LUMO of D, or LUMO of C with HOMO of D ? (Hint: the one
with a smaller energy gap). Would D-A reaction between A and B expected to be faster or
slower than between C and D ?
Share the results with your instructor before leaving to be sure you have all needed for your lab
report.
Type up the lab report and include each of the following items:
1) Title of this experiment (make one up with your own idea)
2) Date on which this experiment was performed
3) Name
4) Class and Section
5) Purpose of the experiment
6) Introduction—Assume your readers to be students taking Organic Chemistry but who have
never had any experience with computational chemistry. The two web sites listed at the
beginning of this handout and discussion presented here should give you enough background to
write 1-2 paragraphs of introduction. Include principle of computational chemistry and what
problems/issues we are trying to address in this lab.
7) Results and Discussion—in this section, present all three tables (hand drawn structures) and
discuss the results by answering all the questions listed throughout this handout.
8) Conclusions—Make conclusions as to what this experiment had achieved and success or
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failure of this experiment. Suggest any improvement that can be done in the future.
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