CHEM 350, Fall 2008
Principles of Organic Chemistry I Lab
Prof. T. Nalli, WSU
Expt #1 - Molecular Modeling of Alkanes
Assigned Reading/Viewing - Lab Manual, #1, Expt 18a. Hyperchem installation
instructions. Hyperchem help tutorials noted on page 3.
Overview
Molecular models can be very helpful for the 3-D visualization of organic molecules.
The models can be manipulated (for example, bonds can be rotated) in order to mimic
the types of dynamic processes the actual molecules undergo.
Computer molecular modeling programs are not as helpful with the visualization of
molecules because the display is two dimensional. However, these programs are
capable of predicting quantitative information about the molecule, for example the
bond angles, total energy, and distances between atoms.
In this lab you will use molecular models in conjunction with Hyperchem molecular
modeling software to discover and learn about some of the most important concepts
that allow us to predict the most stable conformation(s) of an organic molecule.
Pre-lab Assignment
Install Hyperchem on your laptop using the instructions available at
http://course1.winona.edu/tnalli/f08/hyperchem%20install.html.
Some Important Definitions
Conformation - A particular molecular structure that is arrived at through single bond
rotation. Different conformations of a molecule are easily interconverted by single bond
rotation(s).
Conformer - A conformation of a molecule that corresponds to a potential energy
minimum for the molecule.
Molecular mechanics - A computational method that allows the relative energies of
different conformations of a molecule to be approximated. (Note the terms “relative” here!
The energy of a structure calculated using molecular mechanics only has meaning when
compared to similarly calculated energies for other conformations of the same
molecule.) Molecular mechanics is based on the same basic principles that chemists use
qualitatively to judge conformation stability.
Geometry Optimization – Also referred to as “Energy Minimization”. Mathematical
algorithms are available that vary the bond angles, torsion angles, and bond lengths in a
molecule, calculating the energy and continuing until a conformation that corresponds
to an energy minimum (i.e., a conformer) is found. These algorithms, by design, try not
to change the molecule in a way that increases the energy. For this reason, they are not
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guaranteed to find the overall lowest energy conformation of a particular structure (the
“global minimum”). Read more about global versus local minima in the lab manual
reading assignment.
RMS Gradient – In an energy minimization routine, the root mean square (RMS) of the
derivative of the energy with respect to the Cartesian coordinates is used as a criterion
of when to stop looking for a lower energy and accept the current value as representing
the minimum. In theory, the RMS gradient is zero when an energy minimum has been
achieved. In practice, the computer will never achieve a value of zero so we set a
minimum value for the RMS gradient when we set up a geometry optimization. In
simple terms, if we set the RMS gradient to a lower value then the computer will keep
looking longer for a “true” minimum.
Strain – Any interaction in a structure that causes it to have a higher energy is called
strain. The difference in energy between any particular conformation and the lowest
energy conformer of the same molecule is a measure of the amount of strain that
conformation possesses.
PROCEDURES
Record all data, observations, and structural drawings directly in the lab notebook as
you do this experiment. Make all models both with the Molymod kit and on the
computer in Hyperchem. Hyperchem procedures are consistently given in italics
throughout this handout.
When using the Molymod kit make sure to use tetrahedral carbon atoms (the black
balls with 4 holes!)
General Hyperchem Instructions: Complete “cookbook” instructions on how to use
Hyperchem throughout this experiment would be very difficult to put in writing and
counterproductive. You need to get a feel for how to use this program both for this lab and for
future experiments. Please view all of the tutorials circled in the screenshot below menu before
beginning the lab. You will find these under the Hyperchem help menu.
Hyperchem does not have “undo” capabilities. I strongly recommend saving each model first
thing after you have successfully constructed it.
When using Hyperchem it will be easier if all of our models look the same. Under the “Display”
menu, select Rendering and set Atom Rendering to "balls and cylinders". This will give us ball
and stick models that look very much like our Molymod kit models.
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Refer to the following figure as necessary to identify the Hyperchem tool icons.
Build
Select
Free Rotate XY Rotate Translate
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Conformations of Ethane
Staggered Ethane. Construct a model of ethane, CH3-CH3. Look straight down the C-C
bond and rotate it until the C-H bonds in front exactly bisect the H-C-H angles of the
back carbon. You now have a model of the staggered conformation of ethane. This
structure can be represented on paper in a number of ways, including wedge-dash
formulas and Newman projections (see below).
H
H
H
H
H
H
H
H
H
H
H
H
Newman projection
Wedge/Dash formula
In Hyperchem, select the Build tool and then click, drag, and release a short distance away in the
main window. Under the Build menu select “Add H & Model build”. The resulting ethane
model is already in the staggered conformation. The model can be rotated around in space much
like the Molymod model by using either the free rotate tool or the XY rotate tool.
Draw structural representations (Newman and wedge/dash) of staggered ethane in
your notebook.
Eclipsed Ethane. Rotate the C-C bond 1/6th of a turn (60) so that all of the C-H bonds
are lined up. You now have a model of the eclipsed conformation of ethane.
In Hyperchem you can rotate the C-C bond using the procedure shown in the “Using selection
to perform an internal rotation” tutorial. Make a model of eclipsed ethane in Hyperchem using
this procedure. (Hint: you will want to free rotate the molecule so that you are looking straight
down the C-C bond before you do the bond rotation).
Draw structural representations (Newman and wedge/dash) of eclipsed ethane in your
notebook.
Eclipsed vs Staggered Ethane. Observe the two ethane conformations carefully. In
which of the two ethane conformations do the sigma electrons of the C-H bonds on one
carbon come closer to the sigma electrons of the C-H bonds of the other carbon? Which
conformation would you expect to be less stable, the eclipsed or the staggered? (Think
of VSEPR theory in attempting to answer this question.)
Plot a graph of potential energy versus the angle between one of the C-H bonds on the
front carbon and one of the C-H bonds on the back carbon (the dihedral or torsion
angle). Start with the eclipsed conformation (torsion angle = 0) and go through one full
rotation (360). Indicate on the graph where each conformation would be found.
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Hyperchem will allow you to make this graph quantitative by using molecular mechanics to
estimate the relative energy of each conformation. First run an energy minimization on your
eclipsed ethane model. Under the Compute menu select geometry optimization. Use all of the
default parameters and hit OK. Observe carefully what happens to the model and record the
energy value displayed in the bottom left corner of the window.
(All energy values in Hyperchem are in units of kcal/mol. Also please note that these values are
estimates and all of the digits displayed by Hyperchem are not significant. The energy results are
probably only good to ± 0.1 kcal/mol)
Now redo the energy minimization but use a lower value (0.001) for the RMS gradient
termination condition. Record what happens in your notebook as well as the energy obtained.
Based on what you just saw do you think it would be a good idea to run future energy
minimizations with the RMS gradient set to 0.1? Discuss this with the instructor before going
on.
Redetermine the energy of the eclipsed conformation using the following procedure. First lock
the model in an exactly eclipsed conformation by using the select tool to select the 4 atoms that
define the torsion angle (H-C-C-H). Next, under the Build menu select Constrain Bond Torsion
and enter 0° (or cis). Now unselect the selected atoms by clicking with the selection tool
anywhere in the main window not on the molecule. Under the Build menu select “Add H &
Model build”. Finally run a geometry optimization with the RMS gradient set to 0.001. Record
the results in your notebook.
Conformations of Propane
From here on it is assumed that you will record all observations and data from each stage of the
experiment in your notebook! (Remember to note energy values after each geometry
optimization!) Also for all future geometry optimizations set the RMS gradient to 0.001.
Staggered Propane. Remove a hydrogen from the ethane model and add a CH3 group
in its place. You now have a model of propane. Rotate each of the C-C bonds so that
both of these bonds are staggered. A wedge/dash formula of the model should look
like the figure below.
H H
H
H
H
H
H
H
In Hyperchem use the build tool to add a carbon (click on one of the hydrogens of your ethane
model to change it to a carbon atom). Add H and Model Build and then minimize the energy as
before. You should end up with the all staggered propane conformation shown above.
Draw a Newman projection that represents this conformation of propane. Represent the
extra methyl group simply by "CH3". (Note - the Newman projection should look the
same regardless of which C-C bond you sight down.
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Eclipsed Propane. Rotate one of the C-C bonds in this model so that it is now eclipsed.
It should look like the figure below.
H
H
H
H
H
H
H
H
Draw a Newman projection that shows the conformation around the eclipsed bond.
To get to the above model in Hyperchem, you can use selection to perform rotation of the C-C
bond (like you did with ethane). Or more preferably, select 4 atoms to define the torsion angle
around one of the C-C bonds (i.e., H-C-C-H), constrain the bond torsion to 0° (Build menu),
Add H & Model Build, and then run a Geometry Optimization. (You need to unselect atoms in a
molecule before geometry optimization otherwise Hyperchem will only adjust the position of the
selected atoms.)
Eclipsed vs Staggered Propane. Plot a graph of energy versus torsion angle for one of
the C-C bonds in propane. (Assume the other C-C bond stays staggered.) Use the
energy values obtained using Hyperchem to label the scale of the y axis on the last
graph (The graph should show quantitatively the relative energies of the two
conformations.)
How much strain is present in eclipsed propane? In staggered propane?
Conformations of Butane
Remove a hydrogen from one of the end carbons of the propane model and add a CH3
group in its place. You now have a model of butane. Rotate each of the C-C bonds so
that they are all staggered and the two end CH3 groups are opposite each other. A
wedge/dash formula of the model should look like the figure below. This model
represents the anti conformation of butane. We will refer to it as conformation A.
H
H
H
H
H
H
H
H
H
H
Draw a Newman projection that shows the conformation of the bond between the
center two carbons (use "CH3" to represent each of the end carbons).
Now rotate the center C-C bond 60. This is conformation B. Draw a Newman
projection of this conformation.
Rotate the center bond another 60 to give conformation C. This model represents the
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gauche conformation of butane. Draw a Newman projection of this conformation.
Rotate the center bond another 60. This is conformation D. Draw a Newman
projection that shows the conformation of the bond between the center two carbons.
Rotate the center bond another 60° and draw a Newman projection of the resulting
structure. Is this a new conformation of butane or is it the same as one of those already
examined?
Rotate the center bond another 60° and draw a Newman projection of the resulting
structure. Is this a new conformation of butane or is it the same as one of those already
examined?
Rotate the center bond another 60° and what do you have?
Which of the above conformations do you think is the most stable (lowest energy)?
Which should be the least stable? Explain.
In Hyperchem start from scratch and make n-butane using the build tool followed by Add H &
Model Build. Minimize the energy of this model as before. Make sure that you are looking at the
anti conformation (A) by free rotating it so that you are looking at it from the side like in the
above picture and verifying that the four carbons form a zig zag pattern. If this is not the case,
start over or use Constrain Bond Torsion to set the C-C-C-C torsion angle to 180° and repeat the
model build and energy minimization.
Next use selection to rotate the central C-C bond approximately 60º to get conformation B. Run
a geometry optimization and note your results. Does the energy value obtained represent the
relative energy of B? If not come up with a procedure to get an energy value for B.
Now make a model of gauche butane, conformation C. Run geometry optimization and record the
energy. Also measure the C-C-C-C torsion angle in the minimized gauche butane. Do this by
selecting the four carbon atoms in order and noting the message that occurs at bottom left in the
Hyperchem window. (Four atoms bonded sequentially always defines a torsion angle)
Make a model of conformation D and calculate its relative energy. You will need to constrain the
C-C-C-C torsion angle to 0 before energy minimization.
Use your molecular mechanics results to plot a graph of energy versus torsion angle of
the central C-C bond in butane. Use the angle between end CH3 groups to define the
torsion angle (i.e., D= 0, C= 60, etc). Make sure the graph goes through one full
revolution of the C-C bond (goes from 0 to 360 degrees) and that it shows the relative
energies of each conformation.
The instructor will discuss the generally accepted explanation for the relative energies
of the butane conformations. This is also discussed in Chapter 4.9-4.10 of the Smith
textbook.
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Conformations of some other Compounds
Now make models of and then draw a Newman projection of the gauche and anti
conformers (around the C3-C4 bond) of each of the following compounds. Find the
relative energy of each conformer using Hyperchem molecular mechanics and use this
to determine how much excess strain is present in the gauche conformer. Also measure
the torsion angle around the central bond (defined by selecting atoms C2-C3-C4-C5) in
the gauche conformer of each of these.
hexane
2,5-dimethylhexane
2,2,5,5-tetramethylhexane
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Post-lab Questions
1. Compare the difference in energy between the eclipsed and staggered conformations
of ethane to that of propane. Explain.
2. Which of the conformations examined for butane are properly referred to as
“conformers”? Explain.
3. Explain why eclipsed conformations gave very different results when minimized
with the RMS gradient set to a relatively large value of 0.1 versus having this parameter
set to 0.001.
4. Propane has another possible conformation where both C-C bonds are eclipsed. (a)
Predict the amount of strain present in this conformation. (b) This “eclipsed-eclipsed”
conformation is certainly much less important than the two conformations we did
examine in lab. Why is this?
5. The lowest energy conformation of butane is the anti, so why does the Hyperchem
program geometry optimization sometimes terminate with the gauche conformer being
found? In other words, when you start with the molecule in a gauche conformation and
run geometry optimization you end up with gauche. Why?
6. Compare your graph of energy vs bond rotation in butane to that on page 137 of
Smith. Also construct a table similar to Table 4.3 in Smith in which you present your
results for the various strain energies alongside the Smith values. How do your results
compare quantitatively to the book data? Propose explanations for any differences.
7. What was the torsion angle between the methyl groups found in the optimized
gauche butane? The textbook states that the torsion angle for gauche butane is 60°.
Think carefully and try to explain why the value predicted by molecular mechanics is
different.
8. Make a table or chart that compares the difference in energy (i.e., the strain) between
the gauche and anti forms of butane, hexane, 2,5-dimethylhexane, and 2,2,5,5tetramethylhexane. Explain both the general trend seen and the detailed nature of the
trend – is it linear, exponential…? (Hint: all of these molecules are of the form, R-CH2CH2-R with butane having R = Me, hexane having R = Et, 2,5-dimethylhexane having R
= i-Pr, and 2,2,5,5-tetramethylhexane having R = t-Bu).
Note: The simple alkyl groups have standard abbreviations, which I am introducing to
the class using this question:
Methyl = “Me” = CH3;
Ethyl = “Et” = CH3CH2
Isopropyl = “i-“Pr = (CH3)2CHtert-butyl = “t-Bu” = (CH3)3C-
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