CHEM 350
Principles of Organic Chemistry I Lab
Prof. T. Nalli, WSU
Expt #3 - Molecular Modeling of Cycloalkanes
Relevant Reading – Smith, Chapter 4.2, 4.5, 4.11-4.13. Lab Manual, #1, Expt 18b.
Handout for Expt 1.
Overview
Cyclic structures present conformational complexities not present in acyclic molecules.
In this lab you will use models and Hyperchem modeling software to explore the
conformations of some cyclic alkanes, especially cyclohexane and its mono- and disubstituted derivatives.
Definitions
Strain - Any factor that increases the potential energy of a molecule.
Torsional Strain - Strain associated with an eclipsed single bond.
Steric Strain - Strain due to two atoms being too close to each other in space. If the
distance between the atoms is less than the sum of the Van der Waal's radii of the atoms
then there is steric strain.
Angle Strain - Strain due to bond angles in a molecule not being able to attain ideal
values (i.e., the values predicted by VSEPR theory). The strain results from a
combination of extra electron pair repulsion (bonding electron pairs too close) and/or
poor orbital overlap resulting in weak, bent bonds.
Ring Strain - The strain associated with a cyclic structure. This could be due to one or
more of the three fundamental types of strain, torsional, steric, and angle.
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 instructions are consistently given in italics
throughout this handout. Remember to record the energy after every geometry
optimization.
General Guidelines for Examining Models
We are particularly interested in detecting the types of and total amount of strain
present in a particular structure. Since there are only three types of strain, we check for
each, one at a time:
 Torsional Strain. Sight directly down each C-C bond in the molecule to see if any
of them are eclipsed or partially eclipsed. (By partially eclipsed we mean not
perfectly staggered.) On the computer we can check this quantitatively by
checking torsion angles in our optimized molecules. In Hyperchem simply select


any 4 atoms in a row and the torsion angle is displayed at bottom left. Torsion
angles that deviate significantly from 60, 180, or 300 degrees indicate eclipsing
interactions are present and therefore torsional strain.
Steric Strain. Use a space-filling model and check to see if there are any atoms
not bonded to each other that are “bumping” into each other. In Hyperchem you
can measure the distance between atoms that appear close by selecting them and
observing the message at bottom left. Distances closer than the sum of the
Vanderwaals radii of the two atoms would bring about steric strain. For
hydrogen the VDW radius is 1.2 Ǻ so when two hydrogens are closer than 2.4 Ǻ
to each other then there is steric strain present. (Two hydrogens attached to the
same carbon are always closer than this so this rule does not apply in this case.)
Angle Strain. Ball and stick model kits use balls (atoms) with predefined “ideal”
bond angles. Therefore, when a molecular structure requires non-ideal bond
angles the sticks (bonds) are forced to bend. Inspect your models for the presence
of bent bonds as an indication of angle strain. In Hyperchem you can measure
the bond angles by selecting 3 atoms in a row (two bonds to a central atom) and
note the message that appears at bottom left. Bond angles that deviate
significantly from those predicted by VSEPR would indicate the presence of
angle strain.
Conformations of Cyclohexane
1. The Chair
Construct a model of cyclohexane by joining six carbons in a ring and then adding two
hydrogens to each carbon. First force the six carbons all lie in one plane. Note your
observations carefully on this hypothetical planar form of cyclohexane.
You can make planar cyclohexane in Hyperchem by first making a ring of six carbon atoms the
Add H & Model Build. Then select four carbons in a row and constrain the torsion angle
(Build menu) to be 0° (cis). Unselect (right click on it) the first carbon of the 4, select the next
carbon down (#5) so that you again have 4 in a row selected and again constrain the torsion
angle to 0° again. Repeat the last sentence once more. Unselect all atoms and do the Add H &
Model Build. Use molecular mechanics to determine the relative energy of this hypothetical
form of cyclohexane (run a geometry optimization – you will probably need to use a relatively
high RMS gradient setting).
By rotating some of the bonds you should be able to make your cyclohexane model look
like the figure below. The model should sit firmly on the desktop with three hydrogens
serving as legs. This model represents the chair conformation of cyclohexane.
H
H
H
H
H
H
H
H
H
H
H
H
Start from scratch in Hyperchem. Again construct a ring of six carbons, then Add H & Model
Build and you should have a model of cyclohexane in the chair conformation. Minimize the
energy and record the relative energy in your notebook.
Examine the cyclohexane chair conformation carefully and practice drawing it. (The
instructor will present some methods for helping you master this.) Next look for
“strain” in the molecule using the General Guidelines above. What types of strain if any
does cyclohexane possess?
Note that the cyclohexane chair is highly symmetrical. How many ways can you pick it
up rotate it in space (less than a full 360°) and then put it back down so that it was
indistinguishable from the way it looked when it was originally sitting there? How
many planes of symmetry does it possess?
Also note that three of the hydrogens point straight up and three point straight down.
These hydrogens are said to be in axial positions. (Imagine the ring as a wheel. These
hydrogens point out in the same direction as the axis of the wheel would.) The other six
hydrogens radiate outward along the perimeter of the ring. These hydrogens are in
equatorial positions. If you numbered the six carbons of the ring, which carbons would
have axial hydrogens that are on the same side of the ring? Once again, draw the chair
conformation of cyclohexane and this time label all of the hydrogens as equatorial (eq)
or axial (ax).
2. The Boat
By grasping one of the carbons with an axial hydrogen pointing down and forcing it to
point up (bond rotations are required), you should be able to get your model to look
like a boat. (See figure below.) This conformation of cyclohexane is referred to as the
boat.
boat
To make the boat conformation in HyperChem, select the four carbon atoms that make up the
seat of the chair. Under the Select menu, choose Name Selection and Plane. Deselect all atoms
and then select one of the two out-of-plane carbon atoms and its two hydrogen atoms. In the Edit
menu, select Reflect. Optimize the structure and you should have the boat.
Look carefully for strain in the boat conformation using the methods outlined
previously. Record all observations and data in the notebook. Depict any strain you
find with a structural drawing, e.g., a Newman projection for torsional strain.
Other conformations of cyclohexane include the half chair and the twist conformations:
half chair
twist
3. The Twist
The twist (also called the “twist boat”) can be arrived at by starting with the boat,
grasping the carbons that would represent the bow and stern of the boat, and pulling
them slightly away from each other and in opposite directions with respect to the plane
of symmetry which they lie in. (See figure below).
The boat is known to represent a potential energy maximum, therefore, one should be able to run
a geometry optimization on it in HyperChem and end up with the twist conformer. However, the
various minimization algorithms have a difficult time finding “the way down” (perhaps for the
same reasons you probably found it difficult to manipulate the physical boat model and make it
into a twist.) Still it should be possible to get HyperChem to find the twist starting from the boat
simply by setting the RMS Gradient low enough and/or changing the optimization algorithm.
Once you have the twist make sure to record its energy ad well as the exact method by which you
arrived at it.
Look carefully for strain in the twist conformation using the same process as before.
Record all observations and data in the notebook. Depict any strain you find with a
structural drawing, e.g., a Newman projection for torsional strain.
4. The Half Chair
The half chair can be arrived at by stopping halfway on the way from the chair to the
boat. At this point, five of the carbons lie in the same plane. Make a model of the halfchair.
Arriving at the half chair conformation of cyclohexane using this software is difficult so use the
one in the file that the instructor emails you. Click File then Open and double click on the
halfchr.hin file in the folder which contains your email attachments.
Look carefully for strain in the half chair conformation using the same process as before.
Record all observations and data in the notebook. Depict any strain you find with a
structural drawing, e.g., a Newman projection for torsional strain.
Determine the relative energy of the half chair by selecting Compute and Single Point. Now
run a geometry optimization on the half chair. What conformation do you end up with?
Conformations of Monosubstituted Cyclohexanes
For the remainder of the lab consider chair conformations only.
Remove an equatorial hydrogen from the cyclohexane model and add a CH3 group in
its place to form methylcyclohexane. In Hyperchem start with the cyclohexane chair, and
click on one of the equatorial hydrogens with the build tool. Add H & Model Build and run an
energy minimization to get the desired model.
Neatly draw the structure represented by the model.
Now grasp and invert any carbon (C-1) to form a boat conformation. Then take C-4 and
invert it to remake a chair conformation. This process inverts the chair conformation
and is called chair flipping (See figure below).
Flipping the chair to the boat and then flipping the boat to the other chair is nearly impossible
using this software. The instructor will demonstrate these ring flips using a physical model and
a computer animation.
Neatly draw the structure represented by this model. Generalize as to what chair
flipping does to substituents in terms of their equatorial/axial status.
Make a model of the chair-flipped form in Hyperchem by simply starting with a new cyclohexane
chair and this time click on one of the axial hydrogens with the build tool, then Add H & Model
Build and run an energy minimization.
Notice that chair flipping is accomplished easily by single bond rotations and so
happens very rapidly at room temperature (like any conformational interconversion).
Observe both chair conformations of methylcyclohexane looking for strain. Record your
observations using structural diagrams as appropriate to show any strain present.
Which chair conformation of methylcyclohexane is more stable? Why?
Conformations of Disubstituted Cyclohexanes
trans-1,2-Dimethylcyclohexane
Starting with the above model in the chair conformation with the methyl group
equatorial, replace the equatorial hydrogen on an adjacent ring carbon (C-2) with a
second methyl group. Force the ring to be planar for a moment and verify for yourself
that the methyl groups are indeed trans to each other. Look carefully for strain
interactions in this model and note your observations.
In Hyperchem start with chair cyclohexane, and use the build tool to change equatorial
hydrogens on adjacent carbons into carbon atoms. Add H & Model Build and run an energy
minimization.
Flip the ring to its other chair conformation. Observe the positions of the methyl groups
now. Did the methyl groups’ stereochemical relationship (i.e., cis or trans) change?
Again, look carefully for strain interactions in this model and note your observations.
Which of the two chairs do you think is more stable? Explain.
Make a model of the flipped chair in Hyperchem and run an energy minimization.
Check your answer to the previous question against the molecular mechanics results
(the relative energies) for the two chair forms. If it does not agree then revisit the
question and figure out where your prediction went wrong.
cis-1,2-Dimethylcyclohexane
Now make a model of 1,2-dimethylcyclohexane with one of the methyl groups in an
equatorial position and the other in an axial position. Again, force the ring to be planar
for a moment in order to prove to yourself that the methyl groups are indeed cis. Look
for strain and note your observations.
As before build this model in Hyperchem and run an energy minimization.
Flip the ring to its other chair conformation. Did the methyl groups’ stereochemical
relationship (i.e., cis or trans) change? Again, look for strain and note your observations.
Which of the two chairs do you think is more stable? Explain. It is unnecessary to build
this model in Hyperchem. Why?
1,3- and 1,4-Dimethylcyclohexane
Now make a model of cis-1,3-dimethylcyclohexane. Examine ring flipping and draw
both chair conformations. Observe each carefully for strain interactions. Which chair
should be more stable? Why? Use Hyperchem to test your prediction. (Build models of
both conformations, run energy minimizations on each, and compare the resulting
steric energies.)
Repeat the previous paragraph for trans-1,3-dimethylcyclohexane, cis-1,4dimethylcyclohexane, and trans-1,4-dimethylcyclohexane.
Conformations of some other Substituted Cyclohexane Rings
There are two stereoisomers of 1,3,5-trimethylcyclohexane, cis-trans-trans and all-cis.
CH3
H3C
CH3
CH3
all-cis
H3C
CH3
cis-trans-trans
Which isomer is more stable? (Make models to make sure!). Draw the molecule in its
most stable conformation.
Make a model of cis-1-bromo-4-tert-butylcyclohexane. In the most stable conformation
of this compound what type of position does the bromine find itself in? Why? Draw the
molecule in its most stable conformation.
Compared to the difference in stability between alternative chair conformations of the
other compounds examined in this experiment, the difference in stability between the
two chair conformations of cis-1-bromo-4-tert-butylcyclohexane is quite large. Explain
why.
Conformations of some other Cycloalkanes
Make a model of cyclopropane. Are there multiple conformations of the cyclopropane
ring possible like there are with cyclohexane? Identify all strain interactions present in
cyclopropane. Is this a particularly stable molecule?
Make a model of cyclopentane. Can you find a conformation of this ring that is strainfree? Identify the type of strain present in all possible conformations of this molecule.
Post-Lab Questions
1. Draw an energy diagram showing a cyclohexane chair flip. Go from a chair to the half
chair to the twist and then back again to the half chair and the other chair. The half chair
and boat conformations are not properly referred to as “conformers”. Why not?
2. Which isomer of dimethylcyclohexane is the most stable? Rank all six isomers
according to relative stability. Explain thoroughly.
3. Indicate the preferred position (axial or equatorial) of the bromo substituent in each
of the following.
a. trans-1-bromo-4-tert-butylcyclohexane
b. cis-1-bromo-3-tert-butylcyclohexane
c. trans-1-bromo-3-tert-butylcyclohexane
d. cis-1-bromo-2-tert-butylcyclohexane
e. trans-1-bromo-2-tert-butylcyclohexane
f. 1-bromo-1-tert-butylcyclohexane