CHEM 40.1: Basic Organic Chemistry Laboratory
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Module 5
Introduction to Stereochemistry
I.
Introduction
Stereochemistry is concerned with the shapes of molecules and how the differences in shape
can affect the properties and reactions of compounds. Subtle differences in molecular shape
have far-reaching consequences and it is probably in the field of molecular biology that a full
awareness of the importance of molecular shape has emerged.
Molecular structures are so frequently represented in two dimensions (2D) that thinking about
molecules in three dimensions (3D) can be considerably difficult. The purpose of this exercise is
to help organic chemistry students think in three dimensions. This exercise is designed in a
manner that would give step-by-step introduction to the basic concepts of stereochemistry. A
student, however, must first be able to
a. write and interpret molecular and structural formulas and
b. recognize that a compound with a particular Lewis structure can exist in a number of
forms called stereochemical isomers that differ only in the arrangement in space of
the bonded atoms.
Throughout the exercise students should actively participate in the learning process by
answering questions and constructing and inspecting molecular models.
II.
Learning Outcomes
At the end of this module, you are expected to attain the following competencies:
1. to be able to translate three-dimensional models on molecules to two-dimensional
representations (drawings) and vice-versa;
2. to be able to determine chirality of molecules in terms of
a. superimposability/non-superimposability with corresponding mirror image
b. the presence/absence of a simple element of symmetry such as a palne of
symmetry
c. the presence/absence of stereocenters, and
d. the presence/absence of optical activity
3. to be able to predict the existence of enantiomerism and diastereomerism in
certain compounds;
4. to be able to differentiate between
a. enantiomers and racemic mixtures and
b. enantiomers and diastereomers;
5. to recognize that
a. free rotation about C-C single bonds gives rise to different conformations,
b. conformations are continuously and rapidly interconverting, and
c. there is preferred conformation; and
6. to be able to differentiate between conformational and configurational
stereoisomers.
No part of this module may be reproduced without the written permission of the Organic Chemistry and
Natural Products Division, Institute of Chemistry, UPLB, College, Laguna.
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CHEM 40.1: Basic Organic Chemistry Laboratory
Navigation and Use of 3D Simulation
Throughout the exercise, you will actively participate in the learning process by using the
interactive 3D simulation of fundamental stereochemistry concepts and answering questions. The
simulation developed by the Stereoaisier Research Group is designed to provide students with
2D representations of molecules and visualize and manipulate them in 3D. The website can be
accessed at http://stereoaisier.com/. Click this link and you will be directed to this page:
This simulation in particular contains three parts for the learner to explore such as chirality, openchain conformations, and ring conformations. Please make sure that you have a stable internet
connection when you access this website. Otherwise, there might be a problem in loading the 3D
models.
THE DEVELOPERS
These are the faculty members and students who designed and developed the web-based
simulation for this module. You can contact the thesis students through their email address if you
have any questions about the website.
Thesis Students
Benedict S. Cardel
Andrea A. Estorninos
Jose Lorenzo C. Manansala
Email Address
bscardel@up.edu.ph
aaestorninos@up.edu.ph
jcmanansala1@up.edu.ph
Advisers
Assistant Professor Dana C. Punelas
Assistant Professor Hazel Joyce M. Ramirez
No part of this module may be reproduced without the written permission of the Organic Chemistry and
Natural Products Division, Institute of Chemistry, UPLB, College, Laguna.
CHEM 40.1: Basic Organic Chemistry Laboratory
III.
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Exercise Proper
Answer the following on a clean, sheet of paper. Write the corresponding item numbers. Before
starting, make sure you have access to the 3D simulation provided above and use it as you see
fit for this exercise. It is highly recommended to finish each tutorial per simulation in order to
maximize your knowledge for stereochemistry.
Instructions: Carefully read each part in chronological order.
Part I. CHIRALITY
A.1. Superimposability
To begin, click CHIRALITY in the homepage.
Click this to begin.
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CHEM 40.1: Basic Organic Chemistry Laboratory
You will be directed to the simulation page shown below. Familiarize yourself with the
features of this page as indicated by arrows.
Click this to go back to the homepage.
Click this to explore the tutorial.
Pictures only of the
Fischer projection of a
given compound.
3D models, can be
manipulated by dragging
Click this to view the simulation
for different compounds.
Click this to watch an
animation and to know
whether the given compound
is superimposable or not.
Click this to know
the R/S configuration.
Now, click the
and you will be directed to the page below. Go through the webpage
by scrolling downward. Make sure that you finish reading all the lessons presented in this
TUTORIAL.
Disclaimer: It is quite difficult to control the scroll down function in the tutorial and the developers
will try their best to improve this feature soon. Thank you! ☺
This indicates the number of
pages in the tutorial.
Objects that are IDENTICAL are SUPERIMPOSABLE— that is, when we imagine the two
objects “fused” together, all the corresponding parts match exactly. Continue scrolling down to
view the next page.
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CHEM 40.1: Basic Organic Chemistry Laboratory
Note: These are pictures only. ☺
Thus, an Erlenmeyer flask is superimposable on Erlenmeyer flask of the same size. On the other
hand, your left hand is not superimposable on your right hand.
Consider the pages shown below and answer the following questions. Write your answers (letter
only) on a piece of paper. You may click on the following images to view an animation when
objects are superimposed with their mirror images.
Click on these images to watch an animation.
1. Which of the following pairs of objects are identical with each other, that is,
superimposable mirror images?
I.
your left and your right hand
II.
two Erlenmeyer flasks
III.
two spheres with the same diameter
a. I only
b. II only
c. II and III only
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CHEM 40.1: Basic Organic Chemistry Laboratory
2. View your right hand in front of the mirror. Which of the following statement/s is/are
TRUE?
I.
Your left hand is the mirror image of your right hand.
II.
The reflection of your right hand is superimposable on your left hand.
a. I only
b. II only
c. both I and II
So far, we have examined certain simple relationships between the shapes of pairs of objects.
Two objects may be IDENTICAL or DISTINCT. Distinct objects may be related as mirror images
of each other or not related as mirror images at all.
Many molecules can be classified in a similar way. Many molecules are superimposable on their
mirror images, other are not. Those which are related as nonsuperimposable mirror images are
particularly important in biological systems.
A.2. PLANE OF SYMMETRY
Continue reading the TUTORIAL SECTION and consider the page below:
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CHEM 40.1: Basic Organic Chemistry Laboratory
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A PLANE OF SYMMETRY is an imaginary plane or sheet that divides the object so that one half
is the exact reflection of the other half. Consider the webpage below and answer the question.
You can click the letters to verify the correct answers.
3.
Which of the following objects are chiral?
a. A, B, F
b. B, E, F
c. A, C, D
Continue reading by scrolling down through the tutorial. Once you have reached the page shown
below, read the instruction and then go
by clicking the encircled tab.
Click this tab.
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CHEM 40.1: Basic Organic Chemistry Laboratory
You will be directed back to the simulation page. Again, familiarize yourself with the following
features.
Click this to view the simulation
for different compounds.
Pictures of the Fischer
projection of the given
compound.
3D models, can be
manipulated by dragging
1. Drag the molecule
to zoom and rotate
the 3D model.
2. Click this to know
whether the given
compound is
superimposable or not.
Click this to know
the absolute configuration.
Visualize the three-dimensional model of methane (CH4). Follow the instructions below to know
how to navigate the simulation.
Step 1. Manipulate the 3D models by rotating it and zooming in and out of the plane.
Step 2. Click the
function to watch an animation demonstrating that the object is
superimposable to its mirror image. This clearly shows that methane is ACHIRAL.
Step 3. Click the
function and this information will be displayed in your screen.
Take note that the absolute configuration refers to the spatial arrangement of the atoms of a
chiral molecular entity (or group) and its stereochemical description, for example, R or S. Since
methane is an achiral molecule, assigning an absolute configuration is not applicable.
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CHEM 40.1: Basic Organic Chemistry Laboratory
Now, do the same steps described above for chloromethane, bromochloromethane, and
bromochlorofluoromethane. Answer the following questions and complete the table below.
Compound
Has a plane of
Superimposable on its
Chiral or Achiral?
symmetry?
mirror image?
Yes
Yes
Achiral
Yes
Yes
Achiral
4.
5.
6.
7.
8.
9.
Molecules which are related as non-superimposable mirror images are called ENANTIOMERS.
Moreover, please remember that stereoisomers possess the same molecular and structural
formula but have different spatial arrangements of their atoms.
After visualizing the 3D molecules in the simulation, answer the following questions below:
10. Are enantiomers chiral?
11. Do enantiomers have the same molecular formula?
12. Does one structural formula represent both members of a pair of enantiomers?
13. Are enantiomers stereoisomers?
Assigning R or S Configuration to Chirality Centers in Molecules
Absolute configuration is the spatial arrangement of the atoms of a chiral molecular entity (or
group) and is specified by the Cahn–Ingold– Prelog R, S convention and are represented in 2D
by Flying Wedge or Fischer projection. In this section, you will learn how to assign R or S
configuration to a chiral molecule step by step.
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CHEM 40.1: Basic Organic Chemistry Laboratory
Consider the webpage shown below. Pay attention on how the 2D representations are translated
into
3D models.
Particularly, examine the flying wedge representation of
bromochlorofluoromethane and orient the 3D models exactly the same as shown below. You can
observe that the solid lines represent bonds that are in the plane of the screen, dashed
line represents bonds that extend away from the
shaped lines represent bonds oriented facing the viewer.
Cl
Br
Cl
viewer,
and wedge-
Br
H
H
F
F
Drag the molecule to rotate and zoom in or out of the page.
Click this.
Now, click the
for bromochlorofluoromethane. You should be directed to
this page. Follow the instructions to understand how to assign the absolute configuration.
1. Type the
correct
atomic number
for each atom.
2. Click this to show
the 2D structure and
3D model.
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Once GENERATE was clicked, the following page should be displayed in your screen.
•
Orient the 3D model (by dragging the molecule left or right) so that the lowest-priority
atom (#4, hydrogen atom) is projected away from you, and then assign R or S
configuration. As you can see, priorities are assigned to the four substituents, with #1
being the highest priority and #4 the lowest. Priorities are based on the atomic number.
Since bromine has the highest atomic number, it will be assigned with the highest priority
(#1), followed by chlorine (#2), fluorine (#3), and hydrogen (#4).
•
Now, trace a circle from #1 to #2 to #3. Since the direction of rotation is clockwise, the
given molecule has an R configuration. Remember that a counterclockwise circle
corresponds to the S configuration. The designation 'R’ is derived from the Latin rectus,
meaning right-handed while 'S’ is derived from the Latin sinister, meaning left-handed.
Part II. Enantiomerism, Diastereomerism and Optical Activity
For this part, you will not use the simulations, specifically from numbers 14—41. Read the
instructions and questions carefully and write your answer on your answer sheet.
One of the most important properties of chiral molecules in solution is their effect on planepolarized light. Both enantiomers rotate the plane polarized light. Substances with this property
are said to be optically active. Chiral substances have molecules that are not superimposable
on their mirror images and are optically active. Enantiomers are also known as optical
isomers.
Determine whether each of the following if optically active or not.
14. CH3CH(NH2)COOH
15. CH3CH2CHClCH3
The rotation of plane polarized light is used to observe experimentally one of the main
differences between a pair of enantiomers. One enantiomer rotates plane-polarized light
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CHEM 40.1: Basic Organic Chemistry Laboratory
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clockwise (as seen by observer), the other enantiomer, counterclockwise by the same
magnitude. Conventions used to indicate the direction of rotation of the plane of polarization
are:
• clockwise (+), dextrorotatory, d
• counterclockwise (–), levorotatory, l
For example, alanine is a chiral amino acid that has two enantiomers: (+)-alanine and (–)-alanine.
These two are optical isomers.
16. Which enantiomer of alanine rotates the plane polarized light clockwise?
Substances which do not rotate the plane polarized light are said to be optically inactive.
Determine whether each of the following aqueous solutions are likely to be optically active or
inactive.
17. a solution of ethanol, CH3CH2OH
18. a solution of (+) -alanine
19. a solution containing equimolar quantities of (+) -alanine and (–) -alanine
A mixture containing equimolar quantities of a pair of enantiomers is called a RACEMIC
MIXTURE. A racemic mixture is represented as (+) or sometimes dl, e.g. (+)-glucose or dlglucose. A racemic mixture is optically inactive.
20. How is the racemic mixture of alanine represented?
In the preceding section, we have seen that if a substance can be shown to be optically active
in solution, then we know it is chiral. However, absence of optical activity does not prove that
the substance is achiral, since a racemic mixture may be present. It is therefore also useful to
be able to “detect” molecular chirality directly from molecular shape, if necessary, with the aid
of models.
Two methods have been introduced so far. Another method that allows the direction of chirality
from molecular structure (shape) is described below. This method is useful for simple organic
compounds and easily works even without the aid of models.
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CHEM 40.1: Basic Organic Chemistry Laboratory
A carbon linked to four different groups is asymmetric and known as a tetrahedral
STEREOCENTER. The presence of at least one carbon stereocenter renders chirality to the
molecule.
21. Consider the structures above. Which of these two contains a stereocenter? Draw the
structure on your answer sheet and mark the stereocenter with an asterisk.
22. Which of these two is a chiral molecule? Explain your answer.
23. Which of these two can exist as a pair of enantiomers?
24. Draw the pair of enantiomers using three-dimensional representation.
In the preceding section, you have learned to recognize that the presence of a
stereocenter can confer chirality to a molecule. Lactic acid contains one stereocenter (marked
with an asterisk). It is a chiral molecule and therefore can exist as two pure optical isomers:
(+)-lactic acid and (–)-lactic acid.
H
CH3
C
COOH
OH
lactic acid
Now, we will consider molecules with more than one stereocenter.
dihydroxybutanoic acid:
Consider 2,3-
The molecule 2,3-dihydroxybutanoic acid is an example of a substance with two different
stereocenters. Answer the following questions:
25. Copy the structure and mark the first stereocenter with an asterisk. Encircle the four
groups attached to this stereocenter.
26. Copy the structure and mark the second stereocenter (if any) with an asterisk. Encircle
the four groups attached to this stereocenter.
The flying wedge representation is a 2D representation where the solid wedge indicates
a bond projecting up and out of the plane of the paper while a dashed wedge indicates a bond
projecting into the paper. Thus, in the structure given below, –OH and –H are projecting
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CHEM 40.1: Basic Organic Chemistry Laboratory
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towards you, the observer, while the –COOH and –CH3 groups are projecting into the paper.
(Differentiate H, OH, COOH and CH3 by using colored markers, crayons, or pens.)
Answer the following questions:
27. Copy the structure given in the previous page (the one with wedges). Label this as I.
Draw its mirror image. Label this as II.
28. Are I and II chiral?
29. What kind of stereocenters do they represent?
A compound that contains two different stereocenters can exist as four optically active
stereoisomers. The flying wedge representations of the four stereoisomers are given below:
All of the given stereoisomers of 2,3-dihydroxybutanic acid are optical isomers. Some
pairs are related as nonsuperimposable mirror images (enantiomers).
Others, called
DIASTEREOMERS, are also nonsuperimposable and are not related as mirror image.
What is the relationship between:
30. I and II?
III and IV?
31. I and IV?
II and IV?
32. I and III?
II and III?
PART III. OPEN-CHAIN CONFORMATIONS
Atoms within molecules can vibrate and are free to rotate about single bonds. This
rotation may result in the atom taking different positions relative to the rest of the molecule.
Molecular structures that are interconvertible by simple bond rotations are called
CONFORMATIONAL ISOMERS or CONFORMERS.
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CHEM 40.1: Basic Organic Chemistry Laboratory
In the homepage of the simulation, click the tab for the open-chain conformation.
Click this.
This will direct you to this page. Familiarize yourself with the features of this simulation.
different examples
degrees tab
Drag this to
rotate or zoom
in and out of
the page.
full screen
It is recommended that you go through the tutorial first before proceeding to answer the
following questions. This can be accessed by clicking the tutorial tab at the upper right corner of
the page as shown above. You may exit the tutorial once you have grasped the discussions and
proceed to the simulation proper by clicking the back to simulation tab at the upper left corner of
the page, and you will be directed back to the simulation page.
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CHEM 40.1: Basic Organic Chemistry Laboratory
Start by observing and examining the 2D representations of ethane CH3CH3 and visualize its 3D
model by rotating the object. Click the FULLSCREEN
to explore the other features of the
3D models. You may go back to the simulation page by clicking on the FULLSCREEN
again.
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CHEM 40.1: Basic Organic Chemistry Laboratory
To rotate along the carbon-carbon single bond of ethane by 60 degrees, click the degrees tab
as shown below.
rotate along the C-C bond by 60°
The two extreme conformations of ethane, the ECLIPSED and STAGGERED can be seen
by viewing along the C-C axis. Initially, the conformation of ethane is eclipsed. You can observe
that if the carbon-carbon bond in ethane rotates, there is a change in relative positions of the
different atoms. Upon rotation by 60 degrees, the conformation of ethane changed from eclipsed
to staggered. Take note that rotation about the C-C bond changes the shape of the molecule
while rotation about the C-H bond had no effect. Atoms can rotate “freely” about single bonds
as opposed to double bonds (e.g., C=N, C=N), which have restricted rotation. The ethane
molecule can adopt an infinite number of conformations according to the relative positions of the
hydrogen atoms. These conformations can be interconverted by rotating about the C-C single
bond.
Observe these conformations on your 3D models and answer the question below.
2D Representations
Conformation
Sawhorse projection
Newman projection
Eclipsed
Staggered
33. In which of the two extreme conformations are the hydrogen atoms farthest apart from
each other?
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Continue rotating the molecule along the C-C bonds by clicking the other degrees tabs
from 120o to 360o.
Click to rotate along the C-C bond by intervals of 60°.
Notice the changes in the potential energy of the ethane conformations as one methyl
(-CH3) group moves relative to the other about the C-C single bonds can be shown
diagrammatically.
The dihedral angle (or rotation angle, Φ) is illustrated as:
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CHEM 40.1: Basic Organic Chemistry Laboratory
The conformation in which the atoms are farthest apart normally has the lowest potential
energy and is referred to as the preferred conformation. Molecules are continuously and rapidly
changing from one conformation to another, but they spend most of their time in the preferred
conformation.
34. Complete the diagram in your answer sheet by indicating changes in relative potential
energy which occur during a full 360° rotation of one methyl group of ethane relative to
the other ethyl group.
The difference in the potential energy of the staggered and eclipsed conformers of ethane
is 3 kcal/mol. Because this energy is readily attained at room temperature, different
conformations of ethane cannot be isolated. An energy barrier greater than 15-20 kcal/mol is
required to be able to isolate different conformations at room temperature. Thus, the staggered
conformation of ethane has the lowest potential energy and is the preferred conformation.
In the preceding sections, you were able to navigate and use the simulation for ethane.
Now, do the same for chloroethane, 1,2-dibromoethane, and butane. Remember that these
3D models do not actually show the relative sizes of different atoms. View the model along the
carbon-carbon axis and draw the sawhorse and Newman projections of the preferred
conformation.
Conformation
2D Representations
Newman
Sawhorse projection
projection
35.
36.
preferred (most stable)
chloroethane
37.
38.
39.
40.
41.
42.
least stable
preferred (most stable)
1,2-dibromoethane
least stable
In ethane, energy differences between various conformations are mainly due to electronic
interactions between the electron pairs in the C-H bonds. In chloroethane, there are electronic
interactions between the C-H bonds and with the C-Cl bonds. Also, interactions between larger
chlorine atom and hydrogen atoms are greater than any hydrogen-hydrogen interactions.
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CHEM 40.1: Basic Organic Chemistry Laboratory
43.
20
Visualize the 3D model of 1,2-dibromoethane, CH2BrCH2Br. Which of the following
interactions will be the greatest?
a. hydrogen-hydrogen interactions
b. hydrogen-bromine interactions
c. bromine-bromine interactions
PART IV. CYCLIC CONFORMATIONS
Many important organic molecules contain rings of atoms, for example, sucrose,
chlorophyll, nicotine, etc. Rings range in size from three-membered, like cyclopropane, to those
containing more that 30 atoms. However, most cyclic compounds are made up to 5- or 6membered rings. In this exercise, only cyclohexane and its monosubstituted derivatives will be
considered.
To start, click the tab for ring conformations on the homepage. This will take you to the
simulation page.
It is recommended to go through the tutorial first, as indicated in the image above, before
answering the questions that follow. Once you have understood the discussion in the tutorial
provided, click the button at the upper-left hand corner to bring you back to the simulation.
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To begin with, examine the 3D model of cyclohexane.
44. Are there any conformations in which all carbon atoms of the ring are in one plane?
The two extreme conformations of cyclohexane are referred to as the CHAIR and BOAT
conformations. To rotate the carbon atoms and observe the conversion from chair to boat
conformation, click this arrow tab
. To visualize the other 2D representations and 3D models
(e.g. boat, and chair II), click the names below their 2D representations.
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CHEM 40.1: Basic Organic Chemistry Laboratory
45.
46.
47.
22
In which conformation are the hydrogen atoms farthest apart?
Which is the preferred conformation? Give reasons for your answer.
Which is the eclipsed conformation?
In the chair conformation, notice that there are two orientations for the C-H bonds. Bonds
that are oriented vertically are known as AXIAL bonds; the rest are known as EQUATORIAL
bonds. The axial bonds alternate above and below the ring carbons while the equatorial bonds
point away from the ring.
Consider the image above— a screenshot of one of the pages from the tutorial. Check
your understanding of axial and equatorial bonds by answering the question on the website.
Note that there are several pages from the tutorial that include questions provided with answers.
Make sure to check your understanding of the discussion by verifying your answers to the
questions.
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CHEM 40.1: Basic Organic Chemistry Laboratory
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The simulation includes other examples of molecules with their own 3D models that you
can manipulate and examine. Try to observe the conversion from chair to boat conformations
(and vice versa) for each one.
48.
What happens to the axial bonds when a chair conformation is converted to
another chair conformation?
The overall process of converting one chair conformation to another chair conformation is
known as RING INVERSION or ring flipping and is a very rapid process. The cyclohexane ring
inverts approximately 10 time a second at room temperature.
49.
50.
IV.
Show this interconversion by drawing the two chair conformations and putting a
reversible arrow between them to indicate a dynamic equilibrium.
If we have a methylcyclohexane molecule and this undergoes ring inversion, what
will be the resulting structure?
Links to Online Resources
Conformational Analysis of Ethane
(video in Khan Academic Organic Chemistry youtube channel)
https://www.youtube.com/watch?v=vOq6cwT-l2U
Conformations of Cyclohexane
(video in Khan Academy Organic Chemistry youtube channel)
https://www.youtube.com/watch?v=p9NzhA3E-70
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Natural Products Division, Institute of Chemistry, UPLB, College, Laguna.
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Drawing Chair Conformations
(video in Khan Academy Organic Chemistry youtube channel)
https://www.youtube.com/watch?v=AtK0QQYHKCk
Chair Chair Interconversion: Cyclohexane Conformation Animation
(video in DokeDJ youtube channel)
https://www.youtube.com/watch?v=bPLREpfZ63I
No part of this module may be reproduced without the written permission of the Organic Chemistry and
Natural Products Division, Institute of Chemistry, UPLB, College, Laguna.