Lab 3: Molecular Structures
Introduction
There are over a million known organic compounds. The chemical and physical properties
depend on the elements present and their order of arrangement. The representation of the bonding
in molecules can be represented by the Lewis dot structure.
The molecular formula of a molecule may represent the composition of more than one molecule.
For example, the molecular formula, C2H6O2, represents two different compounds: CH3CH2OH
(ethanol) and CH3OCH3 (dimethyl ether). These two compounds possess different chemical and
physical properties. They are isomers (have the same chemical formula but different properties).
The formulas for ethanol and dimethyl ether are referred to as condensed structural formulas
because information is given on the connectivity of the atoms.
Structural isomers are compounds with the same atoms but one or more of the bonds are
different. Stereoisomers are compounds with the same atoms and same bonds but the spatial
arrangements of the atoms are different.
The purpose of this lab is to use molecular models to clarify the theoretical concepts of covalent
bonding and molecular structure. Molecular models are designed to reproduce molecular
structures in three dimensions. If models are correctly assembled, many subtle feature
concerning shapes of molecules (such as dipole moment, polarity, bond angle and symmetry) will
become clearer.
Each student will be supplied with a molecular model set. Familiarize yourself with the
components of the molecular model set with the help of the following tables:
Type
Short Gray (stiff)
Long Gray (flexible)
Colour
Atom
White
Black
Hydrogen
Carbon
Red
Blue
Green
Orange
Purple
Oxygen
Nitrogen
Chlorine/Flourine
Bromine
Iodine
Table 1: Bonds
Use
Single Bonds
Double and Triple Bonds
Table 2:
Number of
Holes
1
4
5
2
4
1
1
1
Length (mm)
30
45
Atoms
Electron-pair
Geometry
Tetrahedral
Trigonal bipyramidal
Angular or bent
Tetrahedral
Maximum # Bonds
in Neutral Molecule
1
4
2
3
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The colour-coded atoms contain from one to five holes drilled at the appropriate bond angles for
angular, tetrahedral and trigonal bipyramidal geometries. By leaving some holes vacant, linear,
trigonal pyramidal, trigonal planar and other molecular geometries can be obtained as well. The
short gray lines are used as single bonds in ball-and –stick models in which the atoms are well
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separated from one another. This makes it easier to see the relative positions of the atoms and to
relate a model of a compound to its structural formula. The long gray links are used to construct
double and triple bonds or highly strained single bonds. The sizes of the major atoms (H, C, O,
and N) correspond closely to actual atomic dimensions.
The models can only be used to illustrate bonding as lone pairs are left out.
Using the models, proceed through the following exercises, answering the question on the report
sheets. The report sheet questions must be answered independently. It is up to the student to
make sure they understand the various concepts during the lab.
Do not mix up the kit parts with a different set.
Part 1 – Covalent Bonding and Molecular Structures
You will construct models of a variety of inorganic and organic molecules and then answer
questions on the report sheet. For each central atom, choose a ball in which the number of holes
equals the total number bonding and non-bonding electron pairs around that atom. Use valence
shell electron-pair repulsion (VSEPR) rules to predict the molecular geometries. Sketches should
be drawn using dash-line-wedge notation to impart a 3-dimensional representation. By this
notation, a solid line represents a bond in the plane of the paper, a wedge represents a bond
coming out of or in front of the plane of paper, and a dashed line represents a bond going into or
behind the plane of paper. For example, methane, CH4, appears as:
H
C
H
H
H
Complete the table on the report sheet for each molecule or ion. You will be required to:

Draw the correct Lewis structure with electrons and any resonance forms.

Construct a molecular model for the compounds. Resonance structures require only one
model.

Sketch the model, using dashed-line-wedge notation.

Assign organic functional groups from table 1(Section 1B)

Indicate the following for each Lewis structure:
o Hybridization on central atom(s)
o Electron pair geometry and overall molecular geometry
Remember, the placement of the electron pairs determines the structure,
but the name of the molecular geometry is based on the positions of the
atoms
o Polarity
Polar means that the molecule has a net dipole
Non-polar means that there is no net dipole, either there are no dipoles
present or that they cancel our resulting in no net dipole
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Table 3: Some Important Organic Functional Groups
Substance
Functional Group
Substance
R
Amide
(RCONH2)
Alcohol
(ROH)
OH
Functional Group
O
R
C
NH2
O
Aldehyde
(RCOH)
R
Amine
(RNH2)
C
R
NH2
H
O
R
Alkane
Carboxylic Acid
(RCOOH)
H
R
R
Alkyl Halide
OH
O
Ester
(RCOOR’)
C
R'''
Alkyne
C
R'
C
Alkene
R
R
C
R''
C
C
R
X
R
Ether
(ROR’)
R'
O
O
R'
R'
O
Ketone
(RCOR’)
R
C
R'
R = rest of molecule
Part 2 – Bond Rotations and Conformations
On paper a molecule may appear to be static but even solids undergo atomic vibrations due to
kinetic energy. Polymers can undergo bond rotation which has an effect on their packing structure
and thermal properties (i.e. glass transition temperature and melting point). When bonds on a
molecule rotate, this is known as a change in the molecular conformation. Some conformations
are higher energy than others. For example, polyethylene chains tend to adopt a zig-zag
conformation for the carbon-carbon backbone because this is the lowest energy arrangement.
H H
H
HH
H H
H
C
C
C
C
C
C
H H
H
C
C
H
H
HH
H
A segment of a polyethylene chain
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Procedure
1. Construct a model of ethane (CH3CH3). Look down the carbon-carbon bond and rotate the
carbon-carbon bond until the hydrogens are lined up behind each other. This in known as the
eclipsed conformation. Rotate the bond until the hydrogens form a 60° angle (known as the
dihedral angle). This is the staggered conformation.
2. Construct a model of cyclopropane (C3H6). Notice how the links must be bent to form the
three-membered ring. Such rings are said to be strained.
3. Now construct a model of cyclohexane. Rotate and rearrange the bonds to produce the boat
conformation and identify the “flagpole” hydrogen atoms on the report. Convert the boat to a
chair conformation and observe the axial and equatorial hydrogen atoms.
Part 3 – Structural and Geometric Isomers
By using models, one can easily construct a number of molecules for one molecular formula. By
comparing the models with each other, identical molecules can be eliminated until the correct
number of molecular structures can be determined.
For example, the molecular formula C3H6 represents only two molecules that can be constructed.
H
C
H
C
H
H
H
H
Propylene
H
C
C
H
H
C
H
H
C
H
Cyclopropane
Procedure
1. Construct a model of propane (C3H8). Examine your model of propane and note how many
indistinguishable hydrogen atoms (hydrogen atoms that cannot be placed in the same location
via simple rotation of the molecule) are present in propane. Construct a model of
chloropropane (C3H7Cl). How many isomers of chloropropane exist? Sketch them on the
report sheet.
2. If a hydrogen atom is replaced with chlorine on chloropropane, how many isomers of
dichloropropane (C3H6Cl2) exist? Sketch them on the report sheet.
3. Determine for yourself that there are five isomers with the formula C3H5Cl3. Sketch them on
the report sheet.
4. Construct a model of ethene (ethylene, C2H4). Note the rigidity of the molecule and that there
is not rotation about the carbon-carbon double bond as there is in ethane or cyclohexane.
Construct models to determine how many isomers there are that correspond to formulas
(a) C2H3Cl and (b) C2H2Cl2. Draw the different isomers on the report sheet.
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Part 4 – Optical Isomerism
Objects that are not superimposable on its mirror image are called chiral, such as the left and right
hands. An achiral object is superimposable on its mirror image.
Optical active compounds are molecules that have non-superimposable mirror images (i.e. they
are chiral molecules). Optical isomers are steroisomers that rotate the polarized light. One
isomer will rotate the polarized light clockwise and the other will rotate it counter clockwise.
In this part the experiment, the more subtle differences in another type of stereoisomer, the
optical isomer, will be studied.
Procedure
1. Build two identical models of CH2ClBr. Looking at only one of the models for now, note
the plane of symmetry that is defined by the C, Cl and Br atoms. This molecule has an
internal plane of symmetry and will be superimposable on its mirror image. Check this fact
by lining up the two models so that the atoms are reflected through an imaginary mirror that
runs between them. The two molecules are mirror images. Try putting one molecule on top
of the other such that all the atoms line up. Are the two molecules superimposable? Is
CH2ClBr chiral or achiral? Does interchanging any two atoms (Cl, Br or H) create a new
molecule?
2. Using a purple ball to represent fluorine, construct two models of CHClBrF, one that is a
mirror image of the other. Check for an interior plane of symmetry. Are these two
molecules superimposable? CHClBrF is chiral.
3. Construct models of the compounds given on the report sheet and answer the questions.
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Lab 3: Molecular Structures
Name:__________________________
Date_____________
Reminder: the models do not show lone pair electrons, only molecular shape. Show the lone pair electrons in the Lewis structure.
Part 1 – Covalent Bonding and Molecular Structure
Molecule or Ion
3D Sketch of
Model
(dash-line-wedge)
Atom
Hybridization
C ________
CHCl3
C ________
CH2O
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Lewis Struture
(include resonance
structures if present)
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Electron Pair
Geometry
Bond Angle of
Central Atom
Molecular
Geometry
Polarity
Molecule or Ion
Lewis Struture
(include resonance
structures if present)
3D Sketch of
Model
(dash-line-wedge)
Atom
Hybridization
NO2¯
N ________
HCCH
C ________
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Electron Pair
Geometry
Bond Angle of
Central Atom
Molecular
Geometry
Polarity
Section 1B – Use Table 1 for a list of functional groups
Molecule or Ion
Lewis Struture
(include resonance
structures if present)
3D Sketch of
Model
(dash-line-wedge)
Hybridization of
Underlined Atom
CH3OH
C ________
CH3NH2
C ________
CH3COOH
C ________
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Functional Group
(Table 3)
Bond Angle of
Underlined Atom
Molecular
Geometry of
Underlined Atom
Strongest
Intermolcular
Force
Molecule or Ion
Lewis Struture
(include resonance
structures if present)
3D Sketch of
Model
(dash-line-wedge)
Hybridization of
Underlined Atom
CH3OCH3
O ________
CH3COCH3
C ________
CH3CHCH2
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C ________
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Functional Group
(Table 1)
Bond Angle of
Underlined Atom
Molecular
Geometry of
Underlined Atom
Strongest
Intermolcular
Force
Part 2 – Bond Rotation and Conformers
1.
Ethane: Circle the conformation of lower energy. Name both conformations.
________________
2.
_____________________
Cyclopropane:
I)
What is the hybridization of C in cyclopropane?
______________
II) What is the ideal bond angle for this hybridization?
______________
III) Based on the bond angle, do you think cyclopropane is stable relative to larger hydrocarbon rings.
3
Cyclohexane: Draw the “flagpole” hydrogens on the boat conformation of cyclohexane:
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Part 3 – Structural and Geometric Isomers
How many groups of indistinguishable hydrogen atoms are present in propane, C3H8?
________________
Sketch of Isomer(s)
C3H7Cl
C3H6Cl2
C3H5Cl3
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How many groups of indistinguishable hydrogen atoms are present in ethylene, C2H4?
________________
How many groups of indistinguishable hydrogen atoms are present in chloroethylene, C2H3Cl?
________________
Sketch of Isomer(s)
C2H3Cl
C2H2Cl2
(Hint 3 isomers)
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Part 4 – Optical Isomerism
Circle the correct answer
1. Bromo-chloro-methane:
Are the two molecules of CH2ClBr superimposable on each other?
Yes
No
Is CH2ClBr chiral or achiral?
Chiral
Achiral
Does interchanging an H atom with either the Cl or Br make a molecule identical to the original molecule?
Yes
No
2. Bromo-chloro-fluoro-methane
Are the two molecules of CHClBrF superimposable on each other?
Yes
No
Is CHClBrF chiral or achiral?
Chiral
Achiral
Does interchanging an H atom with either the Cl or Br make a molecule identical to the original molecule?
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Yes
No
Gylcine
H2NCH2COOH
Alanine
CH3NH2CHCOOH
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(complete)
Optical Active?
(yes/no)
Sketch of Mirror Image
Number of
Chiral Centres
Sketch
(Given)
Internal plane of
symmetry?
(yes/no)
Compound
Is Mirror Image
Superimposable?
(yes/no)
3. Construct the following molecules and complete the table:
Conclusions:
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