Lab#7
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Adelphi University *
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109
Subject
Chemistry
Date
Dec 6, 2023
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Molecular Models
Learning outcomes:
By the end of this activity, students will be able to:
●
Explain the difference between paired and unpaired electrons in a Lewis Dot Structure of an
atom.
●
Determine the number of bonds an atom can form using a Lewis Dot Structure of an atom.
●
Draw a Lewis Structure of a compound when provided the formula of the compound, based
upon the number of bonds each atom can form.
●
Explain the difference between Lewis Structures and Stick Structures in how they represent a
molecule’s structure.
●
Define what a functional group is and their function in structures.
●
Recognize the following functional groups when provided a structure in Lewis Structure format
or Stick Structure format:
○
Alcohol
○
Primary Amine
○
Quaternary Amine
○
Carboxylic Acid
○
Carboxyl
○
Carboxylic Acid Salt
○
Thiol
○
Phenyl
○
Phenol
○
Ester
○
Amide
Model 1: Review - Lewis Dot Structures and Bonding
Core valence models and Lewis Dot structures are both used to portray an atom, however they differ in
terms of what information is being presented. Figures 1A-1D below show oxygen on the periodic table,
the core valence model for oxygen, the Lewis Dot structure of oxygen and a molecule of water showing
how many bonds oxygen forms.
Figure 1A: Oxygen on the periodic table
Figure 1B: Core valence model of oxygen
Figure 1C: Lewis Dot structure of an oxygen atom
Figure 1D: Lewis Structure of a water molecule showing oxygen bonding
Using Figures 1A-1D, answer the following questions:
1.
According to the fig.1B, Core Valence Model of oxygen, how many valence electrons does oxygen
have?
1
2.
Consider the placement of oxygen on the periodic table. How does this quantity of valence
electrons relate to the location of oxygen on the periodic table?
3.
Examin fig. 1C, how many electrons are being represented in the Lewis Dot Structure?
4.
Based upon your answers for questions 1 and 3, what is being represented by the dots in a Lewis
Dot Structure.
5.
In a Lewis Dot structure you have pairs of electrons and unpaired electrons. Paired electrons are
sides of your Lewis Dot structure that have 2 dots forming a pair, whereas unpaired electrons are
when you have a side of the Lewis Dot structure with 1 dot.
a.
How many pairs of electrons does the Lewis Dot structure of oxygen have?
b.
How many unpaired electrons does the Lewis Dot structure of oxygen have?
6.
Compare Figures 1C and 1D, the Lewis Dot of oxygen and oxygen in a water molecule.
a.
How many bonds did oxygen form with other atoms in the water molecule?
b.
Which electrons, paired or unpaired, did the oxygen use to form the bonds with the
other atoms?
c.
Based upon your answer for 6 a and b above, how can you predict the number of bonds
an atom will form from the Lewis Dot Structures?
2
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Model 2: Representing Molecules: Lewis Structures and Stick Structures
Lewis Structures and Stick Structures are two ways in which the structure of a molecule can be
represented, however these two representations differ in how much information is being presented.
Below is the molecular formula and the Lewis Structure and Stick Structure of Propane.
Molecular Formula of Propane: C
3
H
8
Figure 2A: Lewis Structure of Propane
Figure 2B: Stick Structure of Propane
Use the molecular formula and Figures 2A and 2B to answer the following questions.
1.
Draw the Lewis Dot structures for the following atoms:
a.
Carbon
b.
Hydrogen
2.
Based upon the Lewis Dot structures you drew above, determine the number of bonds each of
the following atoms would form:
a.
Carbon
b.
Hydrogen
3.
Examine the Lewis Structure of Propane in Fig. 2A:
a.
Is each carbon fulfilled with the number of bonds determined in question 2 above?
b.
Is each hydrogen atom fulfilled with the number of bonds determined in question 2
above?
4.
Compare the Lewis structure of propane, Fig 2A, to the molecular formula of propane. What
does the Lewis Structure show you that the molecular formula does not?
3
5.
The Lewis Structure in Fig 2A and the Stick Structure in 2B are both representing propane with
the molecular formula C3H8. Compare the Stick structure to the Lewis Structure to see the
difference in representations.
a.
What element is being represented by the ending points of each line and the
intersection point of the lines?
b.
What do each of the lines in the stick structure represent?
c.
What element is not shown or represented at all in this stick structure?
6.
Summarizing the information: Complete the table below to summarize what is being
represented by a molecular formula, lewis structure and stick structure.
Table 1: Summarization of Molecular Representations
Molecular
Representation
What is being shown in this representation of the molecule?
Molecular Formula
Lewis Structure
Stick Structure
4
Figure 2C: Stick Structure of an organic molecule
7.
Examine the Stick Structure in Fig 2C above. Compare this to the stick structure in Fig 2B.
a.
What element symbols are never written in a stick structure?
b.
What element symbols should always be written in a stick structure?
c.
When is the symbol for hydrogen written?
d.
When is the symbol for hydrogen not written?
5
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Model 3: Modeling Organic Molecules - Isomers and Hydrocarbons
Organic Chemistry is the study of carbon containing compounds. The most common elements found in
organic molecules are shaded in the periodic table below:
1A
2A
Group
3A
4A
5A
6A
7A
8A
H
He
Li
Be
B
C
N
O
F
Ne
Na
Mg
Al
Si
P
S
Cl
Ar
K
Ca
Sc
Ti
V
Cr
Mn
Fe
Co
Ni
Cu
Zn
Ga
Ge
As
Se
Br
Kr
Rb
Sr
Y
Zr
Nb
Mo
Tc
Ru
Rh
Pd
Ag
Cd
In
Sn
Sb
Te
I
Xe
Figure 3: Partial periodic table highlighting elements common to organic chemistry
Hydrocarbons are molecules composed of carbon and hydrogen atoms in a long chain that can be
branched or unbranched. There are two classes of hydrocarbons that we will be investigating: alkanes
and alkenes. Alkanes and alkenes are the main component of fats and fatty acids.
●
Alkanes
: also known as saturated hydrocarbons, are hydrocarbons that contain only
carbon-carbon single bonds within the chain.
●
Alkenes
: also known as unsaturated hydrocarbons, are hydrocarbons that contain 1 or more
carbon-carbon double bonds
We will be using molecular modeling kits to help observe the shape of the hydrocarbon molecules we
are going to observe. Model kits contain different colored spheres to represent different atoms and two
different types of connectors:
●
Carbon – black
●
Hydrogen – white
●
Oxygen – red
●
Nitrogen - blue
●
Single bonds –
short
grey connectors
. Use 1 to represent a single bond.
●
Double bonds – long grey flexible connectors.
Use two between the same 2 atoms to represent a
double bond.
Isomers of Alkanes:
1.
Obtain 15 carbon atoms, a handful of single bond connectors and a handful of hydrogen atoms.
Use beakers for organizing your atoms and bonds so they don’t end up all over the table, floor
and sinks.
6
2.
Using 5 of the carbon atoms you obtained, connect the 5 carbon atoms in a straight chain using
single bond connectors.
3.
Fill in the remaining holes on the carbon atoms by connecting a hydrogen atom to each hole
using single bond connectors.
4.
You have now built the ball and stick model of the hydrocarbon called PENTANE. Fill in table 2A
below based upon your structure of pentane.
Table 2A: Pentane Structure
Molecular
Formula
Picture of Model Kit Structure
Built
Lewis Structure
Stick Structure
5.
Obtain another 5 carbon atoms. Connect 4 of these carbon atoms together in a straight chain
using the single bond connectors.
6.
Connect the 5th carbon atom as a branch coming off the chain of carbons.
7.
Fill in the remaining holes on the carbons by connecting a hydrogen atom to each hole using
single bond connectors.
Show your 2nd model to your instructor to ensure it was built correctly.
8.
Compare the two structures you have built, they should have the same molecular formula, but
completely different structures (bonding patterns). The 2 models you have built are called
structural isomers
.
9.
Fill in table 2B below based upon the structure of the isomer you built in steps 5-7.
Table 2B: Pentane Isomer 1
Molecular
Formula
Picture of Model Kit Structure
Built
Lewis Structure
Stick Structure
7
10. Using the last 5 carbon atoms you obtained, connect 3 of the carbons in a straight chain using
single bond connectors.
11. Add the 4th and 5th carbons as two separate branches off of the carbon chain.
12. Complete the model by filling in the empty holes using hydrogens and single bond connectors.
Show your 3rd model to your instructor to ensure it was built correctly.
13. You have now built a 2nd structural isomer of pentane. Complete table 2C regarding the 3rd
model you have built.
Table 2C: Pentane Isomer 2
Molecular
Formula
Picture of Model Kit Structure
Built
Lewis Structure
Stick Structure
14. Compare the 3 models you have built:
a.
What is the same for all 3 models?
b.
What is different for the 3 models?
c.
In your own words provide a definition for structural isomers:
15. Keep the first model you built of pentane for the next part. Break down the 2nd and 3rd model
of the isomers you made.
8
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Isomers of Alkenes
16. Obtain a handful of the flexible long connectors for double bonds.
17. Take your 1st model from the alkane section of the lab and replace the bond between the 1st
and 2nd carbon in the chain with 1 of the long flexible bonds. Add a 2nd flexible bond between
the same 2 carbons. This will require you to remove hydrogens from the model. You have now
created a model of the alkene called PENTENE.
18. Compare the molecular formula of the model of propene you just built to the formula of the
models in table 2A-2C.
a.
What happened to the number of hydrogens in the formula when you added a double
bond?
b.
This new model of pentene is called unsaturated while the models built for tables 2A-2C
were saturated. In your own words, explain the difference between a saturated and
unsaturated hydrocarbon in terms of bonds and number of hydrogen atoms.
19. Using another 5 carbons, connect the 5 carbons with a double bond between carbon 2 and
carbon 3 in the chain. The remainder of the carbon-carbon bonds should be created using single
bond connectors.
20. Fill in the remaining holes with hydrogens and single bond connectors.
21. Using the last 5 carbons, connect the 5 carbons again with a double bond between carbon 2 and
carbon 3 in the chain with the remainder of the carbon-carbon bonds being single bonds. When
you are adding the 4th carbon to the chain, connect it differently than you did in the model you
built in step 19 by switching the placement of the carbon and the hydrogen connected to carbon
3 in your chain.
22.
Show both models to your instructor to ensure they are correctly built.
23. The 3 models you have just built are again isomers of one another. When hydrocarbons have a
double bond, not only can you create structural isomers that differ in bonding patterns, but you
can also observe stereoisomers. Stereoisomers have the same sequence of bonded atoms but
differ in their 3-dimensional shape. The models built in steps 19 and 21 are a type of
stereoisomer called cis/trans isomerism.
Cis/Trans Isomers:
In cis/trans isomers, the double bond restricts free rotation around the bond creating a plane with 4
bonding positions. The plane created by the double bond can be seen in Fig. 4 below.
9
Figure 4: Carbon-carbon double bond showing the plane created by the double bond in red.
In cis/trans Isomers, 1 of the bonding positions on each carbon must be a hydrogen while the other
bonding position must be a non-hydrogen atom or group of atoms. Cis/trans isomers differ in how those
2 non-hydrogen groups appear with respect to the plane of the bond. If either of the carbons have 2
hydrogens or 2 non-hydrogen groups connected to them, cis/trans labelel does not apply
Trans Isomer
: the 2 non-hydrogen groups are on opposite sides of the plane created by the bond.
Cis Isomer
: the 2 non-hydrogen groups are on the same side of the plane created by the bond.
Figure 5: Examples of a cis and trans isomers of hexene.
24. Examine the cis and trans isomers of hexene in Fig. 5. Draw the plane of the bonds by drawing a
line that follows the “equal sign” you see for the double bonds similar to the red line you see in
Fig 4.
a.
How do the hydrogens appear with respect to one another across the double bond in
the Trans isomer?
b.
How do the hydrogens appear with respect to one another across the double bond in
the Cis isomer?
10
25. Complete table 3 regarding your 3 models of pentene. If one of the models doesn’t abide by
cis/trans rules, label it as neither.
Table 2C: PENTENE Isomers
Molecular
Formula
Picture of Model Kit
Structure Built
Lewis Structure
Stick Structure
Cis, Trans
or Neither
11
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Model 4: Functional Groups
Functional Groups are groups of atoms in a specific pattern that give the molecule certain properties and
allow us to organize molecules into families. In representations of functional groups “R” is a placeholder
that represents the rest of the molecule. Below is a table containing many of the common functional
groups in organic chemistry.
Figure 6: Table of Functional Groups taken from Frost
12
Identifying functional groups
1.
Examine the organic structures below in Fig 7. Label the following functional groups on these
compounds: alkene, amide, alcohol, phenyl, phenol, primary amine, ester, thiol, and a carboxylic
acid.
Tetracaine
Cysteine
13
Post Lab Questions:
1.
For the following provided structures
a.
Draw the corresponding Lewis Structure and Stick Structure.
b.
Circle and label the functional group(s) in each of the Lewis and Stick Structures you
drew
Condensed Structure
Lewis Structure
Stick Structure
CH
3
CH
2
OH CH
3
CH
2
CH
2
COOH Note: COOH is a condensed
structure for
CH
3
CH
2
CH
2
NH
3
+
HOCH
2
CH
2
N
+
(CH
3
)
3
Note: -N
+
(CH
3
)
3
indicates
there are 3 separate CH
3
groups attached to the same
Nitrogen atom
2. Classify each compound as a cis isomer, a trans isomer, or neither.
a.
14
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b.
c.
d.
15
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