1. Investigation III: Building Molecules
Smells Unit
Investigation III: Building Molecules
Lesson 1: New Smells, New Ideas
Lesson 2: Molecules in Three Dimensions
Lesson 3: Two’s Company
Lesson 4: Let’s Build It
Lesson 5: Shape Matters
Lesson 6: What Shape Is That Smell?
Lesson 7: Sorting It Out

2. Smells Unit – Investigation III
Lesson 1:
New Smells, New Ideas

3. ChemCatalyst
Do you think any of these molecules will smell similar? What evidence do you have to support your prediction?
(cont.)
Unit 2 • Investigation III

4. (cont.) citronellol C10H20O geraniol C10H18O menthol C10H20O
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5. The Big Question
How do we refine our hypothesis about how smell works?
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6. You will be able to:
Evaluate the usefulness of functional groups in predicting the smell of a molecule.
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7. Activity
Purpose: In this lesson you will be introduced to five new molecules. These molecules will lead you in the direction of new discoveries about the relationship between smell and chemistry.
(cont.)
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8. Molecular formula and name
Vial
Molecular formula and name
Functional group
Structural formula
Actual Smell O
C10H20O
citronellol
alcohol P
C10H18O
fenchol Q
geraniol
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9. Molecular formula and name
(cont.)
Vial
Molecular formula and name
Functional group
Structural formula
Actual Smell R
C10H20O
menthol
alcohol S
C10H18O
borneol
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10. Making Sense
Review the results of the smell investigation to date by indicating on the following chart:
(1) how molecular formulas can be used to predict smell, (2) how name can be used to predict smell, (3) how functional group can be used to predict smell, (4) what other information might be important. Examples are given for molecules that smell fishy.
(cont.)
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11. Smells Summary Chart smell Chemical Name “ine” = fishy
Molecular Formula
1 N = fishy
Chemical Name
“ine” = fishy
Functional Group
amine = fishy
Another property of molecules?
Smells Summary Chart
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12. Check-In
No Check-In.
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13. Wrap-Up
Molecular formula and functional group are not always sufficient information to predict the smell of a molecule accurately.
It appears that the overall shape of a molecule may be related to its smell.
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14. Smells Unit – Investigation III
Lesson 2:
Molecules in Three Dimensions

15. ChemCatalyst
This is a new way to represent one of the molecules that you smelled in the last class. Which molecule is this? Give your reasoning.
Molecule #1
sweet
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16. The Big Question
Why do some molecules with the same functional group have different smells?
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17. You will be able to:
Name some differences between a structural formula and a ball-and-stick model.
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18. Notes (cont.)
A ball-and-stick model is a 3-dimensional model that a chemist uses to show how the atoms in a molecule are arranged in space.
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19. Activity
Purpose: In this class you will be introduced to 3-dimensional molecular models. These particular molecular models are called ball-and-stick models. This type of model gives us more information than a structural formula. It shows how the atoms in a molecule are arranged in space.
(cont.)
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20. (cont.)
Molecule #1
Sweet smelling
(cont.)
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21. (cont.)
Molecule #2
Minty smelling
(cont.)
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22. (cont.)
Molecule #3
Camphor smelling
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23. Making Sense
What information do you need to know about a molecule in order to build a ball-and-stick model of it?
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24. Check-In
List the molecular model pieces you would need to build a model of ethanol—C2H6O.
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25. Wrap-Up
A ball-and-stick model is a 3-dimensional representation of a molecule that shows us how the atoms are arranged in space in relationship to one another.
Molecules have complex 3-dimensional shapes. The atoms are not necessarily lined up in straight lines and molecules are not flat as depicted in a structural formula.
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26. Smells Unit – Investigation III
Lesson 3:
Two’s Company

27. ChemCatalyst
Here is the structural formula of ethanol. Which is the correct ball-and-stick model for ethanol? Explain your reasoning.
(cont.)
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28. (cont.) 2. 1. 4. 3.
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29. The Big Question
Why are molecules in a ball-and-stick model crooked rather than straight?
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30. You will be able to:
Build a ball-and-stick model showing lone pair electrons for a molecule.
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31. Notes
Electron pairs are sometimes called bonded pairs. Both of these terms are a bit inaccurate because not all covalent bonds consist of a pair of electrons.
Electron charge is another area of potential confusion. We cannot fully explain why two particles with identical negative charges remain in such close proximity to one another within a covalent bond.
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32. Notes (cont.)
Sets of electrons that remain together in bonds or in lone pairs are referred to as electron domains. Electron domains “prefer” to be as far apart as possible from each other.
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33. Activity
Purpose: In this class you will gain practice creating three dimensional models of some small molecules. The concept of electron domains helps to explain why molecules actually exist in crooked and bent shapes, rather than straight lines.
(cont.)
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34. (cont.)
CH4 NH3 H2O
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35. Making Sense
Explain how the lone pairs affect the shape of your molecules.
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36. Notes
The underlying shape in all three of the molecules we created today is called tetrahedral.
A paddle represents a lone pair.
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37. Notes (cont.)
CH4
NH3
H2O
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38. Check-In Build a model for HF. Be sure to show all of the lone pairs.
Build a model for Ne. Be sure to show all of the lone pairs.
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39. Wrap-Up
Electron domains represent the space occupied by bonded electrons or a lone pair.
Electron domains are located as far apart from one another as possible.
The 3-dimensional shape of a molecule is determined by both bonding electrons and lone pairs.
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40. Smells Unit – Investigation III
Lesson 4:
Let’s Build It

41. ChemCatalyst
Remove the lone pair paddles from all five models. Now describe the remaining geometric shape.
CH4
NH3
H2O HF Ne
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42. The Big Question How do we describe the shape of a large molecule?
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43. You will be able to: Predict the shape of a molecule.
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44. Notes tetrahedral pyramidal bent linear point (cont.)
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45. Notes (cont.)
Lone-pair paddles are not generally included in ball-and-stick models. We have included them in order to illustrate how lone pairs affect molecular shape.
A linear molecule has three atoms in a row, with two electron domains around the central atom.
(cont.)
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46. Notes (cont.)
A trigonal planar shape is flat and consists of four atoms bonded together in a single plane. The central atom is bonded to three atoms but unlike ammonia there are only three electron domains in these molecules as shown below.
3 electron domains
A model of a trigonal planar molecule as seen from above.
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47. Activity
Purpose: In this lesson you gain practice creating actual ball-and-stick models from molecular formulas, using Lewis dot structures to assist you.
(cont.)
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48. Molecular Formula Lewis Dot Structure Describe/Draw Shape
methane: CH4
tetrahedral
water: H2O
bent
ethane: C2H6
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49. dichloromethane: CH2Cl2
Molecular Formula
Lewis Dot Structure
Describe/Draw Shape
chloromethane: CH3Cl
dichloromethane: CH2Cl2
methanol: CH3OH
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50. Molecular Formula Lewis Dot Structure Describe/Draw Shape
methyl amine: CH3NH2
formaldehyde: CH2O
ethene (ethylene): C2H4
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51. ethyne (acetylene): C2H2
Molecular Formula
Lewis Dot Structure
Describe/Draw Shape
hydrogen cyanide: HCN
ethyne (acetylene): C2H2
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52. Making Sense Number of domains Number of lone pairs Shape Example
Sketch 4
tetrahedral
CH4 1
pyramidal
NH3 2
bent
H2O 3
trigonal planar
CH2O
linear
CO2
Making Sense
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53. H2S Check-In What is the shape of the following molecule?
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54. Wrap-Up
Knowing the Lewis dot structure of a molecule allows one to predict its 3-dimensional shape.
The shape of large molecules is determined by the smaller shapes around individual atoms.
While lone pairs affect the positions of the atoms, they are not included in describing the shape of a molecule. The shape refers only to the positions of the atoms.
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55. Smells Unit – Investigation III
Lesson 5:
Shape Matters

56. ChemCatalyst Write chemical formulas for the following two molecules.
Are these two representations of the same molecule? Why or why not?
Do you expect these two molecules to have similar properties? Why or why not? C O H
maleic acid
fumaric acid
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57. The Big Question
What evidence suggests that chemical properties are related to the shape of a molecule?
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58. You will be able to:
Name some chemical properties that are related to shape.
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59. Activity
Purpose: To compare the properties of maleic acid and fumaric acid, two compounds with identical molecular formulas.
Safety note: Everyone will wear safety goggles at all times.
(cont.)
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60. (cont.) maleic acid fumaric acid thymol blue magnesium
sodium carbonate
(cont.)
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61. (cont.) Property Maleic Acid (C4H4O4) Fumaric Acid (C4H4O4) Solubility
Reaction with thymol blue
Reaction with magnesium
Reaction with Na2CO3
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62. Making Sense
What evidence do you have that molecular shape is related to chemical properties?
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63. Notes
The H atoms on the C atoms on either side of the double bond can both point in the same direction or they can point in opposite directions. These two forms are called isomers.
The form with both H atoms pointing in the same direction is referred to as the cis isomer.
When the H atoms point in opposite directions, the isomer is referred to as a trans isomer.
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64. Check-In
No Check-In.
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65. Wrap-Up Chemical properties are related to shape.
Twisting (or rotation of) the ends of a molecule around a C=C double bond is restricted.
Isomers are molecules with the same chemical formula but different shapes.
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66. Smells Unit – Investigation III
Lesson 6:
What Shape Is That Smell?

67. ChemCatalyst
What obvious differences do you see between these two different types of models?
space-filling model of citronellol
ball-and-stick model of citronellol
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68. The Big Question
Is there a relationship between the 3-dimensional shape of a molecule and its smell?
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69. You will be able to:
Discuss how the three-dimensional model of a molecule relates to its structural formula.
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70. Notes
A space-filling model is a 3-dimensional model that a chemist uses to show how the atoms are arranged in space and how they fill this space.
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71. Activity
Purpose: In this lesson you will be introduced to space-filling models of six molecules. By comparing and contrasting these models, you will learn more about the relationship between smell and chemistry.
(cont.)
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72. Molecule #5 and #2 - camphor
Questions:
Molecule #1 and #6 - sweet
Molecule #3 and #4 - minty
Molecule #5 and #2 - camphor
1. Using the molecular information sheets from Lesson III-1, identify the molecules in the photos.
2. What similarities do you notice?
3. How would you describe the overall shape of the entire molecule for both molecules in the set?
(cont.)
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73. One molecule from each set (for example, #1, #3, and #5)
(cont.)
Questions:
One molecule from each set (for example, #1, #3, and #5)
4. What similarities do you notice?
5. What major differences do you notice?
6. If you were to describe the overall shapes of the three molecules, what words would you use?
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74. Making Sense
On the basis of your examination of these space-filling models, do you think there is a connection between molecular shape and smell? Provide evidence for your answer.
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75. Notes
These three larger shapes are referred to as stringy, flat, and ball-shaped.
Sweet smells are associated with stringy molecules, minty smells are associated with flat molecules, and camphor smells are associated with ball-shaped molecules.
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76. Check-In
What smell do you predict for the substance in Vial V? Explain your reasoning.
(cont.)
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77. 1. Molecular formula: C12H20O2 2. Chemical name: bornyl acetate
Vial V
1. Molecular formula: C12H20O2
2. Chemical name: bornyl acetate
3. Structural formula:
4. Molecular model:
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78. Notes
A pheromone is a chemical substance that is produced by an animal and serves as a form of chemical communication to other individuals of the same species, often stimulating specific behavioral responses.
It is called an aggregation pheromone because it causes large numbers of insects to collect in one place.
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79. Wrap-Up
Space-filling models provide another way of looking at the 3-dimensional shape of molecules—one that represents the space occupied by atoms.
Smell appears to be directly related to the 3-dimensional molecular shape of a substance.
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80. Smells Unit – Investigation III
Lesson 7:
Sorting It Out

81. ChemCatalyst
What smell(s) do you predict for a stringy molecule? Explain your reasoning.
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82. The Big Question
What chemical information is most useful in predicting smell?
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83. You will be able to: Predict the smell of a mystery molecule.
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84. Activity
Purpose: In this lesson you will try to determine which pieces of chemical information are most valuable in determining the smell of a molecule. You will examine information on all of the smell molecules you’ve encountered so far, in order to come up with specific relationships between chemical information and the five smell categories.
(cont.)
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85. (cont.) Smell Classification Shape(s) Functional Group(s)
Molecular Formula(s)
Sweet
Minty
Camphor
Putrid
Fishy
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86. Making Sense
In what ways are shape, functional group, and molecular formula related to smell?
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87. Notes
Sweet:
Minty:
Camphor:
Fishy:
Putrid:
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88. Check-In Write down the number on your Mystery Card.
Predict the smell of the mystery molecule.
Explain your reasoning.
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89. Wrap-Up
Molecular shape can be used to predict smells for esters, alcohols, ketones, and aldehydes.
Amines and carboxylic acids have distinctive smells.
For stringy molecules it is necessary to look at functional group as well as molecular shape in order to determine smell.
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