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

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

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

(cont.) citronellol C10H20O geraniol C10H18O menthol C10H20O Unit 2 • Investigation III

The Big Question How do we refine our hypothesis about how smell works? Unit 2 • Investigation III

You will be able to: Evaluate the usefulness of functional groups in predicting the smell of a molecule. Unit 2 • Investigation III

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.) Unit 2 • Investigation III

Molecular formula and name Vial Molecular formula and name Functional group Structural formula Actual Smell O C10H20O citronellol alcohol P C10H18O fenchol Q geraniol Unit 2 • Investigation III

Molecular formula and name (cont.) Vial Molecular formula and name Functional group Structural formula Actual Smell R C10H20O menthol alcohol S C10H18O borneol Unit 2 • Investigation III

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.) Unit 2 • Investigation III

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 Unit 2 • Investigation III

Check-In No Check-In. Unit 2 • Investigation III

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. Unit 2 • Investigation III

Smells Unit – Investigation III Lesson 2: Molecules in Three Dimensions

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 Unit 2 • Investigation III

The Big Question Why do some molecules with the same functional group have different smells? Unit 2 • Investigation III

You will be able to: Name some differences between a structural formula and a ball-and-stick model. Unit 2 • Investigation III

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. Unit 2 • Investigation III

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.) Unit 2 • Investigation III

(cont.) Molecule #1 Sweet smelling (cont.) Unit 2 • Investigation III

(cont.) Molecule #2 Minty smelling (cont.) Unit 2 • Investigation III

(cont.) Molecule #3 Camphor smelling Unit 2 • Investigation III

Making Sense What information do you need to know about a molecule in order to build a ball-and-stick model of it? Unit 2 • Investigation III

Check-In List the molecular model pieces you would need to build a model of ethanol—C2H6O. Unit 2 • Investigation III

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. Unit 2 • Investigation III

Smells Unit – Investigation III Lesson 3: Two’s Company

ChemCatalyst Here is the structural formula of ethanol. Which is the correct ball-and-stick model for ethanol? Explain your reasoning. (cont.) Unit 2 • Investigation III

(cont.) 2. 1. 4. 3. Unit 2 • Investigation III

The Big Question Why are molecules in a ball-and-stick model crooked rather than straight? Unit 2 • Investigation III

You will be able to: Build a ball-and-stick model showing lone pair electrons for a molecule. Unit 2 • Investigation III

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. Unit 2 • Investigation III

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. Unit 2 • Investigation III

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.) Unit 2 • Investigation III

(cont.) CH4 NH3 H2O Unit 2 • Investigation III

Making Sense Explain how the lone pairs affect the shape of your molecules. Unit 2 • Investigation III

Notes The underlying shape in all three of the molecules we created today is called tetrahedral. A paddle represents a lone pair. Unit 2 • Investigation III

Notes (cont.) CH4 NH3 H2O Unit 2 • Investigation III

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. Unit 2 • Investigation III

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. Unit 2 • Investigation III

Smells Unit – Investigation III Lesson 4: Let’s Build It

ChemCatalyst Remove the lone pair paddles from all five models. Now describe the remaining geometric shape. CH4 NH3 H2O HF Ne Unit 2 • Investigation III

The Big Question How do we describe the shape of a large molecule? Unit 2 • Investigation III

You will be able to: Predict the shape of a molecule. Unit 2 • Investigation III

Notes tetrahedral pyramidal bent linear point (cont.) Unit 2 • Investigation III

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.) Unit 2 • Investigation III

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. Unit 2 • Investigation III

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.) Unit 2 • Investigation III

Molecular Formula Lewis Dot Structure Describe/Draw Shape methane: CH4 tetrahedral water: H2O bent ethane: C2H6 Unit 2 • Investigation III

dichloromethane: CH2Cl2 Molecular Formula Lewis Dot Structure Describe/Draw Shape chloromethane: CH3Cl dichloromethane: CH2Cl2 methanol: CH3OH Unit 2 • Investigation III

Molecular Formula Lewis Dot Structure Describe/Draw Shape methyl amine: CH3NH2 formaldehyde: CH2O ethene (ethylene): C2H4 Unit 2 • Investigation III

ethyne (acetylene): C2H2 Molecular Formula Lewis Dot Structure Describe/Draw Shape hydrogen cyanide: HCN ethyne (acetylene): C2H2 Unit 2 • Investigation III

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 Unit 2 • Investigation III

H2S Check-In What is the shape of the following molecule? Unit 2 • Investigation III

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. Unit 2 • Investigation III

Smells Unit – Investigation III Lesson 5: Shape Matters

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 Unit 2 • Investigation III

The Big Question What evidence suggests that chemical properties are related to the shape of a molecule? Unit 2 • Investigation III

You will be able to: Name some chemical properties that are related to shape. Unit 2 • Investigation III

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.) Unit 2 • Investigation III

(cont.) maleic acid fumaric acid thymol blue magnesium sodium carbonate (cont.) Unit 2 • Investigation III

(cont.) Property Maleic Acid (C4H4O4) Fumaric Acid (C4H4O4) Solubility Reaction with thymol blue Reaction with magnesium Reaction with Na2CO3 Unit 2 • Investigation III

Making Sense What evidence do you have that molecular shape is related to chemical properties? Unit 2 • Investigation III

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. Unit 2 • Investigation III

Check-In No Check-In. Unit 2 • Investigation III

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. Unit 2 • Investigation III

Smells Unit – Investigation III Lesson 6: What Shape Is That Smell?

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 Unit 2 • Investigation III

The Big Question Is there a relationship between the 3-dimensional shape of a molecule and its smell? Unit 2 • Investigation III

You will be able to: Discuss how the three-dimensional model of a molecule relates to its structural formula. Unit 2 • Investigation III

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. Unit 2 • Investigation III

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.) Unit 2 • Investigation III

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.) Unit 2 • Investigation III

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? Unit 2 • Investigation III

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. Unit 2 • Investigation III

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. Unit 2 • Investigation III

Check-In What smell do you predict for the substance in Vial V? Explain your reasoning. (cont.) Unit 2 • Investigation III

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: Unit 2 • Investigation III

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. Unit 2 • Investigation III

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. Unit 2 • Investigation III

Smells Unit – Investigation III Lesson 7: Sorting It Out

ChemCatalyst What smell(s) do you predict for a stringy molecule? Explain your reasoning. Unit 2 • Investigation III

The Big Question What chemical information is most useful in predicting smell? Unit 2 • Investigation III

You will be able to: Predict the smell of a mystery molecule. Unit 2 • Investigation III

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.) Unit 2 • Investigation III

(cont.) Smell Classification Shape(s) Functional Group(s) Molecular Formula(s) Sweet Minty Camphor Putrid Fishy Unit 2 • Investigation III

Making Sense In what ways are shape, functional group, and molecular formula related to smell? Unit 2 • Investigation III

Notes Sweet: Minty: Camphor: Fishy: Putrid: Unit 2 • Investigation III

Check-In Write down the number on your Mystery Card. Predict the smell of the mystery molecule. Explain your reasoning. Unit 2 • Investigation III

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. Unit 2 • Investigation III