5.2: Lab - Molecular Shape, Polarity, and Intermolecular Forces
- Page ID
- 438409
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)Equipment and Materials
Prepare 12 sets of equipment and materials for 24 students per class section. Include a few more for backup if needed. Each set should include
Equipment
Provide
- 12 Laptop or other suitable device with internet connection
- 12 Hotplates
- 24 cut pieces of aluminum foil (each piece large enough to completely cover surface of hot plate
- 2 packs of medium or small sized test tubes (on cart in front of room)
Materials
Provide 100 mL squeeze bottles of the following liquids
- Distilled water (12)
- Hexanes (12)
- Methanol (12)
- Cyclohexane (12)
- Hydrogen peroxide (12)
Provide about 25 mL vials filled with solid samples (powdered or crystalline) of
- Sucrose
- Fructose
- Glucose
- Lactose
- Catalase
- Sodium chloride (\(\ce{NaCl}\))
- Naphthalene
- Recognize the importance of structure-function relationship in compounds and their receptors
- Know the different intermolecular forces
- Identify polar and nonpolar compounds
Laboratory Skill
- Correct use of hot plate
Equipment and Materials
- Laptop or other suitable device with internet connection
- Hotplate
- Aluminum foil
- Test tubes
- Distilled water
- Hexanes
- Methanol
- Cyclohexane
- Sucrose
- Fructose
- Glucose
- Lactose
- Catalase
- Hydrogen peroxide
- Sodium chloride (\(\ce{NaCl}\))
Safety and Hazard Information
- Personal Protective Equipment (PPE) required: Safety goggle, closed-toe shoes.
Background Information
The action of medicines (aspirin), harmful chemicals (viral toxins), and neurotransmitters (dopamine) all depend on polarity and intermolecular forces displayed by the molecules. These interactions are critical for the processes that keep our cells alive. For example, drugs modify the action of proteins (molecular machinery) through binding based on their shape, polarity and intermolecular forces (Figure \(\PageIndex{1}\)). Click the link that follows to view a simulation of the picture in Figure \(\PageIndex{1}\).
These interactions explain why different medications have different impacts on the body. When we suffer from pains, we take pain relieve medications like aspirin, Tylenol, ibuprofen or any other medication that treats the underlying cause of the pain. In drug design, when chemists and other scientists set out to develop new a new drug they ask themselves several questions. A few basic ones include
- What is the drug expected to treat?
- Where in the body will the drug (or its active component) bind?
- What is the nature (shape and polarity) of the binding site? A binding site is also referred to as a receptor or active site.
- How will the drug interact or influence the chemical reactions in the body after binding?
Table \(\PageIndex{1}\) summarizes the different types of intermolecular forces.
Table \(\PageIndex{1}\): Types of intermolecular forces and sample properties affected
| Type of Force | Particle Arrangement | Example | Properties affected | Strength |
|---|---|---|---|---|
|
Dispersion Forces Major force in nonpolar molecules |
Temporary Dipoles
Partial Charges |
 |
Melting point = low Boiling point = low Solubility = low in water Vapor Pressure = high |
Weakest \[\downarrow\nonumber\]Strongest |
|
Dipole-Dipole Forces Major force in polar molecules |
Permanent Dipoles
Partial charges |
\(\ce{Br^{\delta +}-Cl^{\delta -} ... Br^{\delta +}-Cl^{\delta -}}\) | ||
|
Hydrogen Bonding Polar molecules with \(\ce{H}\) connected to \(\ce{F,O,N}\) |
\(\text{X}= \ce{F,O,N}\)
Partial charges |
 |
||
| Ionic Bonding |
Permanent Charges
Full Charges |
\(\ce{Na^+ Cl^-}\) |
Melting point = highest Boiling point = highest Solubility = high in water Vapor Pressure = low |
Dispersion Forces are very weak intermolecular forces that occur in all molecules. They are the dominant intermolecular force in nonpolar molecules whose elements have similar electronegativities, or the molecular structure is symmetrical such that its dipoles cancel out.
Dipole-dipole forces occur in polar molecules. A molecule is polar when it is non-symmetrical and has elements whose electronegativities are different. Dipole-dipole forces are stronger than dispersion forces.
Hydrogen bonding occurs in molecules that contain the less electronegative element, hydrogen directly bonded (or attached) to the very electronegative element \(\ce{F}\), \(\ce{O}\) or \(\ce{N}\). As a result, the \(\ce{F-H}\), \(\ce{O-H}\), and \(\ce{N-H}\) bonds are very polar, hence hydrogen bonding can be considered as a stronger version of dipole-dipole.
Ionic Bond occurs in ionic compounds. An ionic compound is formed when positively charges ions (cations) and negatively charged ions (anions) attract each other. The ionic bond is the strongest of all intermolecular forces. The stronger the intermolecular force present in a molecule, the higher its melting and boiling points.
In this laboratory exercise, we will use a PhET simulation to explore molecular shapes. There are several molecular shapes, but some of the common ones we will deal with include linear, trigonal planar, bent, tetrahedral, trigonal pyramidal, and octahedral.
We will also deduce the polarity of substances by adding them to polar and nonpolar substances. Two or more substances that are miscible are said to have similar polarities. Polar substances (such as water) are miscible with other polar substances, and non-polar substances (such as hexanes) are miscible with other non-polar substances. Polar and non-polar substances are immiscible. In chemistry, the expression “like dissolves like” is commonly used to explain the miscibility of liquids. If two substances are miscible, the resulting mixture is uniform throughout and displays only one phase. If two substances are immiscible, the resulting mixture displays more than one phase with a thin visible layer or border separating them. Interestingly, when drug molecules interact with receptors (Figure \(\PageIndex{1}\)), polar-polar contacts or nonpolar-nonpolar contacts are favorable, while polar-nonpolar contacts are not favorable. This is in line with “like dissolves like.”
We will then examine how intermolecular forces play a role in determining melting point by examining different sugars ranging from simple (glucose) to more complex (lactose) shown in Figure \(\PageIndex{2}\) below.
Lastly, we will look at a biochemical example of these intermolecular forces and molecular geometries in action. The reaction examined will be the decomposition of hydrogen peroxide by the enzyme catalase. Hydrogen peroxide is a highly reactive compound that damages biological systems. This is why it is sometimes used to clean small cuts and scrapes (it kills bacteria!). Within our bodies, the enzyme catalase is responsible for breaking down hydrogen peroxide to minimize its damage to our bodies.
Sucrose
Fructose
Glucose
LactoseSpecial Instructions (if any)
N/A
Procedure
\(\PageIndex{A}\): Molecular Shapes
1. Click to open the molecular shapes PhET simulation link.
2. Then click on model. This will display a molecule with a purple central atom (CA) and two white surrounding atoms that are directly connected (bonded) to the CA.
3. Using the menu provided, you can click to increase or decrease the number of atoms bonded to the CA. You could also click to add or remove electron lone pairs. By checking the molecular geometry box, the molecular shape of each molecule will be displayed. Take a few moments to play with the simulation by randomly building molecules through adding and removing atoms bonded to the CA. Click the reset button, then proceed to step 4.
4. You will complete Table \(\PageIndex{1}\) on the experimental report. Begin by drawing the Lewis structure of the displayed molecules.
5. Use the PhET simulation to build your molecule then report the corresponding molecular shape on Table \(\PageIndex{1}\).
6. Complete Table \(\PageIndex{1}\) by placing the molecule from the that best fits a description.
\(\PageIndex{B}\): Polarity
1. Gather the following items for this part of the experiment:
- Squeeze bottles of distilled water, hexanes, methanol, and cyclohexane.
- Vials of lactose, catalase, and glucose.
- 10 small or medium sized test tubes in a test tube rack.
2. Mixing liquids: Refer to Table \(\PageIndex{2}\) in the experimental report to deduce the substances to mix. In each test tube mix equal portions (approximately 2 mL each) of two liquid substances, shake to mix and allow to settle for about a minute. In each corresponding box on Table \(\PageIndex{2}\), report if the two substances are miscible or immiscible.
3. Mixing liquids and solids: In each test, add about 5 mL of liquid followed by a peanut size amount of solid on the tip of a spatula. Stir the mixture with a glass rod until solid dissolves. Stop if solid has not dissolved after stirring for 2 minutes. Report on Table \(\PageIndex{2}\) if substances are miscible (solid dissolved) or immiscible (solid did not dissolve).
4. State if the substance is polar or non-polar. The first two substances (water and hexanes) have been completed as an example.
\(\PageIndex{C}\): Intermolecular Forces and melting points
1. Obtain two sheets of aluminum foil, a hot plate, sucrose, glucose, napthalene, and \(\ce{NaCl}\).
2. Cover the hotplate with both sheets of aluminum foil.
3. Place a few crystals (just enough to be visible!) of each solid on separate spots on the hotplate. Plug in the hotplate and turn the heat to 8.
4. Observe and record the melting point from 1 to 5 of each substance on Table \(\PageIndex{3}\), with 1 being the 1st to melt and 5 being the last to melt.
\(\PageIndex{D}\): Catalase and hydrogen peroxide
1. In an additional test-tube, add catalase and a few drops of 2% hydrogen peroxide. Describe your observations in the report sheet.
Experimental Report
\(\PageIndex{A}\): Molecular Shapes
To complete the Example column, choose from the molecules below. The first has been completed as an example.
Molecules for the Example column: \(\ce{SO2, H2S, PH3, CF4,}\) and \(\ce{BCl3}\).
Table \(\PageIndex{1}\): Molecular Shapes
| Bonded Atoms on CA | Lone Pairs on CA | Lewis Structure | Molecular Shape | Example |
|---|---|---|---|---|
| 2 | 0 |  |
Linear | \(\ce{CS2}\) |
| 2 | 1 | |||
| 2 | 2 | |||
| 3 | 0 | |||
| 3 | 1 | |||
| 4 | 0 |
\(\PageIndex{B}\): Polarity
Table \(\PageIndex{2}\): Polarity of compounds
| Substance | Water | Hexanes |
State if Polar or Non-polar? |
|---|---|---|---|
| Water | N/A | immiscible | Polar |
| Hexanes | immiscible | N/A | Non-polar |
| Methanol | |||
| Cyclohexane | |||
| Lactose | |||
| Catalase | |||
| Glucose |
C. Intermolecular Forces and melting points
See Figure \(\PageIndex{2}\) for structures of sugars.
Table \(\PageIndex{3}\): Intermolecular forces and melting points
| Substance |
Order of Melting (1st, 2nd, etc) |
Molar Mass |
State if Polar or Non-polar? |
Strongest intermolecular force present |
|---|---|---|---|---|
| Sucrose | ||||
| Glucose | ||||
| Naphthalene | ||||
| \(\ce{NaCl}\) |
\(\PageIndex{D}\): Catalase and Hydrogen peroxide
Describe the reaction below:
Follow-up questions
Below are the structures of glucose (blood sugar) and lactose (the sugar in milk). You’ll notice these structures make rings, in 1152 you will study these structures in more detail, for now you will only need to examine the \(\ce{OH}\) groups as discussed below.
|
Glucose |
Lactose |
a. Circle every \(\ce{OH}\) group in each structure above.
- How many \(\ce{OH}\) groups does glucose have?
- How many does lactose have?
b. \(\ce{OH}\) groups allow these sugars to participate in hydrogen bonding. Which sugar would be able to perform more hydrogen bonds?
c. Given your answer to b, which would you expect to have stronger intermolecular forces?
d. Which sugar would you expect to have a higher melting point? Is this consistent with your findings?
Sucrose and fructose (structures in Figure \(\PageIndex{2}\)) also have hydrogen bonding. From your results above, which do you expect to have more hydrogen bonding?
Glucose (blood sugar) is dissolved in your blood and transported around your body to provide your cells with energy. Your blood is an aqueous solution made of mostly water. Given this, what would you expect about the solubility of glucose in water? Is this consistent with your findings in Table \(\PageIndex{2}\)?
Below is the Lewis structure of hydrogen peroxide. Given that the electronegativity of oxygen is 3.4 and the electronegativity of hydrogen is 2.1, which of the below atoms do you expect to be negatively charged? (Draw a partially negative sign on these atoms).
The active site of catalase contains what is called a heme group, and at its center is a positively charged iron ion (shown below). This iron is responsible for splitting apart hydrogen peroxide into water and oxygen. What atom on hydrogen peroxide will bind to this iron based on the charges you wrote in preceding question?
\[\ce{Fe^{3+}}\nonumber\]
Once the iron in catalase binds to oxygen, it is bonded to six separate atoms and has zero lone pairs. What is the molecular geometry of the active site of catalase at this point?
Was catalase soluble in water? Given that our body contains catalase to remove hydrogen peroxide, why is this important?