Summer Research Program for Science Teachers/Partners in Science

Denice A. Gamper

Bishop Kearney High School, Brooklyn, NY

August 1998

MOLECULAR MODELING ACTIVITY

OVERVIEW: Molecules and polyatomic ions are not all flat structures. Each has a three dimensional shape that helps account for its various chemical and physical properties. Students often find it difficult to concretize the abstract concept of molecular geometry and that many molecules and polyatomic ions have a three-dimensional shape. For students to grasp this concept, it becomes necessary to introduce molecular modeling as a way to enable students to visualize that which they cannot see. This Action Plan is designed to introduce students to the concept of molecular modeling. [Content Standard Unifying Concepts- Models] Students will learn how to generate three-dimensional images of some simple inorganic and organic molecules they encounter in their introductory chemistry class. They will accomplish this through the use of traditional molecular modeling kits as well as computer generated images downloaded from the internet . [Teaching Standard D- Make accessible science tools]

ACTION PLAN COMPONENTS:

• Cooperative learning activity
• Laboratory exercise
• Computer/internet activity

Cooperative learning activity:

OVERVIEW: The carbon atom is special in that each atom can form four bonds to other atoms. These can be single, double, or triple bonds. The multiple bonding of carbon allows it to form an unlimited number of compounds that vary in molecular complexity, size, and shape. The study of carbon and its compounds is called organic chemistry. [9-12 Content Standard B- Structure of atoms]

The simplest organic compounds are those that contain only the elements hydrogen and carbon. These compounds are known as hydrocarbons and serve as the parent compounds from which most other organic compounds are named. The alkanes, alkenes, and alkynes represent three of the simplest homologous series of hydrocarbons. The members of each group have related structures and properties.

In this activity students will work in groups to compare and contrast the physical and chemical properties of the alkanes, alkenes, and alkynes. [9-12 Content Standard B- Structure and properties of matter]

TIME FRAME: Two 40 minute periods or the equivalent

OBJECTIVES:

• Differentiate between saturated and unsaturated compounds.

• Compare the general formulas and chemical and physical properties of the alkanes, alkenes, and alkynes.

• Recognize structural, condensed, and molecular formulas of the continuous-chain

hydrocarbons containing up to five carbons.

• Organize their information in the form of a chart. [Content Standard Unifying Concepts- Systems, order, and organization]

MATERIALS:

• pens and pencils
• textbook and other reference books provided for this activity

PROCEDURES:

Have students work in groups to:

1. classify the alkanes, alkenes, and alkynes as either saturated or unsaturated hydrocarbons based on the bonding between the carbon atoms, determine their general formulas, and use these general formulas to find the molecular formula for each of the first five members of each series.
2. organize a chart for each homologous series that includes the molecular formula, IUPAC name, molecular formula, condensed formula, and structural formula for the first five members in each series.

SAMPLE CHARTS:

COMPARISON OF ALKANES, ALKENES, AND ALKYNES

LABORATORY EXERCISE

TIME FRAME: Two 40 minute periods or the equivalent

OBJECTIVES:

• Construct models of simple hydrocarbon molecules using molecular model kits.

• Interpret molecular models depicting shape, bonding, and ability of atoms to rotate about the bonds in the molecule.

• Draw the shorthand, structural, and condensed formulas for each molecule constructed.

• Differentiate between saturated and unsaturated compounds.

MATERIALS:

• pens and pencils
• textbook and other reference books provided for this activity
• laboratory assignment
• molecular model kits

PROCEDURES:

1. Have students work in groups to construct models of the first three members of the

alkanes, alkenes, and alkynes.

2. Construct a table with the shorthand, structural, and condensed formulas for each

homologous series.

3. Complete a worksheet based on the lab activity.

INTERNET ACTIVITY

OVERVIEW: RasMol is a molecular graphics program which can be used to visualize small organic molecules like the alkanes, alkenes, or alkynes as well as larger more complex molecules like proteins and nucleic acids. [9-12 Content Standard E- Understandings about science and technology] RasMol displays the molecule of interest on the screen in a variety of color schemes and representations. The loaded molecule may be shown as wireframe, cylinder (Dreiding) stick bonds, alpha-carbon trace, spacefilling (CPK) spheres, macromolecular ribbons (either smooth shaded solid ribbons or parallel strands), hydrogen bonding and dot surface. The displayed molecule may be rotated, translated, zoomed, z-clipped (slabbed) interactively using either the mouse, the scroll bars, the command line or an attached dials box. RasMol is a powerful educational tool that can be used in conjunction with traditional molecular modeling kits to reinforce and concretize the concept of molecular geometry.

TIME FRAME: Five 40 minute periods or the equivalent

[Teaching Standard D- Structure time for extended investigations]

OBJECTIVES:

• Learn how to use the Internet to view molecular modeling images simplest to the most complex molecules.

• Interpret molecular models depicting shape, bonding, and ability of atoms to rotate about the bonds.

• Learn how scientists use high-powered computers to study microscopic structures.

• Compare images downloaded using RasMol to actual molecular models of the alkanes,

alkenes, and alkynes.

PROCEDURES:

Each student will:

1. Download the RasMol program from its web site onto a floppy disk.

2. Then be taught how to operate RasMol

a) Download images from different web sites

b) Move and rotate structures

c) Change display options and color schemes

d) Export and print images

3. Set up three separate folders on his or her floppy disk and label them alkanes, alkenes, and alkynes.

4. Download the first three members of each homologous series into its appropriate file.

5. Practice procedures 2b and 2c using downloaded structures.

6. Submit the floppy disk and printouts of the structures downloaded into their files.

7. Complete a worksheet that is related to the topic covered.

EXTENSION:

As a follow-up to this exercise, students will be taught how to use the molecular modeling program Hyperchem Lite to generate the same molecular images they downloaded from the Internet.

EVALUATION:

The students will be evaluated on their group activities (cooperative learning and laboratory assignment) using a general performance tasks scoring rubric. Students will receive a numeric grade for floppy disks and worksheets submitted for the computer portion of the action plan. In addition, students will be tested on their knowledge of the similarities and differences between the alkanes, alkenes, and alkynes. [Teaching Standard C- Use multiple methods to gather data about student understanding]

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