Summer Research Program for Science Teachers

Denice A. Gamper 

Bishop Kearney High School

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. [9-12 Content Standard B- Structure and properties of matter] 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 aims to reinforce the concept of molecular geometry through the use of traditional molecular modeling kits as well as computer generated images downloaded from the internet. Students will also learn how to generate three-dimensional images of some simple inorganic molecules they encounter in their introductory chemistry class using HypeChem Lite.

COMPONENTS INCLUDED IN PLAN

· Cooperative learning activity

· Laboratory exercise

· Computer/Internet activity

Cooperative learning activity:

OVERVIEW:

Electron dot structures and structural formulas usually show a given molecule in only two dimensions. In reality, many molecules and polyatomic ions exist in three dimensions. The VSEPR (valence shell electron pair repulsion) theory does not attempt to explain how bonds form but it does provide an explanation for the shape of many molecules and ions. According to the VSEPR theory, valence shell electron pairs will stay as far apart as possible so that the repulsions between them are minimized. [Content Standard Unifying Concepts- Models and explanation]

TIME FRAME: Two 40 minute periods or the equivalent

OBJECTIVES:

· Define the VSEPR theory and explain its relationship to the shape of molecules.

· Differentiate electron pair geometry from molecular geometry.

· Name and describe the five electron pair geometries which can surround the central atom.

· Use balloons to illustrate the different electron pair geometries around the central atom.

· Show how molecular geometry is a function of electron pair geometry.

· State the two factors that determine the polarity of a molecule.

· Explain how the geometry of a molecule helps to determine its properties.

· Organize their information in the form of a chart.

MATERIALS:

· pens and pencils

· textbook and other reference books provided for this activity

· six pear shaped balloons

PROCEDURES:

As part of this cooperative activity students will:

· define the VSEPR theory and explain its relationship to the shape of molecules.

· use balloons to visualize electron pair geometries with the following shapes:

linear, trigonal planar, tetrahedral, trigonal bipyramidal, and octahedral.

· differentiate between electron pair and molecular geometry.

· see that the shape of a given molecule will depend on the number of bonding and nonbonding electron pairs around the central atom.

· state the two factors that determine the polarity of a molecule.

· organize their information into a chart.

SAMPLE CHARTS: Students will be expected to fill in a chart similar to the one below.

[Teaching Standard B- Orchestrate scientific discourse]

LABORATORY EXERCISE

TIME FRAME: Two 40 minute periods or the equivalent

OBJECTIVES:

· Construct models of simple inorganic molecules with the following molecular geometries using molecular modeling kits and HyperChem Lite: linear, trigonal planar, tetrahedral, trigonal pyramidal, bent or V-shaped, trigonal bipyramidal, and octahedral.

· Interpret molecular models depicting shape, type of bonding, and polarity of the molecule.

· Draw the Lewis dot and structural formulas for each molecule constructed.

MATERIALS:

· pens and pencils

· textbook and other reference books provided for this activity

· laboratory assignment

· molecular model kits [Teaching Standard D- Make accessible science tools]

PROCEDURES:

1. Have students work in groups to construct models of the with the aforementioned molecular geometries.

2. Construct a table with the Lewis dot and structural formula, number of bonding and lone pairs, electron pair and molecular geometry, shape, type of bond, and polarity for each assigned molecule.

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 inorganic molecules like water, ammonia, or methane as well as larger more complex molecules like proteins and nucleic acids. 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. [9-12 Content Standard E- Understandings about science and technology]

RasMol Home Page: www.umass.edu/microbio/rasmol/index2.htm

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 from the simplest to the most complex molecules.

· Interpret molecular models depicting shape, type of bonding, and polarity of the molecule.

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

· Compare images downloaded using RasMol to actual molecular models constructed during the previous laboratory activity.

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 a folder on their floppy disk and label it Molecular Geometry.

4. download molecules similar to each of the molecules constructed during the laboratory exercise into the Molecular Geometry folder.

5. will be allowed to practice procedures 2b and 2c using their 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:

[9-12 Content Standard A- Identify questions and concepts that guide inquiry]

As a follow-up to this exercise, students will be allowed to choose a class of molecules or compounds ie: amino acids, proteins, sugars, explosives, hormones, vitamins, insecticides. They will then download the RasMol molecular files for their compounds and create either a PowerPoint presentation or a Chime presentation for their molecules. Chime is a plug-in for either Netscape or Internet Explorer and can be downloaded free from the following site:

http://www.mdli.com/. Chime allows the student to convert their RasMol images into a web page.

As part of this activity, students will be expected to research each of the compounds they have chosen and include in their presentations the following kinds of information:

a) physical and/or chemical properties ie: melting point, boiling point, density, specific gravity, etc.

b) molecular weight and chemical formula for each compound. [9-12 Content Standard B- Properties of matter]

c) biological, industrial, technological, medical significance of the compounds chosen.

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 understanding of the concepts of molecular geometry using multiple choice and free-response type questions. [Teaching Standard C- Use multiple methods to gather data about student understanding]

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