Molecular Models

Preface

The directions in your laboratory book are just fine for preparation for this laboratory. However, in addition, you will be doing the investigation using both computer models of molecules and building them from plastic parts in a commercial kit. There are advantages to building molecular models from model kits. When you build them yourself, you have to decide how to connect the atoms so that they represent the target structure, and the result is a tangible object that you can hold in your hands.

Using the computer to examine molecular models also has advantages. The models can be obtained quickly, and several different kinds of representations can be examined. Since every “model” of a molecule represents only some aspects of its nature, it is good to see molecules represented in different fashions. The computer facilitates this by allowing you to switch quickly between different representations. Like a physical model, the computer representations can be viewed from all angles, showing their three-dimensional character.

Both of these kinds of models have limitations, of course. In neither kind are the relative motions of the atoms represented. In “real” molecules, the atoms do not have exactly fixed distances from one another, but they “vibrate” around their equilibrium distances in a complicated motion that you may learn about in future courses. In real molecules, the bond lengths of a given type (C-C, or C-O, for example) are not exactly all the same. In plastic models, they are. Another important distinction between these models and real molecules is that rotational motion around single bonds between atoms is allowed. In physical models, one can twist the atoms around such bonds. The computer models we will be using do not depict that motion, but it is something that you can imagine.

Goals

In completing this investigation you will:

  1. Use molecular models to illustrate the structures of various molecules.

Materials

In addition to building physical models from kits, you can obtain all of the structures for this laboratory from the Web site of Professor Emeritus David Woodcock at Okanagan University College, in British Columbia, where hundreds of simple molecules are available in a format viewable using the Chime viewer. Chime is a plug-in application for Web browsers such as Netscape or Internet Explorer. It has been installed on the UMSL network, for Mozilla Firefox. If you want to use this plug-in on your computer at home, you can download and install the program from

The Okanagan University College collection of molecules is at Use Firefox to go this site, and choose the molecules of interest using the Index, which is ordered by the number of atoms of each kind, beginning with C, then, H, then O, etc. (Molecules that have no carbon atoms follow those that do.) Clicking on a molecule of interest opens a new window in which the molecule is displayed. Clicking within the window while moving the mouse will rotate the molecule in space. Right-click within the window to open a menu where you can change display options, make the molecule rotate continuously, and so forth. Experiment!

Getting Started

Start by obtaining models of C2H6, C2H4, and C2H2 (ethane, ethene, and ethyne, respectively). Use these models to explain differences in atom arrangement and bond angles. What are the bond angles in these molecules? How would you describe the shapes of each structure? How do they compare to the Lewis structures you have drawn?

Using models of CH4, NH3, and H2O, develop an explanation for the shapes of molecules Compare the arrangement of the hydrogens around the central atom for each of the structures. What is the arrangement of atoms and valence electron pairs around the central atom? What are the approximate bond angles? What are the shapes of the molecules?

The chemical formulas listed in the table are shorthand notations for the arrangement of atoms along the carbon chain. The stick model below shows the attachment of hydrogens around the backbone structure for the first molecule listed in Table 1. Note that the structural formula as shown is written in two dimensions and does not represent the three-dimensional arrangement of atoms needed to explain the properties of the molecule.

CH3CH2OH =

Look up the structures of the following molecules; make models of the those in the first column

Table 1

Name / Condensed Formula / Name / Condensed Formula
ethanol / CH3CH2OH / Valium / C16H13ClN2O
propanol / CH3CH2CH2OH / morphine / C17H19NO3
cyclohexane / C6H12 / benzocaine / C9H11NO2

As you explore the formula index for the molecules you need for this experiment, you will discover that there are often several molecules that have the same elemental composition. These are called “isomers” of one another, and it may not be immediately obvious which possibility is the one that it was intended for you to visualize. What are the differences between the various structures that all have the formula C3H8O and all include the –OH group, which makes them all “propanol”? Which one of these corresponds to the structure that is given in Table 1?

Can you discover the meaning of (R) and (S)? [This is a question that goes well beyond Chemistry 1111; it is interesting, aspect of molecular structure and can be determined from these models.]

Look up the structures of CCl4, CH2Cl2, COCl2 , C2H4Cl2, andSF6 (at the end of the index)

Make models and draw 3 D stick models for all of the compounds listed below. Be sure to include all the bonds to the central atoms.

C2H6,

C2H4,

C2H2

CH3CH2OH

CCl4

CH2Cl2

COCl2

C2H4Cl2

SF6