CHEM 1103 - Structures of
Molecules CHEM 1103 - Structures of
Molecules 
Guidelines for Laboratory Notebooks
Guidelines for Laboratory Reports
Introduction
Chemists use models to describe many phenomena. We have studied several models for the structure of the atom. We began with Dalton's atomic theory, which described the atom as a small, impenetrable particle. This type of description is called a model. Next, Thomson described the atom as "plum pudding" or as a "raisin bun" where the majority of the volume contained the negative charge and was punctuated with small particles of positive charge. Both of these models explained the observations of the day, but were not experimentally well-tested. They did, however, provide straightforward explanations of observations. Later, by his experiments with gold foil, Rutherford conceived the beginnings of the modern picture of the atom as a small, positive core, surrounded by a large sphere of negative charge. Bohr studied the hydrogen atom, simplest of the atoms, and developed the first model describing the structure of the possible orbits of the electron. You calculated the energies of these orbits a few weeks ago. We then realized that the Bohr model for hydrogen, while it describes hydrogen accurately, is too simplistic to describe more complex atoms. The wave-mechanical model, which describes the man orbitals and their energies is currently used by most chemists to describe the structure of the electrons in an atom. Thus, we have considered several models for the structure of the atom.
Since atoms combine to form molecules, ionic compounds and ions, it is useful to construct models that can be used to describe the structure of the complete molecule. ionic compound or ion. In class, we are discussing models for the bonding in molecules and ions. We have used Lewis structures to describe the bonding in molecules that obey the octet rule. We can use electronegativity and bond order to describe the polarity and strength of a bond. We can use the VSEPR (Section 10.1) model to predict the shapes of molecules. In this experiment, we will use the Molecules 3D software that is available on Mathsci to draw Lewis structures and use those structures to construct computer models of some molecules. We will then describe the bonding and shapes of the molecules. In the lab manual, this is Chapter 12.
Accessing the Software
You must log into a server to access this software. It is not available through Netscape. It is not available over the modem lines or the internet in any fashion.
Log into your server. When you have logged-in a screen including Novell-delivered applications should appear. Double click on the icon (looks like a molecule) called "Molecule." The software should load. Click once to remove the Mosby logo from the screen. If you have trouble loading the software, contact the help desk.
When the software has loaded properly, the screen should look something like this:
Click here for a picture (150K gif format)
Making a Lewis Structure
First, for each sample, we will construct a Lewis structure. Use the "Coach Lewis" tool to construct the structure. First, "click" on the Coach Lewis tool (the C with eight dots around it). You will then be assisted through the process of creating one of the possible Lewis structures for your sample. As is done in the lab manual, the structure for formaldehyde, CH2O is described here.
Click here for a picture (83K gif format)
1. When prompted, input the formula for your sample, the number of valence electrons and the total charge of your sample (remember that ions have charges). Use the usual capital and small letters in the formula. If you make any obvious mistakes, Coach Lewis will help you.
Click here for a picture (149K gif format)
2. A work area will appear with all of the necessary atoms and electron pairs at the top. Drag and drop the atoms from the top to the work area. Arrange them roughly in the skeleton that you think the sample should have. Click "next step" when ready.
Click here ofr a picture (149K gif format)
3. Drag and drop electron pairs to make the single bond skeleton for your sample. Click "next step" when ready, or click "pervious step" if you want to go back and fix something.
Click here for a picture (149K gif format)
4. Drag and drop 3 electron pairs to every non-H atom that is external (has only 1 bond). Remember that you cannot violate the octet rule. If you violate the octet rule, Coach Lewis will respond with a "too many connections" error message. Click "next step" when done, or "previous step" to go back.
Click here for a picture (150K gif format)
5. Assign formal charge to each atom. Double click on the atom symbol. You will be prompted to choose a formal charge. If you are incorrect, you will have the opportunity to try again or to accept the value given by the program. If you use the program value, be sure that you understand where the number comes from. Click on "next step" to continue. Click on "pervious step" to go back.
Click here for a picture (150K gif format)
6. Minimize the formal charges by dragging electron pairs to form multiple bonds between negative and positive formal charge atoms. The formal charges will be updated by Coach Lewis as you go. When finished, click on "next step" to continue or click on "previous step" to go back.
Click here for a picture (150K gif format)
7. You will be prompted to tell Coach Lewis how many resonance structures you expect to be able to make. Copies of your structure will appear and you can move electron pairs to generate resonance structures. Be aware that you will NOT be stopped from violating the octet rule.
8. Choose "done" to return to the molecule layout with your finished structure, or to return without your structure, choose "quit."
Viewing the Models
After you have finished the Lewis and resonance structures, you return to the molecule layout. A skeleton of your molecule will appear on the screen. To view the molecule as a ball and stick model, click on the ball and stick tool. To view it as a space filling model (which more accurately represents the shapes) click on the space filling tool. To rotate the molecule, click on the free rotate tool. Use the molecule viewer to help you answer the information required for each molecule in the lab manual. You can also save and print your molecules by using the appropriate Windows commands.
Click here for a picture showing skeleton model (150K gif format)
Click here for a picture showing ball and stick model (150K gif format)
Cliick here for a picture showing space filling model
(150K gif format)
You do not need to wear safety goggles when performing this experiment. Work
by yourself on the computer portion of the experiment. For the most part, we will
perform the experiment as described in Chapter 12 of the lab manual, except that we will
use the computer instead of the wooden or plastic ball and stick models. Read the
introduction on pages 91-94. You might want to use the software to draw some of the
molecules described in the introduction for practice and to further illustrate the
authors' points. The procedure (pp. 94-96) illustrates a method using ball and stick
models for making a molecule. Use the example molecule described there to make your first
computer model. Once you have successfully made this molecule (formaldehyde), move on to
the other molecules and ions given in the lab manual. In your lab notebook, complete a
table similar to that on pp. 97-98. Your TA will provide a list of unknowns for part C.
The report should have the usual sections. For results, complete a table of the format shown on pages 97-98. Look up the appropriate sections in the textbook to help you discuss how the arrangement of electrons leads to the shape of the molecule or ion. Discuss why some of the molecules or ions have resonance structures and some do not. Discuss why some are polar and some aren't. Be sure discuss your conclusions from parts B and C of the procedure.
These pages are maintained by Dr. Nicholas H. Snow. For more information or to make a comment, please send email.
(nhs) 11/3/98
