LABORATORY SCHEDULE

Professor Charles E. McKenna
Department of Chemistry
Last updated Sept. 26, 2003

All labs are in SGM 121

Week of September 29: The structure, bonding and conformation of molecules
Due date: Your lab date plus one week

The structure, bonding and conformation of molecules is crucial to the study of organic chemistry. In this lab you will work through a wide variety of online problems using 3-D computer models of molecules. You will be given structures to draw using a computer program (ISIS draw).ISIS draw is a program that can draw 2-d chemical structures very quickly and easily. It is  available on all the Windows PCs and Macs in SGM 121. You can also Download ISIS draw from the web at http://www.mdli.com/. 

We have a page that can help you learn how to use it by drawing the LSD molecule. This will cover:

• Structure: Understanding how molecules fit together and the differences between similar molecules.
• Bonding: Covalent vs. hydrogen bonding, dispersion forces and how they affect the geometry of molecules.
• Chirality: Molecules with the same connectivity and formula can still differwidely in biological activity: the mirror image of a potent drug may have no value whatsoever.

You will also use a more sophisticated program called Chemsketch. Your TA will introduce this program to you.

The Lab:

Carbon is the main element that sustains life. One reason is its versatility. In nature, it exists as allotropes: graphite and diamonds. “Organic” compounds of carbon show enormous diversity due to the special ability of carbon to make multiple bonds, as discussed in the lecture. The 3D shapes of drugs, which help to determine their activity, selectivity, and toxicity, are very dependent on the type of bonding to their carbon atoms. This lab explores carbon-based structures. In Part 1 of this lab, you will use a 2D chemical structure drawing program–ISIS Draw–to construct an AIDS drug, after finding the structure via a Web search. In Part 2, you will will use a more sophisticated, 3D drawing program–Chemsketch–to create three simple organic molecules, allowing the program to find their most stable 3D structures, and you will be asked to correlate carbon bonding mode with compound structure. In Part 3, you will use Chemsketch to make the image and mirror image forms (“enantiomers”) of an amino acid found in proteins, and show that they are (or are not) superimposable.

In lecture we mentioned that “orbitals” are really math equations. Chemsketch uses a built-in math package to calculate the most favorable structure for each molecule that you create, and shows you the final result. This structure corresponds to the lowest energy calculated for the molecule, by minimizing mutual repulsion between electrons in different atoms. The math is invisible to you, but you will be able to watch the structure change in real time as the calculation proceeds.

Your TA will explain some functions of ISIS Draw and Chemsketch that you will need in order to answer several questions that are part of this lab. Please note that Chemsketch may only be found on the lab computers.

Be sure to create a single document containing all your work for electronic submission to your TA. If you have any questions about what to submit, ask your TA.

Part 1: AIDS Drug Structure

a) Reproduce the structure of the AIDS drug Viracept with ISIS Draw (find structure on Web) (4 points).

b) Calculate the molecular weight of Viracept using the “chemistry” command of ISIS draw (1 point).

Part 2: Carbon Bonding Modes

a) Carbon bonded to 4 atoms (3 points).

When carbon is bonded to 4 atoms, it adopts a tetrahedral geometry. This geometry optimizes the distance between each of four atoms forming a single bond with the carbon. Hydrocarbon (C,H) compounds in which all the carbon atoms are singly bonded are called “saturated”. Examples are methane (natural gas), ethane, propane, butane, and octane. Using the Chemsketch software, your task is to create ethane (C2H6) and analyze its structure.

•Draw the ethane molecule and optimize its geometry using the built-in program function.
•Copy and paste a ball-and-stick representation into a Word file.
•Measure the following parameters and record them in your file.
(a) C-C bond distance
(b) C-C-H angle

b) Carbon bonded to 3 atoms (3 points).

When carbon is bonded to 3 atoms, it adopts a trigonal planar geometry. The carbon atom forms two single bonds with two other atoms, and a double bond with the third one. Hydrocarbon compounds that contain one or more C=C bonds are called “unsaturated”. Ethylene (C2H4) is the simplest example of an unsaturated hydrocarbon compound with a double bond.

•Draw the ethylene molecule and optimize its geometry.
•Copy and paste a ball-and-stick representation into your Word file.
•Measure the following parameters and record as above.
(a) C-C bond distance
(b) C-C-H angle

c) Carbon bonded to 2 atoms (3 points).

When carbon is bonded to 2 atoms, it adopts a linear geometry. only forming a single bond with the first atom and a triple bond with the second one and adopting a linear geometry. You can verify this by drawing acetylene (C2H2), a gas commonly used in welding.

•Draw the acetylene molecule and optimize its geometry.
•Copy and paste a ball-and-stick representation into your Word file.
•Measure the following parameters
(a) C-C bond distance
(b) C-C-H angle

Questions (2 points). Record your answers in your Word file.

&Mac183; How do the C-C bond distances vary with carbon geometry?
&Mac183; How do the C-C-H bond angles vary with carbon geometry?

Part 3: Chirality

Using Chemsketch, draw the amino acid alanine in both its image (natural, “L”) and mirror image (unnatural, “D”) forms, label them and optimize their geometries. Try to superimpose the two structures. Can you do it? Submit your answer with ball-and-stick pictures of your structures, oriented to prove that your answer is correct (4 points).

(C) CE McKenna, Ph.D. USC, Chemistry Dept., 2002-3