Organic Structures 1.0

This HTML-based presentation provides students with basic background on bonding, methods of representing (i.e., drawing, writing and naming) function groups, and types of isomerization possible in in organic molecules. These connections are all beautifully tied together in the final section of the module which provides an interactive presentation of name, structural drawing, and 3-D rendering of selected pharmaceutical products.

There are two versions of this module provided on Release 1.0. The 'regular' version uses PDB structure files, which are viewed using RasMol (RasMac, or RasWin) as a helper application to the web browser. This helps users get a sense of the three dimensionality of molecules.

Although the exercise itself has a number of intricate parts, the premise of the exercise is simple. In thinking of, and communicating about, organic molecules, chemists use a set of tools--including words, parts of words, and pictures of varying levels of complexity. This module helps students explore the interrelation among these tools of thinking and communication, so that they will become familiar both with the tools and with the concepts that stand behind their use.

For the two dimensional representation (line notation) of organic molecules students may want to brush up on the the bonding patterns observed for atoms commonly found in organic molecules. In order to be able to understand the naming of organic compounds some knowledge about functional groups (about 20 of them are described), and isomers of molecular structures is important.

The medicinal drug structures section is the capstone. This section presents a list of 11 ethical drugs, some over-the-counter and some prescription. For each, there is provided a line-drawing structure and a systematic name in one frame (left), and a RasMol viewable link for the three-dimensional structure and a summary of the medical purpose of the drug in another (right). Also included are some of the names under which the drug may have been marketed. The line-drawing structure with systematic name is a clickable image map where by clicking on a portion of the line-drawing structure, the corresponding portion of the name will be highlighted and vice versa. In both cases, the word "explain" may be displayed below the name/structure panel, and clicking on that link will display the information on that functional group from the previous section where functional groups were discussed in the right hand frame.

Table of contents:

• Acknowledgments
• Purpose
• RasMol Viewing Instructions
• Review of Bonding
• Line Notation
• Functional Groups
• Isomerization
  • Functional Isomers
  • Positional Isomers
  • Stereo Isomers
• Naming
• Medicinal Drug Structures