About those images ...

I believe that most of my fellow chemists "see" molecules within their brains. Indeed, I have often joked that if one popped open the front of the cranium of a practicing chemist, you could see the TV used for visualizing molecules. The data that comes to a chemist doesn't just sit around as tables and 2-D drawings on a piece of paper or a balckboard, it gets integrated into 3-D models, and chemists move these "real" molecules around within the cranium as they argue about properties and reactions. Students need to learn this visualization skill, and many do not aquire it until they are near the end of their college career.

All of the images are of the common molecule ETHANOL, the active ingredient in beer and wine. It contains two carbon atoms, one oxygen atom, and six hydrogen atoms.

These images are scattered throughout the website in order remind users that chemists use multiple "views" of molecules in order to work with chemical reactions. There isn't just one molecule to "see"; chemists call up various representations in order to emphasize relevant properties for a particular application.

All the images were generated with Spartan '06 ®

This called the Van der Waals view. The gray surfaces shows -- more or less -- where the repulsive forces between molecules become dominant. If one is thinking about how molecules move when they are next to one another -- as in pure liquid ethanol -- this image can help guide the reasoning.

This is called the Ball & Stick view. Chemists call on this view to help visualize the bond lengths and bond angles within a molecule -- the structure of a molecule. The oxgyen atom is shown in red, the carbon atoms in gray, and the hydrogen atoms are not shown -- we chemists know enough about such molecules to put them in by ourselves. Of course, we know that the colors are just to help us tell the atoms apart in a picture -- assigning real colors to individual atoms is not simple.

This is an alternate Ball and Stick view. This time the hydrogen atoms are shown. Which view is better? Perhaps novice chemists need to be reminded that the hydrogens are there, and perhaps experienced chemists think that showing the hydrogen atoms complicates the picture too much.

This the Tube View. Sometimes we want to concentrate on the bonds between atoms and minimize the attention we pay to the atoms.

The Electrostatic Map uses colors to show the density of electrons mapped onto the Van der Waals surface. Views like this are important in considering which types of reactions will be favored (or disfavored.). In this case the red shows a high electron density, the green a medium electronic density, and the blue a low electron density.

The Space Filling View combines elements of the Ball & Stick view and the Van der Waals views. It carries the sense of how molecules push against each other and identifies the atoms through colors.