Organic Chemistry/Foundational concepts of organic chemistry/Visualization

Visualization
Visualization is absolutely crucial in organic chemistry. Being able to picture the 3-dimensional structure of a molecule in your head, rotating it around, seeing how it interacts with other molecules; these are really important skills that you need to develop if you want to understand what's really happening in organic chemistry.

Some people are born with this skill naturally, but even if you aren't, like anything else, with practice, you can become better at it. So if this is difficult for you, spend time working on it. Most people willing to put the effort in, before long, have that "Aha!" moment, where they suddenly just get it. Once you "get it", you really don't have to work at it anymore. You'll be able to look at a molecule, regardless of how it's drawn, and you'll just know what it looks like in 3-dimensions.

Many people find models very useful. As mentioned in the foreword of this book, there are places where you can buy molecular model kits and there are sites that offer free online software like Jmol, for moving models around virtually, with your mouse. Take advantage of these kinds of tools, because if you don't understand the 3-dimensional aspects of organic chemistry, you're not going to really understand organic chemistry.

Organic chemists have developed a number of ways for describing molecules. Some of them explicitly show the 3-dimensional structure, some imply it, and some don't show it at all and simply assume that that the reader has enough background to be able to visualize it without aids.



For example, in the figure above, the simplest organic molecule, Methane, is shown rendered in 5 different ways. At the far left, simply the text CH4. This indicates 4 hydrogen atoms attached to a carbon atom. But this doesn't tell you anything about how it looks. An organic chemist doesn't need more information than that. Any organic chemist knows what a methane molecule looks like. However, for more complex molecules, even for the best organic chemists, knowing the components often isn't enough to visualize the structure.

The second drawing provides a little more information. You have the carbon in the center and 4 hydrogens attached to it. This provides a little more information, but it provides no insight into the 3-dimensional structure. This kind of drawing is called a Kekulé structure, after Friedrich August Kekulé, or a line-bond structure.

The third drawing is a very common rendering in organic chemistry, often called dash-wedge notation. The 3-dimensional structure of a methane molecule is that of a tetrahedron. Think of it as a pyramid with a triangle as the base (as opposed to a square base, like the pyramids in Giza). Then picture the hydrogen atoms at the 4 corners of that pyramid, one at each corner of the bottom and one at the point at the top, and finally, the carbon in the very center. The angle between each hydrogen bond in a methane is at what's called a tetrahedral angle, which is 109.5°.

That's what the dash-wedge model is a little better at showing. To picture a molecule in dash-wedge notation, think of the carbon and two hydrogens connected by solid lines (the one on the right and the one below the carbon) as being all in the same plane as the screen (or paper). The solid wedge represents a bond coming out of the screen (or paper) towards us, and the dashed-wedge is that of a bond going away from us.

This common form of rendering will frequently give the reader a good idea of the 3-dimensional structure of a molecules of moderate complexity.

For more complex structures, sometimes 3-dimensional renderings are needed like the 4th and 5th images. For methane, this is a bit overboard, but as the structures start to get more complex, a more complex method of rendering is needed to accurately describe the shape. The 4th image is called a ball and stick model, with the hydrogens represented by white balls and the carbon in the center is represented by a grey ball.

Finally, in the 5th image, called a stick model, forgoes the actual atoms and simply shows the bonds. Color changes represent different atoms. In this case, the grey near the center, represents the carbon and the white on the ends represents hydrogen.



The figure above shows 5 different renderings of the cyclohexane molecule. Cyclohexane consists of a ring of 6 carbon atoms, each with 2 hydrogen atoms attached to them. The hexagon on the left shows the carbons with their 2 hydrogens. Often, however, a cyclohexane is drawn as simply a hexagon, with the carbons and hydrogens simply implied.

The second image shows the ring at an angle, but like the first, gives little insight into the structure beyond the fact that it's cyclic.

The third is a ball and stick figure, much like we saw for methane. As you can see, the carbons are not all flat. This particular conformation of cyclohexane is called the chair configuration. Conformations of cyclohexane will be discussed more later on.

The fourth is a stick figure of cyclohexane, also in the chair conformation.

Finally, we have the filled version of the cyclohexane molecule. The surfaces represent a sort of field around the molecules that represent the boundaries of how close atoms can approach, also called Van der Waals surfaces. This representation isn't used as often as others in organic chemistry.

Summary
As we've seen, there are a variety of ways to represent molecules in organic chemistry. If any one method is most important to learn, it's the dash-wedge notation, as this will be used throughout this and other books when describing the 3-dimensional nature of organic molecules. You should be able to look at it and immediately know which bonds lie in the same plane, which ones are coming towards us and which are going away. Once you're comfortable with that, you'll find that further visualization of more complex molecules becomes much easier.