Chemical Structures

Slide3Chemical structures can be represented visually in a variety of ways. Therefore, it is important for readers to have mental flexibility when describing chemical images.

For example, the following three images express the same structure (adenosine triphosphate):ATP-xtal-3D-ballsAtp_exp.qutemol-ball2000px-Adenosintriphosphat_protoniert.svg

Each structure uses different visual cues to express the same information. I and my readers quickly get used to thinking about and describing structures in different ways. Sometimes colors are most pertinent, sometimes sizes, sometimes letters and line shading. With  large or complex structures, it is often important to be able to describe the same figure in different ways, approaching it repeatedly from different angles until all the descriptions synergies in my mind and give me a well-formed, comprehensive image.

Generally to begin approaching a unfamiliar structure, I have the reader identify the longest chain of repeating components, and then describe what branches off from this chain. This can work very well for organic compounds, but it is not always useful. It is always important to follow the logic of the molecule. If there is a central ring structure, begin with that and describe what branches out from it in a clockwise progression. If there isn’t a clear central pattern, I usually ask them to describe everything working from the left  to the right.

For large and complex structures, it can become difficult to keep track of details all the way through to the end of a long verbal description. Sometimes it helps me to write information down, even thought I can’t see what I’m writing. This is how my brain works. Another thing that helps is getting the general shape first, and then coloring it in with details. Often I will ask readers to trace the general shape of the molecule or compound onto the back of my hand or arm, and then to touch the part of the figure they are describing in detail. It gives me a frame of reference to hang newer details upon.

It is most convenient when my readers know the names of organic substituents. If they know chemical nomenclature, all the better. If they do not (or if they have any uncertainty) I expect them simply to name exactly what they see, atom by atom and bond by bond. In some cases, I might ask my readers to do some “homework,” aka. to memorize the names of certain common structures and chemical substituents. Being able to begin a description with, “It’s a phospholipid,” or “It’s a polysaccharide,” can streamline the process a lot. When readers know chemical terminology, it also makes it much easier for me to ask questions about pertinent information.