Drawing Molecules

Introduction

Organic chemists routinely use simplified line diagrams to represent molecules. These diagrams rapidly convey a surprising amount of data while still being clean and quick to draw. The key to these drawings is understanding that they highlight the functionality within a molecule and minimise the carbon skeleton that supports this functionality. This summary will re-iterate the key points. Like all these summaries it is not a comprehensive overview but is rather to jog your memory.

Skeletal or line diagrams

Let’s start with the simplest of molecular representations and start adding more useful information until we reach the structures seen in organic textbooks.

Various representations of L-leucine (naughtily drawn in non-zwitterionic or uncharged form)

The molecular formula simply tells you what atoms are present in your compound. It has no information about connectivity or shape. The condensed formula adds connectivity, it indicates the order the atoms are joined. Its limitations include a lack of information about shape, it isn't easy on the eye, and it rapidly becomes overly complicated (just imagine trying to draw compounds with fused rings).

The Lewis structure tells you about the valence electrons, it shows you the discrete covalent bonds as well as the position of the lone pairs of electrons. It is a wonderful representation at the start of your organic chemistry odyssey. But Lewis structures are time-consuming to draw and soon become very messy. The next is the structural representation, this is effectively a cleaned up version of the Lewis diagram. It replaces the shared electrons with lines to represent the bonds (each line is two electrons). There is little wrong with the structural diagram when drawn well (please stop drawing those hideous crosses you were taught at high school). Its downsides come apparent when you draw more complex molecules; it takes time to draw every atoms, and showing every carbon and hydrogen atom can overwhelm the structure, leading to the important functionality being hidden.

The skeletal or line diagram is the simplest representation of an organic molecule. But within its code is all the information organic chemists require. The goal of the skeletal diagram is to emphasize the functionality that adorns a molecule, leaving the carbon framework in the background. In the drawing of leucine above, the carboxylic acid is in red and the amine in green. The carbon framework has been left in black.

Most molecules are not flat so our representations must indicate their shape. Bold wedges are used to indicate bonds that are pointing towards the viewer while dashed wedges show that the bond is going backwards, into the page.

Drawing skeletal or line diagrams

How do you convert a structural representation, showing all the atoms and bonds, into a skeletal diagram? A skeletal representation ignores the hydrogen atoms and their bonds to carbon. It also misses out all the carbon atoms. All other atoms, including the hydrogen atoms of functional groups and all other bonds (unless incorporating condensed formula) must be shown.

Converting a structural representation into a skeletal or line diagram

Points to remember when drawing a skeletal or line diagram:

1. A chain of carbon atoms should always been drawn as a zig-zag. Every kink or corner is a carbon atom and it is more realistic.

2. Always draw bonds as far apart as possible on multiple bonds

Common errors when drawing multiple bonds

3. You musty include hydrogen atoms in functional groups (or at least bonded to heteroatoms)
4. You can include other hydrogen atoms or carbon atoms if they are important (the site of a reaction for instance)

Skeletal drawings to full structural representations

Students often struggle with the reverse process, deciphering a skeletal representation. The key is remembering all atoms except carbon and the hydrogen atoms of C–H bonds are shown. Then noting that a neutral carbon atom (not an carbanion or carbocation) must have four bonds. If the bond is not shown it is a C–H bond (unless the carbon is part of condensed formula).

Understanding a skeletal drawing

Below is an example of ‘reading’ a skeletal or line diagram. It is the reverse of the diagram above. First show where each carbon atom is. Then add the hydrogen atoms.

Converting a line diagram into a structural diagram

While the stepwise approach shown above is helpful, the middle drawing is problematic and teaches students some bad behaviour. This kind of representation shouldn’t be drawn as it is meaningless to chemists. Which brings us onto …

Common mistakes

1. Never draw a pentavalent carbon. Carbon will have four bonds or less.

2. Always draw hydrogen atoms attached to any heteroatom (an atom that is no carbon) on both structural and line diagrams.

3. Make sure the shape is correct. Chains of carbon atoms joined by single bonds should be kinked. Bonds off a multiple bond should be as far apart as possible.

4. Either draw a line diagram or show every single atom and bond. There is no middle ground. Below shows a number of bad examples:

Three poor and two acceptable molecular representations

Mixed representations

It is common for skeletal representations to include condensed formula as well. It is shorthand that speeds up drawings and can make our drawings look cleaner. You must remember that any condensed formula included lists every atom in that section. Condensed formula cannot miss carbons or hydrogen atoms. For example, the CN in the molecule below is a nitrile. It has one carbon atom and a triple bond to nitrogen. There are no missing hydrogen atoms. Likewise CHO is an aldehyde, you cannot add extra atoms (it is not an alcohol drawn backwards - one of the most common misconceptions).

Expanding condensed formula - you cannot add extra atoms

Conclusion

Skeletal or line drawings are the most common way to represent organic molecules. They are quick and simple to draw. They codify a lot of information. This is useful if you understand them but can be frustrating at the start of your career. It is an important skill to learn. Please practice and have a go at the worksheet.

The future of line diagrams

For thirty years, largely since the advent of ChemDraw, the ‘go to’ app for drawing molecules, the way chemists have displayed molecules has remained unchanged. We use a stylistic representation that flattens the molecule and forces bond angles of 120° and multiples of 30°. It gives rise to all the diagrams that look like chicken-wire or honeycomb. These diagram are clean and easy to read but they obliterate the beauty of the real shape of molecules. There is a welcome trend to try and depict molecules more realistically. Below are several representations of sparteine, an alkaloid with antiarrhythmic properties and a useful reagent in asymmetric synthesis. There are also two representations of morphine. In each case, the first drawing shows a standard representation, the second a more ‘realistic’ representation. (it should be noted that ChemDraw have recognized this trend and now have a feature that ‘models’ 3D structure. Can’t wait until they enable ChemDraw to open .cif files (used to record data from X-ray crystallography ‘pictures’ of molecules)).

Representations of sparteine and morphine

At this stage in your career we strongly recommend that you master the traditional drawings and worry about the more realistic three-dimensional representations at a later stage.

The ‘Drawing Molecules’ worksheet can be downloaded HERE.

Please check out the summary of the summary with the ‘Drawing Molecules’ cheatsheet on the Handouts page of this blog.