Drawing molecules

Drawing molecules
Be realistic
Below is another organic structure—again, you may be familiar with the molecule it represents; it is a fatty acid commonly called linoleic acid.

We could also depict linoleic acid as

You may well have seen diagrams like these last two in older books—they used to be easy to print (in the days before computers) because all the atoms were in a line and all the angles were 90°. But are they realistic? We will consider ways of determining the shapes and structures of molecules in more detail in Chapter 3, but the picture below shows the structure of linoleic acid determined by X-ray crystallography.

You can see that the chain of carbon atoms is not linear, but a zig-zag. Although our diagram is just a two-dimensional representation of this three-dimensional structure, it seems reasonable to draw it as a zig-zag too.

This gives us our first guideline for drawing organic structures.

Realism of course has its limits—the X-ray structure shows that the linoleic acid molecule is in fact slightly bent in the vicinity of the double bonds; we have taken the liberty of drawing it as a ‘straight zig-zag’. Similarly, close inspection of crystal structures like this reveals that the angle of the zig-zag is about 109° when the carbon atom is not part of a double bond and 120° when it is. The 109° angle is the ‘tetrahedral angle’, the angle between two vertices of a tetrahedron when viewed from its centre. In Chapter 4 we shall look at why carbon atoms take up this particular arrangement of bonds. Our realistic drawing is a projection of a threedimensional structure onto flat paper so we have to compromise.

Be economical
When we draw organic structures we try to be as realistic as we can be without putting in superfluous detail. Look at these three pictures.

(1) is immediately recognizable as Leonardo da Vinci’s Mona Lisa. You may not recognize
(2)—it’s also Leonardo da Vinci’s Mona Lisa—this time viewed from above. The frame is very ornate, but the picture tells us as much about the painting as our rejected linear and 90° angle

diagrams did about our fatty acid. They’re both correct—in their way—but sadly useless. What we need when we draw molecules is the equivalent of (3). It gets across the idea of the original, and includes all the detail necessary for us to recognize what it’s a picture of, and leaves out the rest. And it was quick to draw—this picture was drawn in less than 10 minutes:
we haven’t got time to produce great works of art! Because functional groups are the key to the chemistry of molecules, clear diagrams must emphasize the functional groups and let the hydrocarbon framework fade into the background. Compare the diagrams below:

The second structure is the way that most organic chemists would draw linoleic acid. Notice how the important carboxylic acid functional group stands out clearly and is no longer cluttered by all those Cs and Hs. The zig-zag pattern of the chain is much clearer too. And this structure is much quicker to draw than any of the previous ones!
To get this diagram from the one above we’ve done two things. Firstly, we’ve got rid of all the hydrogen atoms attached to carbon atoms, along with the bonds joining them to the carbon atoms. Even without drawing the hydrogen atoms we know they’re there—we assume that any carbon atom that doesn’t appear to have its potential for four bonds satisfied is also attached to the appropriate number of hydrogen atoms. Secondly, we’ve rubbed out all the Cs representing carbon atoms. We’re left with a zig-zag line, and we assume that every kink in the line represents a carbon atom, as does the end of the line.

We can turn these two simplifi cations into two more guidelines for drawing organic structures.

Be clear
Try drawing some of the amino acids represented on p. 16 in a similar way, using the three guidelines. The bond angles at tetrahedral carbon atoms are about 109°. Make them look about 109° projected on to a plane! (120° is a good compromise, and it makes the drawings look neat.)
Start with leucine—earlier we drew it as the structure to the right. Get a piece of paper and do it now. Once you have done this, turn the page to see how your drawing compares with our suggestions.

It doesn’t matter which way up you’ve drawn it, but your diagram should look something like one of these structures below.

The guidelines we gave were only guidelines, not rules, and it certainly does not matter which way round you draw the molecule. The aim is to keep the functional groups clear and let the skeleton fade into the background. That’s why the last two structures are all right—the carbon atom shown as ‘C’ is part of a functional group (the carboxyl group) so it can stand out.
Now turn back to p. 16 and try redrawing the some of the other eight structures there using the guidelines. Don’t look at our suggestions below until you’ve done them! Then compare your drawings with our suggestions.

Remember that these are only suggestions, but we hope you’ll agree that this style of diagram looks much less cluttered and makes the functional groups much clearer than the diagrams on p. 16. Moreover, they still bear significant resemblance to the ‘real thing’—compare these crystal structures of lysine and tryptophan with the structures shown above, for example.

Structural diagrams can be modifi ed to suit the occasion
You’ll probably fi nd that you want to draw the same molecule in different ways on different occasions to emphasize different points. Let’s carry on using leucine as an example. We mentioned before that an amino acid can act as an acid or as a base. When it acts as an acid, a base (for example hydroxide, OH-) removes H+ from the carboxylic acid group in a reaction we can represent as:
The product of this reaction has a negative charge on an oxygen atom. We have put it in a circle to make it clearer, and we suggest you do the same when you draw charges: + and – signs are easily mislaid. We shall discuss this type of reaction, the way in which reactions are drawn, and what the ‘curly arrows’ in the diagram mean in Chapter 5. But for now, notice that we drew out the CO2H as the fragment on the left because we wanted to show how the O–H bond was broken when the base attacked. We modifi ed our diagram to suit our own purposes.
When leucine acts as a base, the amino (NH
2) group is involved. The nitrogen atom attaches itself to a proton, forming a new bond using its lone pair.
We can represent this reaction as:

Notice how we drew in the lone pair this time because we wanted to show how it was involved in the reaction. The oxygen atoms of the carboxylic acid groups also have lone pairs but we didn’t draw them in because they weren’t relevant to what we were talking about. Neither did we feel it was necessary to draw CO2H in full this time because none of the atoms or bonds in the carboxylic acid functional group was involved in the reaction.

Structural diagrams can show three-dimensional information on a two-dimensional page
Of course, all the structures we have been drawing give only an idea of the real structure of the molecules. For example, the carbon atom between the NH2 group and the CO2H group of leucine has a tetrahedral arrangement of atoms around it, a fact which we have so far completely ignored.

We might want to emphasize this fact by drawing in the hydrogen atom we missed out at this point, as in structure 1 (in the right-hand margin). We can then show that one of the groups attached to this carbon atom comes towards us, out of the plane of the paper, and the other one goes away from us, into the paper.

There are several ways of doing this. In structure 2, the bold, wedged bond suggests a perspective view of a bond coming towards you, while the hashed bond suggests a bond fading away  from you. The other two ‘normal’ bonds are in the plane of the paper.
Alternatively we could miss out the hydrogen atom and draw something a bit neater, although slightly less realistic, as in structure 3. We can assume the missing hydrogen atom is behind the plane of the paper because that is where the ‘missing’ vertex of the tetrahedron of atoms attached to the carbon atom lies. When you draw diagrams like these to indicate the three dimensional shape of the molecule, try to keep the hydrocarbon framework in the

plane of the paper and allow functional groups and other branches to project forwards out of the paper or backwards into it.
These conventions allow us to give an idea of the three-dimensional shape (stereochemistry) of any organic molecule—you have already seen them in use in the diagram of the structure of palytoxin at the beginning of this chapter.

The guidelines we have given and the conventions we have illustrated in this section have grown up over decades. They are not arbitrary pronouncements by some official body but are used by organic chemists because they work! We guarantee to follow them for the rest of the book—try to follow them yourself whenever you draw an organic structure. Before you ever draw a capital C or a capital H again, ask yourself whether it’s really necessary!
Now that we have considered how to draw structures, we can return to some of the structural types that we find in organic molecules. Firstly, we’ll talk about hydrocarbon frameworks, then about functional groups.

All the big American textbooks have early chapters on structure, shape, and the drawing of molecules but they tend to use Lewis structures with all atoms and electrons in bonds shown and often
right angles between bonds.
A short and sensible introduction is in the Oxford Primer
Foundations of Organic Chemistry by M. Hornby and J. Peach, OUP, Oxford, 1996.
For more on palytoxin: E. M. Suh and Y. Kishi,
J. Am. Chem. Soc., 1994, 116, 11205–11206.
For an account of the competing claims to the fi rst proposal of a cyclic structure of benzene, see Alfred Bader’s article ‘Out of the Shadow’ in the 17 May 1993 issue of
Chemistry and Industry.