Artwork

Chemical Structure from the inside out

Chemistry is one of those words that make a lot of people shudder, presenting it on a poster in a cool and interesting way can be a tricky task. Here are some tips to give your organic molecules a little bit of pop! First of all though you need to know what you want to communicate, are you comparing a couple of molecules? More than a couple? Or just displaying the attributes and features of one alone. Also how much space do you have to display them? A small diagram won’t fit buckets of detail, so best to stick to a more basic design. However, if you’re working on a larger area a skeletal design will leave a lot of dead space, and look pretty boring. In this post we’re going to use Caffeine, a personal favourite of ours to explain.

Skeletal Structure: The Bare Bones

Great for when you want to show a complicated process or mechanism without crowding your page with letters.

Koffein_-_Caffeine.svg

The simplest way to display the structure of any organic molecule is skeletal. In this format we don’t write a letter ‘C’ wherever there’s a carbon, we draw chains of Carbons as zigzagging lines. Each line represents a bond (or two) and each corner represents a Carbon. We don’t draw the hydrogens that are attached to the carbon chain. We do write them on when they are bonded to any other atom though, such as Oxygen or Nitrogen. In these instances they define the type of functional group we have attached, so aren’t as predictable as the standard hydrocarbon chain.

Full Display Diagrams

All the atoms in the molecule.

caffeine

Full display is exactly what it says on the tin, it shows every bit of detail and you don’t get to take any short-cuts with writing out the hydrocarbon chains. Could be a bit annoying it you’re doing something really long and repetitive like a fatty acid or a dense hydrocarbon. Typically you try to get all the bond angles correct, although this can be a bit tricky when doing constrained shapes. Sometimes allowances have to be made if you have a particularly bulky group. In the 3D structure this would probably project out of the plane, but because you have to get all the atoms in you’re going to have to do some creative rearranging. These diagrams are brilliant for detailed descriptions of individual molecules, but be wary if presenting on a poster they can look make it look crowded and busy on the page especially if using a large molecule. You can make allowances with some hydrocarbon groups. Usually you’d write a methyl group as -CH3 rather than drawing out at the C-H bonds.

Stick and Ball Diagrams

Great for comparing structures and shapes.

caffeine silhouetteThese diagrams are more three dimensional than traditional skeletal diagrams, yet still get the full detail from full display diagrams in. They can look a bit more interesting and make it easier to compare molecules that might look a little bit too similar under the skeletal system (zigzags all look the same after a while).

These diagrams usually use the CPK colouring scheme to show you what atoms you have rather than using letters. This means that you don’t end up disrupting the structure of molecule, and you can show the different sizes of various atoms (hydrogens are tiny). Because you’re only trying to see the colours rather than read letters, you’ve got more scope for overlapping different atoms and therefore getting a more accurate 3D shape.

Typically the colours are as followCaffeine Ball and sticks:

  • Black – Carbon
  • White – Hydrogen
  • Blue – Nitrogen
  • Red – Oxygen
  • Yellow – Sulfur
  • Purple – Phosphorus

Obviously you could use your own colours, as long as you use a key. If you’re going to pick your own, make sure you’ve made it obvious which is which. People might get very confused if you’re suggesting your molecule has a sulfur backbone rather than a carbon one.

Empty spaces

PrintOf course if we were really trying to be accurate we wouldn’t be drawing atoms as balls and sticks at all. Atoms are mostly empty space. If you atom is the size of a football pitch, most of it is empty space. The only solid part of it is the football sized nucleus in the middle. Electrons are somewhere in the orbitals around the edges of the pitch, although you can’t really draw them as particles zipping around. Chemists typically represent orbitals as areas where the electron is probably, possibly, somewhere – they just can’t say where exactly.