Reading a structure diagram: displayed, structural and skeletal formulas

A chemical formula can be written in several ways, and each shows a different amount of detail. C₂H₆O tells you which atoms are in ethanol. A drawing tells you how they are joined. This guide explains the four common ways of writing a formula, from the plainest to the most compact. It then shows how to read the skeletal drawing of a peptide, like the one on each of our product pages.

Terms are defined in the glossary.

Chemical formula: four ways to write one

Each step down the table hides a little more and shows the shape more clearly. Chemists use whichever suits the job. A molecular formula is enough for working out a molar mass. A skeletal formula is better for anything bigger than a few atoms.

Molecular formula

A molecular formula lists each element and how many atoms of it there are, written in Hill order: carbon first, then hydrogen, then the rest alphabetically. It is the formula given on our product pages and certificates, for example C₁₆H₃₀N₄O₄ for KPV.

What it can't show is how the atoms are connected. Many different molecules can share one molecular formula. These are called isomers. For how a molecular formula relates to the simplest ratio of atoms, see empirical and molecular formulas.

Structural formula

A structural formula, sometimes called a condensed formula, writes the molecule on one line in the order the groups are joined. Ethanol is CH₃CH₂OH: a CH₃ joined to a CH₂, joined to an OH. Acetic acid is CH₃COOH: a CH₃ joined to a carboxylic acid group.

This form is quick to type and makes the functional groups easy to spot. It becomes hard to read once a molecule has branches or rings.

Displayed formula

A displayed formula draws every atom as its symbol and every bond as a line. A single line is a single bond, which is one shared pair of electrons. A double line is a double bond. See chemical bonds and polarity for what a bond is.

Displayed formulas show every connection, so they are good for learning and for checking a small molecule. They are drawn flat, though, and the angles on paper don't match the real shape of the molecule. For anything with more than a dozen or so atoms, they become crowded.

Skeletal formula

A skeletal formula shows the carbon framework as lines, with the carbon atoms and the hydrogens on them left out. The rules are:

• Carbon atoms aren't written. Each corner where lines meet, and each line end with no symbol, is a carbon.
• Hydrogens on carbon are left out. Each carbon is assumed to have enough hydrogens to make four bonds in total.
• Every other atom is shown, such as oxygen, nitrogen and sulfur, along with any hydrogens attached to them.
• Zigzags show chains. A straight run of carbons is drawn as a zigzag, which is closer to the real shape than a straight line.

Ethanol becomes a two-segment zigzag ending in OH. Acetic acid becomes a short V: one end is the CH₃, the corner is the carbonyl carbon with a double bond to O, and the other end is OH.

Skeletal formulas are the standard way to draw organic molecules. They are compact enough for large molecules such as peptides, and the carbon framework stands out.

How to draw a skeletal formula

1. Draw the carbon chain as a zigzag, one line for each carbon–carbon bond, with a corner or line end wherever a carbon sits. Draw rings as polygons.
2. Add double and triple bonds as two or three parallel lines.
3. Write in every atom that isn't carbon or hydrogen-on-carbon, such as O, N, S or a halogen, at the end of its line, with any hydrogens it carries (OH, NH₂). Then check that each carbon has no more than four bonds.

For ethanol, CH₃CH₂OH, that gives two lines at an angle with OH at the end. For acetic acid, CH₃COOH, it gives a V with a double line up to O at the corner and OH on the far end, as in the figure above.

Wedges and hashes

A flat drawing can't show which way a group points in three dimensions. Skeletal formulas use two extra kinds of line for this:

• A solid wedge is a bond coming out of the page towards you.
• A hashed wedge is a bond going behind the page.

They matter at a stereocentre, a carbon whose four different groups can be arranged in two mirror-image ways. L- and D-amino acids differ only there, and the wedges are what tell them apart on paper.

Reading a peptide's structure diagram

Most of our product pages show the compound's skeletal formula in the Technical data section. The drawing follows the same rules as above, with a few changes so that it stays readable:

• No letters on the drawing. Instead of writing O, N and S, the figure marks each with a symbol, and a key under the drawing says which is which.
• Unlabelled corners are carbon, as in any skeletal formula.
• Wedges and hashes show stereochemistry where the molecule has it.
• Hover over, or tap, a residue to lift it out and see its name.

A worked example: KPV

KPV is a tripeptide: three amino acid residues, lysine, proline and valine, joined in that order. Its molecular formula is C₁₆H₃₀N₄O₄. This is the same drawing as on the KPV product page:

KPV structure

Hover a residueTap a residue

Read it from one end to the other:

1. Find the backbone. A peptide's backbone repeats the same pattern for each residue: a nitrogen, then the alpha carbon, then a carbonyl carbon with its double-bonded oxygen. In KPV that pattern appears three times.
2. Find the peptide bonds. Each carbonyl carbon is joined to the next residue's nitrogen. That C(=O)–N link is the peptide bond. KPV has two.
3. Find the ends. At the start is a free amine (–NH₂) on lysine's alpha carbon: the N-terminus. At the other end is a carboxylic acid (–COOH) on valine: the C-terminus. KPV ends in a free acid, not an amide. See C-terminal amides and N-terminal acetylation for how that would look different.
4. Read the side chains. Each alpha carbon carries one side chain:
   • Lysine: a chain of four carbons ending in a second amine.
   • Proline: a ring of carbons that loops back and bonds to its own backbone nitrogen. This is why proline's nitrogen has no hydrogen in the chain.
   • Valine: a short branch, two carbons on one, which makes a small Y.
5. Check the stereocentres. Each of the three alpha carbons has a wedge or hash showing that it is the L form.

The same method works for longer peptides. The drawing just has more repeats of the backbone pattern. For the side chain of every standard amino acid, see the 20 amino acids. For the codes used to write sequences, see amino acid codes.

Which formula to use

Databases such as PubChem give all of these for a compound, along with machine-readable forms such as SMILES and InChI.

Related guides

For formulas and percentage composition, see empirical and molecular formulas. For the groups named in a structure, see functional groups in peptides. For the 3D side of a structure, see stereoisomers.