Chalk−1

Chemistry · General chemistry II · Worked example

Write a SMILES string for a ring

Write a SMILES string for toluene, a benzene ring that carries one methyl group. Then show that a different-looking string describes the same molecule.

Start outside the ring

Begin with the methyl carbon, C. The next atom is the ring carbon it is bonded to.

Open the ring

Write that ring carbon lowercase, because it is aromatic, and give it the digit 1 to mark one end of the bond you are breaking. The string so far is Cc1.

Walk around and close

Write the other five ring carbons in order and put the same digit on the last one, Cc1ccccc1. The two atoms that carry the 1 are bonded, which closes the six-membered ring.

Check the hydrogens

An aromatic carbon with only its two ring neighbors takes one hydrogen, and the one bonded to the methyl group takes none. That is five ring hydrogens and three on the methyl group, C7H8.

C7H8

Write it another way

Starting in the ring gives c1ccccc1C, and writing the alternating bonds out gives CC1=CC=CC=C1. All three strings are toluene, and RDKit writes each of them as the same canonical SMILES.

Three strings for toluene
StringWhat it does differentlyCanonical SMILES (RDKit)
Cc1ccccc1Starts at the methyl groupCc1ccccc1
c1ccccc1CStarts in the ringCc1ccccc1
CC1=CC=CC=C1Writes the double bonds outCc1ccccc1

Result

Cc1ccccc1 is one SMILES for toluene, and c1ccccc1C and CC1=CC=CC=C1 are others.

Your turn

1. One like the example

Write a SMILES string for chlorobenzene, a benzene ring that carries one chlorine atom.

Show the answer and explanation

Clc1ccccc1 is one, and c1ccccc1Cl is another.

Start at the chlorine, then open the aromatic ring on the carbon it is bonded to and walk around to close it. The formula comes to C6H5Cl, because the ring carbon that holds the chlorine has no hydrogen. Chalk names Clc1ccccc1 chlorobenzene.

2. A variation

Write a SMILES string for cyclohexanol, a six-membered ring of carbons with an OH on one of them.

Show the answer and explanation

OC1CCCCC1 is one, and C1CCCCC1O is another.

Start at the oxygen, then write the ring carbon it is on, which opens the ring with a 1, then five more carbons, the last one carrying the closing 1. The ring is not aromatic, so its carbons are capital letters, and the formula is C6H12O.

3. Somewhere new

Naphthalene is two benzene rings that share one edge, ten carbons in all. Write a SMILES string for it.

Show the answer and explanation

c1ccc2ccccc2c1, with the formula C10H8.

Open the first ring with 1 and walk four carbons to the first shared carbon. Open a second ring there with 2, because ring 1 is still open, walk around the second ring and close it with 2. Then close ring 1. The two shared carbons carry no hydrogen and the other eight carry one each.

Keep exploring

Import Cc1ccccc1 and CC1=CC=CC=C1 as two drawings, then choose Analyze → Compare on one of them. Chalk reports “Same compound” and notes that one drawing shows aromatic ring bonds while the other uses alternating single and double bonds. To check a practice string of your own, import it and set the compound’s name as its target, such as chlorobenzene, then turn Check on.

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Sources and scope

Authored study material. Tool results depend on the stated inputs and model assumptions.

After reading

Study it, then try it

Practice the key terms as flashcards, then open the example in its tool, change a value and keep a useful result on your board.

Study the 7 key terms Import Cc1ccccc1 into the Skeletal tool Import CC1=CC=CC=C1 beside it See toluene in every representation Open worked example on a board Organic nomenclature in Chemistry Reference

Your existing work stays on this device. Examples open as editable copies.