Chalk−1

Chemistry · General chemistry II · Worked example

Read a SMILES string

What molecule is CC(C)C(=O)O? Give its condensed structure, molecular formula and name.

Walk the main chain

Leave the parentheses out for a moment and the string reads C, C, C, O. Three carbons in a row end in an oxygen.

Attach the branches

(C) follows the second carbon, so that carbon carries a methyl group. (=O) follows the third carbon, so that carbon has a double bond to one oxygen as well as its single bond to the final O. A branch always hangs on the atom written just before its parenthesis.

Fill in the hydrogens

Give each bare atom enough hydrogens to reach its normal valence, four bonds for carbon and two for oxygen. This is allowed because a bare atom in SMILES always means its normal valence.

Hydrogens implied in CC(C)C(=O)O
AtomBonds writtenHydrogens added
First C13
Second C31
C in the branch13
Third C4 (two single, one double)0
Double-bonded O20
Last O11

Write it out

The condensed structure is (CH3)2CHCOOH. Counting atoms gives four carbons, 3+1+3+1=8 hydrogens and two oxygens.

C4H8O2

Name it

The –⁢COOH carbon is carbon 1 of a three-carbon chain, and the methyl group sits on carbon 2, which makes 2-methylpropanoic acid. Chalk reads the string the same way and writes the same name.

Result

2-Methylpropanoic acid, (CH3)2CHCOOH, with the formula C4H8O2.

Your turn

1. One like the example

What molecule is CC(C)CCO? Give its condensed structure, molecular formula and name.

Show the answer and explanation

(CH3)2CHCH2CH2OH, C5H12O, 3-methylbutan-1-ol.

The main chain is C, C, C, C, O, with a methyl branch on the second carbon. Filling in hydrogens gives 3+1+3+2+2+1 =12. Numbered from the carbon that holds the OH, the chain has four carbons and the methyl group sits on carbon 3.

2. A variation

Write a SMILES string for 2-methylpropan-1-ol, (CH3)2CHCH2OH.

Show the answer and explanation

CC(C)CO is one, and OCC(C)C is another.

Start at a methyl carbon, C. Next comes the branching carbon with its other methyl group in parentheses, C(C), then the CH2 and the oxygen, CC(C)CO. Starting from the oxygen gives OCC(C)C. Both are correct, and RDKit writes both as CC(C)CO.

3. Somewhere new

A classmate types CH3CH2OH into Chalk’s SMILES box. What does Chalk say, and what should they type?

Show the answer and explanation

Chalk says “H goes in square brackets in SMILES: write [H].” They should type CCO, the SMILES of ethanol.

CH3CH2OH is a condensed formula. In SMILES each H would have to be an atom of its own in brackets, and hydrogens on bare atoms are implied anyway. Writing only the heavy atoms in bonding order gives CCO.

Keep exploring

Import the string into the Skeletal tool, then choose Analyze → Name: Chalk writes 2-methylpropanoic acid, and it reports the formula C4H8O2 and a molar mass of 88.10 g/⁢mol. Then type the string from the other end, OC(=O)C(C)C: it is the same compound. Practice 1 imports its string without a name, for your own name to be checked. A string you write yourself is checked the same way, imported with the compound’s name as its target.

Return to the concept →
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 CC(C)C(=O)O into the Skeletal tool See it in every representation Practice 1: import the string and check your name Open worked example on a board Organic nomenclature in Chemistry Reference

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