Chalk−1

Chemistry · General chemistry II · Worked example

Read brackets and stereo marks in SMILES

What do the brackets and marks say in CC(=O)[O-], in F/C=C\F and in N[C@@H](C)C(=O)O?

A charge in brackets

[O-] is an oxygen with a charge of −1 and no hydrogen, because nothing is implied inside brackets. That makes CC(=O)[O-] the acetate ion, CH3COO−, with the formula C2H3O2 and one negative charge.

Cis or trans

In F/C=C\F the two marks lean opposite ways, so the two fluorines are on the same side of the double bond. This is the cis isomer, (Z)-1,2-difluoroethene. With both marks leaning the same way, F/C=C/F, it would be the trans isomer, (E). Ethene has only one place for its double bond, so IUPAC writes the letter without a number. Chalk’s name adds the 1, as (1Z), and its check accepts both.

A stereocenter

[C@@H] is a carbon with one hydrogen and a stated arrangement. The atom written before it is N, and the atoms that follow are H, then the CH3, then the COOH carbon. Looking from N, @@ says those three run clockwise. That fixes the arrangement in space, but it does not yet say R or S.

Let the priorities decide R or S

The groups rank NH2, then COOH, then CH3, then H, and with that ranking this arrangement is S. The molecule is (S)-alanine, the L-alanine found in proteins. Chalk draws the center with a wedge and labels it S.

The same molecule with the other mark

C[C@H](N)C(=O)O lists the neighbors in a different order and uses @, yet it is the same (S)-alanine. RDKit writes C[C@H](N)C(=O)O as the canonical SMILES of both strings. The mark belongs to the string’s atom order, not to the molecule.

Result

CC(=O)[O-] is the acetate ion, F/C=C\F is cis-1,2-difluoroethene (Z), and N[C@@H](C)C(=O)O is (S)-alanine.

Your turn

1. One like the example

Is C/C=C/C cis-but-2-ene or trans-but-2-ene?

Show the answer and explanation

trans-But-2-ene, the E isomer, (2E)-but-2-ene.

Both marks lean the same way, so the two methyl groups are on opposite sides of the double bond. The cis isomer is C/C=C\C.

2. A variation

Write a SMILES string for sodium acetate, the sodium salt of acetic acid.

Show the answer and explanation

CC(=O)[O-].[Na+], with the formula C2H3NaO2.

The acetate ion is CC(=O)[O-], with the charge and the missing hydrogen stated in brackets. Sodium is not in the organic subset and carries a charge, so it is [Na+]. The dot says the two ions are separate pieces, not bonded.

3. Somewhere new

Chalk names C[C@@H](O)CC (2R)-butan-2-ol. Is O[C@@H](C)CC the same compound or its mirror image?

Show the answer and explanation

Its mirror image, (2S)-butan-2-ol.

The second string lists the methyl group and the OH in swapped places around the center. Swapping two neighbors reverses what a mark means, so the same @@ now describes the other arrangement. Chalk’s Compare calls the pair “Enantiomers”.

Keep exploring

Open the Skeletal tool, import N[C@@H](C)C(=O)O, then N[C@H](C)C(=O)O beside it, and choose Analyze → Compare. Chalk calls the pair “Enantiomers”. Analyze → Stereochemistry shows the ranking that makes the first one S. The difluoroethene and L-alanine buttons import each string with its name as the target, so Check reads the Z and the S. The Practice buttons import the practice strings without a name, for your own name to be checked.

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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 the acetate ion into the Skeletal tool Import cis-1,2-difluoroethene and check its name Import L-alanine and check its name Import its mirror image beside it Practice 1: import the string and check your name Practice 3: import the second string and check your name Open worked example on a board Organic nomenclature in Chemistry Reference

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