Module 4a: Assignment

1.3. Exercises (Module 4a)

1.3.1. Exercise 1


Without looking in a database, draw the structural formulas of at least ten isomers with the molecular formula: C3H6O.  Don’t include isotopes or radicals.


1.3.2. Exercise 2


Expand the following contracted label to form the full 2D structural formula:


  1. In which direction did you read the contracted label?
  2. How does the full structural formula appear if the label is read the other way?
  3. Which direction is the IUPAC convention?
  4. Re-write the contracted label to clarify the intended meaning.
  5. What is the useful lesson here?


1.3.3. Exercise 3


Resolve each of the following the systematic names listed for Vitamin C into structural formulae using each of the systems below.  Is the expected stereochemistry represented?

  1. (R)-3,4-dihydroxy-5-((S)-1,2-dihydroxyethyl)furan-2(5H)-one
  2. (R)-5-((S)-1,2-dihydroxyethyl)-3,4-dihydroxyfuran-2(5H)-one
  3. (2R)-2-[(1S)-1,2-dihydroxyethyl]-3,4-dihydroxy-2H-furan-5-one
  4. (5R)-[(1S)-1,2-dihydroxyethyl]-3,4-dihydroxy-3-oxolen-2-one


  1. openmolecules:
  2. OPSIN:
  3. CACTUS:
  4. ChemSpider:
  5. PubChem:
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Comments 7

John House (not verified) | Thu, 10/01/2015 - 17:09
For 1.3.3. question a, the 2-D resolved structure from opsin indicates that the cyclized oxygen is coming out of the plane. On the other hand the 3-D resolved structure from NIH shows a planar ring. Would this qualify as the stereochemistry not showing up as expected?

Evan Hepler-Smith's picture
Evan Hepler-Smith | Thu, 10/01/2015 - 18:52
Hi John, The short answer: both structures display the same, *expected* stereochemistry. In terms of R/S configuration of stereocenters, the wedged ring bond (with H left implicit) is the same as a dashed bond to H (with the ring bond in the plane of the page). You can verify this for yourself by building a model. (I try to keep four distinct pens and pencils with me to use in making ad-hoc models of stereocenters....) The longer answer: you're right that these structures sure **look** different, even if they convey the same chemical information in terms of connectivity and stereocenter configuration. If you're communicating with other (human) chemists, you'll want to depict stereochemistry consistently - when you're dealing with rings, it's often easiest to keep the entire ring in the plane of the page and dash or wedge hydrogens and substituents, even though only a few rings (e.g. benzene, cyclopropane) actually have planar conformations. Evan

Otis Rothenberger's picture
Otis Rothenberger | Thu, 10/01/2015 - 20:24
Hi John, Resolver does not really compute structures. It's a super fast approximation of reasonable geometry. This is done by first using an algorithm to break a connectivity identifier (SMILES, IUPAC, InChI) into library building blocks called ensembles. The ensembles are then reassembled into the approximate 3d model, carrying with them their respective geometries. One quick way to see the approximate nature of this is to measure bond angles in simple substituted alkenes. For example, load 2-methylprop-1-ene from PubChem and NIH/CADD Resolver and check the C-C-C bond angles. The "computed" 3D models that we get from databases all carry the weight of the their respective calculation algorithms. Take a look at the 3D model of allene fromPubChem and NIH/CADD Resolver. Otis

John House (not verified) | Thu, 10/01/2015 - 17:20
For 1.3.3., question b, I am receiving different resolved structures from Chemspider and NIH. I am assuming that this indicates the expected stereochemistry as not being represented.

Evan Hepler-Smith's picture
Evan Hepler-Smith | Thu, 10/01/2015 - 19:01
John, Are you sure you're getting different structures? Or rather, are you getting 1) **different R/S configurations** of stereocenters, or 2) **different ways of drawing the same** R/S configuration? (You may be getting multiple tautomers, which is worth noting. But if the tautomerism doesn't involve stereocenters, then the "expected stereochemistry" would be a consistent R/S configuration for each of the tautomers.) Evan

Joshua Henrich (not verified) | Thu, 10/01/2015 - 17:47
Hi Dr's McEwen and Hepler-Smith, I'm confused about what you mean when you say "How does the full structural formula appear if the label is read the other way?" What is the other way the contracted formula can be read? I read it right to left.

Evan Hepler-Smith's picture
Evan Hepler-Smith | Thu, 10/01/2015 - 19:06
Hi Joshua, You've read it in the "correct" (i.e. the usual, conventional, expected) direction. Good! However, try drawing the structure based on reading the contracted formula from left to right, starting with the H3C methyl group and working your way toward the ring system, and see what you end up with. Evan