Partial Pet Molecule Paper

The following is a scheme from the synthesis of ouabain. I cut and pasted it from the pdf version of the journal article. The molecule is fairly complicated and the steps I will be describing are just a small part of it. In your paper you would have the introduction stating the importance of the molecule, the overall synthetic strategy, and then you would start talking about its synthesis. There are some general guidelines below and then I show you how I want synthetic steps described. Try to follow my example—you will probably get a better grade! Your paper will probably be 5-8 pages.

  1. Be sure to show a picture of the molecule early in the paper (preferably the introduction). You can copy/paste it out of the journal article, draw it on the computer, or draw it by hand. Your drawings must be large enough for me to read easily.
  2. Your introduction should tell the reader why the molecule is important.
  3. You should have some discussion about the overall strategy of the synthesis.
  4. You do not have to describe every step in the synthesis, just the ones you understand. If you bring a copy of the pdf version of the article I can tell you the steps you can figure out. You must describe at least 10 steps in your paper. For the rough draft, I will accept at least 5 steps.
  5. You need to show the reader (me) the part of the larger molecule that you are discussing. Don’t make me keep flipping back to the main molecule to find out where you are. I used Adobe Photoshop to highlight the section of the molecule I’m talking about. You can just draw by hand.
  6. You must have your drawings very near your discussion—do not put them at the end of the paper. Be sure to use the same numbering scheme that’s used in the paper.
  7. Do not use quotes in your paper! Everything should be in your own words. If you have to use quotes that means you did not understand what the authors were doing, and therefore should not be discussing that part of the molecule.
  8. After each step, you must show the new structure of the molecule even if it isn’t shown in the paper. If the molecule is really large, you can abbreviate the rest of the molecule and just focus on what’s changing.
  9. Whenever you don’t understand some steps, just use 3 parallel offset arrows, write how many steps, and then the new structure.
  10. Always try to link a reaction you are talking about to one that you have learned in class.
  11. Do NOT start every paragraph with “In the next step,” or some variation of that!
  12. If there is an abbreviation you don’t understand, you can go to Dr. Workman's webpage to see the list of common abbreviations I have listed ( http://web.centre.edu/workmanj/CHE%20241/ABBR.html). You can find another list of common abbreviations at the Journal of Chemical Education website. Do NOT use abbreviations in the mechanisms—draw out what the molecule looks like!
  13. Whenever you use this or these, use a noun to convery your subject clearly. “This was a success” is much less informative than “This synthetic approach was a success”.
  14. Don’t capitalize chemical names or other random words unless they are at the beginning of a sentence.
  15. Reference your work according to the ACS journal style (look at how your paper references articles and books). You may use footnotes or endnotes. You do not have to keep referencing the paper you are discussing—once is enough.
  16. You will be graded on the correctness of your science, general organization, neatness of drawings, and English.

OUABAIN

The synthesis of ouabain starts with the two rings highlighted above. The starting material is 3-butyn-2-ol (I got that name from the paper) and the first step is to protect the alcohol. The mechanism is an electrophilic addition. Dihydrofuran (DHP) is protonated by the toluenesulfonic acid (TsOH) and the resulting carbocation is attacked by the nucleophilic alcohol oxygen. Subsequent deprotonation yields the protected alcohol.

The phenyldimethylsilyl group of 7 is added by deprotonating the alkyne with the strong base methyl lithium (MeLi), and then doing an SN2 reaction with phenyldimethylsilyl chloride. The chloride ion is the leaving group. This last reaction is similar to the alklylation of acetylide anions that we learned about in Chapter 8 in our textbook. (note how I link the reaction to something you have already learned).

Molecule 7 undergoes two steps to form 8. The ketone in molecule 9 is formed by oxidizing the alcohol in 8 with pyridinium chlorochromate (PCC).

That’s it for the examples. I have explained 3 steps from the paper (the alcohol protection, the SN2 reaction, and the oxidation). If you’re curious to see what it looked like in the paper itself, I’ve copied the pertinent section below.