Chemistry Blog



Aug 05

Organic Chemistry Reactions Mind Map

by azmanam | Categories: chem 2.0, chemical education, fun, synthetic chemistry | (83572 Views)

Well… this oughta cover it.

I was reading comments to my reddit submission of the many oxidation states of carbon, and Aa1979 asked if the functional groups could be arranged logically according to actual chemical transformations.  I replied that would be too reaction dependent… alcohols can be turned into a great many things (chlorides, alkenes, ketones, acids, aldehydes…), then aldehydes themselves could be turned into a great many things (alcohols, alkenes, acids, imine/enamine, acetal…).  I pointed the commenter to a post by James over at Master Organic Chemistry where he has a picture of a whiteboard-mind map of most of the reactions in a standard undergrad text.  Very impressive.

Feeling crazy, and deciding to put of lab work I should be doinghaving nothing to do, I expanded on James’ mind map and tried to get as many reactions as I could on one map.  It took about a full day’s work using Compendium, and here’s the result (click for larger):

These are just about all the reactions you’d encounter in your standard, two semester undergraduate organic chemistry course.  Sure I probably missed a few, or maybe your institution covers reactions a bit differently, but this is fairly comprehensive.  Enjoy.


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  1. James

    Great job on version 1.0 ! These types of things are fun to put together, but there are often so many overlapping lines that it starts to get extremely Recently I put together another sheet, trying to organize reactions by oxidation state. I ended up omitting a lot of functional groups in the process but covered the main ones. The post will be up in a week or two, but a sneak peek of the image is here:

  2. azmanam

    Love it! Well done. Only addition: all roads lead to CO2 (O2 + ignition source!) ;)

    The nice part of using Compendium, not ChemDraw, is the ease with which I could add labels, arrows, and colors with almost one click. The feature I wish I had was control over placement of labels and the ability to curve arrows.

    I agree it’s really easy for arrows to overlap real quick and get real confusing real quick. That’s why I went to colors. Arrows from each functional group get a different color. It’s also why the map ended up so large. I had to spread them out enough to minimize overlap of words.

  3. Kenneth Hanson

    That really is a heroic effort given all your spare time. You might want to check out this paper ( titled “Using Concept Maps in Teaching Organic Chemical Reactions”, Acta Chim. Slov. 2005, 52, 471–477. They included color coded arrows for the changes in oxidation state of carbon.

    On a related note, Aldrich sells two significantly more complex reaction maps titled the “Atlas of Organic Conversions: An Aid in Perspective” (|BRAND_KEY&N4=Z258660|ALDRICH&N25=0&QS=ON&F=SPEC). It is separated into two posters: aliphatic and aromatic compounds. For an organic chemistry student they are probably more intimidating than useful but they are still amazing works of art. I was lucky enough to inherent them from a researcher that was leaving our group and someday, when I have an office, I definitely going to hang them on the wall.

  4. azmanam

    Thanks for the links. We’ve got Aldrich’s poster of metabolic pathways hanging in our hallway. I’ll often stop and gaze at a different corner of the poster for a while as I walk to or from class.

  5. Geoff Hutchison

    Do you think I could get the original file? I’d like to add a feature to the Avogadro molecular modeling tool which checks the current molecule and gives a list of potential transformations to execute.

    For example, if you have a halohydrin, it would show “NaH” and the result would be an epoxide.

    Right now, the limit on implementing the feature is having an open source list of reactions, which you have in your map file. We’d transform them into “Reaction SMILES” for use in Avogadro.

    We would definitely provide whatever credit you might want.

  6. azmanam

    Yeah, sure. That can be arranged. Shoot me an email (azmanam {at} chemistry-blog {dot} com)

  7. organic.chemist

    James (Master Chemist) later came up with a more refined reaction map that includes visual cues regarding oxidation states of the various functional groups as they are permutated:

  8. minhaj

    i love these type of jobs.its a fun and amazing work to put together these compounds in such a fantabuls way.

  9. anne s

    Just wanted to say I really appreciate this – I hate chemistry but I am stuck in this degree and I damn well need to know these reactions to get out of it!
    So thank you haha

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