Organizing Organic Chemical Reactions?

thethinkingilia asks: "I am studying organic chemistry and I am seeking an intelligent way to organize all the reactions that I am responsible for memorizing. In general, one can think of this as a directed state machine where a functional group can be transformed to another functional group given set conditions. It must be robust enough to allow for tens of states, the possibility of connection between any of said states, and be able to display not only the states, but conditions for transition between these states. This could be accomplished with HTML hyperlinks, but it would be great to have an elegant flow chart-type solution. Please, help me bring some software sanity to the life sciences!"

Comments

Now you want us to do your studying for you?

[Bootle]

Come on, this is ridiculous...

I took Organic in school, the only way to get through it is to suffer. My course was meant not to teach, but to weed out pre-meds. Damn! Don't forget the 5 hour labs where you sneeze and your whole yield is gone POOF!

Here's a great studying tip: suck it up! The alternative is to grow a pair and realize chemistry is crap and jump ship to the real science, physics! Everything else is stamp-collecting, as Rutherford said.

If I sound bitter it's just because I am. Goddamn pre-meds...

Re:Now you want us to do your studying for you?

[ChuckleBug]

IAAC, the memorizing is a terrible way to learn chemistry (actually it's a bad way to learn anything). you'll never learn anything by memorizing rules.

This is partially true, but I think your generalization is too broad. There are some things in organic chem you just have to memorize. Easy things like names of functional groups and stuff, but also some named reactions are just too complex to be able to just derive from basic principles. Especially knowing reaction conditions. Do you need heat, a catalyst, an oxidizer or reducer, or what? You have to memorize what Tollen's reagent is, and so on. I agree that it's important to understand the broader concepts, but there's no way around a lot of memorization in organic.

I'm one of those weirdos who always loved this stuff. Organic labs produce the most wonderfully indescribable odors. Even something mundane, like pyridene, has an odor I have never been able to adequately describe to anyone. You have to experience it. (DISCLAIMER: I do not recommend inhaling large amounts of pyridene vapor.)

Directed Graph Layout

[tfinniga]

http://www.google.com/search?hl=en&q=directed+grap h+layout

Electrons

[Rick_T]

My (graduate level) organic professor told us that the only thing we needed to remember was that "electrons flow from the electron source to the electron sink".

By and large, he was right - and organic made a lot more sense than it did to me as an undergraduate. Undferatanding HOW the reactions worked was easier than memorization dozens of twisty little reaction types, all alike.

But if you're taking about sophomore level organic - come on, is there really THAT much stuff to memorize?

Re:Electrons

[Daedala]

Paul Scudder's Electron Flow in Organic Chemistry is the textbook you want. It's all about electrons going from source to sink.

(New, the book is overpriced. Even the author thinks so -- he was complaining back when they raised the price to $30, and now it's $50. So get it used and send him a nice email if it helps.)

Microstructured cellulose + patterned graphite

[amide_one]

You'll need four things, all readily available: Microstructured cellulose sheets, a device for depositing thin layers of graphite in controlled patterns, a flexible optical transducer (broad spectral response, high spatial resolution) to read out the data, and a sophisticated neural network to bring them all together.

Nothing beats the flexibility of writing stuff down on paper. Over and over again, if need be. Flash cards, notes, whatever. If you're determined to use a computer, you don't need a program to build a fancy directed graph with HTML hyperlinks and SMILES structures and ... -- I did it just fine with a text editor and a bit of creativity in the notation.

You'll also find that the reactions are generally organized pretty well in the textbook or lecture material.

Finally, "organizing" means either "doing pretty pictures" or "recognizing that this is SN2". It's very easy to spend so much time making pretty pictures that you don't actually learn any of the content. If you recognize reactions by type (mechanism) and substrate (secondary amine with a phenyl ring two carbons away), then all that's left is "reflux this at 120C in toluene with SnCl2", and... well, you'll have to memorize that anyway.

In short -- get through organic first, then (with a bit of background to understand what's important in "organizing" and "presenting", and better knowledge of what's already available) go on and write your own tool to "bring bring some software sanity to the life sciences". Don't expect to take the world of chemistry by storm, though; that sort of thing's been tried before, and the general reaction is "can't kids these days memorize anything?"