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

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.)

graphviz

[CaptainPinko]

i take maybe a half-hour to learn the syntax, but if you name the transition arrows you'll get great graphs. http://www.graphviz.org/

The Obvious Solution

[Frumious Wombat]

(from someone who teaches Chemistry for a living)

You're taking your courses in the wrong order. You need P-Chem and Inorganic to understand _why_ Organic works. Once you can understand which way the electrons flow, you're halfway done. Look for Woodward and Hoffman's book on orbital symmetry interactions, and the old Ian Fleming (different one) "Frontier Orbitals and Organic Chemical Reactions". Albright, Burdett, Whangbo, "Orbital Interactions in Chemistry" is also a good general source, though it's rather inorganic in focus.

The other half is to actually memorize 2000 reactions, if you're going to be a professional organic chemist. You have to know solvent, temperature, and related reactions. You need to know how mechanisms work, what transition states look like, and how both steric and electronic effects interact. To this you can add metal-mediated transformations (organometallic). This is why organic (so say my female colleagues) is overwhelmingly male; the same ability that makes you able to remember 2000 random movie quotes or baseball statistics allows you to memorize organic reactions instead.

Take a deep breath, and start making flash cards. Remember, Organic is just Inorganic with boring elements.

As to the software question, CambridgeSoft (http://www.cambridgesoft.com/ and Accelrys (http://www.accelrys.com/ are two examples of people with expert systems that do some of what you're asking. You will not like the price.

Try this software...

[qx128]

I think you might find GraphViz interesting. It's a pretty easy-to-use program that allows you to produce graphs from a text file. You can add labels, color, edge weights, etc. All you'd have to do is write a text file "linking" the reactions. You can even name the nodes of the graph in an intuitive manner. Here would be an example:

digraph {
NaCl [label = "table salt"];
Na -> NaCl;
Cl -> NaCl;
}

And then GraphViz turns that into a picture. Specifically, you'll be intrested in the program called "dot" that comes with the GraphViz package.

Hope this helps!

-- Dylan