from the dept. 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!"
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: 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...
(Last Journal: Thursday July 10, @07:37PM ) 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.
(http://rickandpatty.com/ ) 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?
(http://www.orangewallaby.net/ ) 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?" [ Reply to This ] (Score:2) by john_is_war (310751) on Tuesday November 22, @08:35PM (#14097080 ) called pencil and paper. You take the paper, and you write down things ontot he paper. You can write letters, numbers, circles, squares, and pointed arrows (and you can lable them too). There you go, everything you need to draw a state diagram [ Reply to This ] Re:There are these great inventions... by tektrix (Score:1) Tuesday November 22, @09:20PM (Score:1) by highwindarea (732127) on Tuesday November 22, @08:42PM (#14097117 ) I found This book [amazon.com] very useful while studying organic.
More generally, don't try to memorize tens of different reactions. Just remember the important principles, like how to draw lewis structures, which atoms are nucleophiles and which are electrophiles and Markonikov's rule etc. And solve as many mechanism/synthesis problems as you can find.
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/ [cambridgesoft.com] and Accelrys (http://www.accelrys.com/ [accelrys.com] are two examples of people with expert systems that do some of what you're asking. You will not like the price. [ Reply to This ] Re:The Obvious Solution by SilverspurG (Score:2) Tuesday November 22, @09:34PM (Score:3, Funny) by Darius Jedburgh (920018) on Tuesday November 22, @09:46PM (#14097459 ) The rest is just footnotes. [ Reply to This ] (Score:2) by lilmouse (310335) on Tuesday November 22, @09:58PM (#14097521 ) Would something like Visio work? You know, draw pretty flowcharts, you can put in whatever arrows you like.
There's a free option out there, but I can't remember what it is, so I'll have to leave that for you to figure out.
(Last Journal: Monday March 25, @10:47PM ) Flashcards.
Sucks, eh? [ Reply to This ] (Score:2) by PIPBoy3000 (619296) on Tuesday November 22, @10:22PM (#14097668 ) I had two Organic Chem classes. The first two terms were over a summer and involved pure memorization. It was a stupid waste of my time and money. Anyone who becomes a chemist will have tons of reference books at their fingertips. As they that knowledge, they'll have to stop referring to the material.
The second class was the final term of Organic Chem, taught by a completely different professor. It was far more interesting and relevant, focused on the process of why things work they way they do. It was much easier to understand the material and apply it to science in general.
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