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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!"
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...
butyric acid (nasty smelling chemical in vomit and rancid dairy products) + ethanol + sulfuric acid (IIRC; I know it's one of the strong acids) -> ethyl butyrate (essence of pineapple)
http://www.google.com/search?hl=en&q=directed+grap h+layout
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Instead of focusing efforts on finding ways to organize all the information you have to memorize, just memorize it. Whatever time you've allotted, use to just study the stuff over and over again.
If brevity is the soul of wit, then how does one explain Twitter?
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?
-- Rick
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.
... -- I did it just fine with a text editor and a bit of creativity in the notation.
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
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?"
First I must state that, according to my employee agreement, anything I say on this topic is the intellectual property of the company.
Next I must recognize that you're asking for an organizational system for something which, you've acknowledged, is difficult to organize in a fashion that makes it easily memorizable. There's a reason textbooks haven't simplified the organization any further: the principles of the material are more important than the brevity at a textbook level.
Finally I must say that this is probably a matter of public record and, should you get caught attempting to make a few million by implementing this categorical conceptualization, I'm not going to get a dollar out of it but my company may decide to look into their ownership of it.
Really people. I'd love to release this as GPL but my company pays my rent and electricity every month.
In organic reactions the electrophile is your zero and the nucleophile is your one.
An organic reaction starts with bit1 bit2 NOT.
The result is then acted upon using logical functions with the contents of other registers. Those registers hold values which are applied using various algorithms and represent mitigating factors of the reaction. One of the most difficult registers is simply to compute the varying nucleophilicity or electrophilicity of one of the entities represented by one of the initial two bits. I suggest segregating them by individual atom. Note that textbooks tend to classify them in terms of functional groups. The nature of any given functional group and, to some extent, each individual atom may be influenced by the nature of the solvent or any other co-reactants. For example, carbon is usually the electrophile but, given proper circumstances, it can be made into the nucleophile. One very difficult classification is when the electron density of a bond, rather than a particular atom, is the nucleophile. You will have to figure out how you want to set the first two bits. While the first two bits may be a zero or a one it is up to you to decide based upon the environment of the reaction which species is the zero and which is the one. Other important factors are: temperature, mixing, solvenet characteristics, and the contribution of any surrounding co-reactants or catalysts. In years past it was necessary to calculate these interactioins with surrounding co-reactants or catalysts as a separate reaction process. As the instruction set of the core CPU has grown we've been able to create custom functions for the addition of metal catalysts, coordination complex catalysts, and levels of some simple salts in the surrounding solution.
It is possible that a reaction sequence being processed is fully evaluated at intermediate points called transition states. These transition states are the Reimann sum of the two interacting species from the point of initial chemical interaction to the point of chemical separation. It is especially necessary to interate the full process of evaluation when there are multiple reaction components involved. Current research is underway to create more sophisticated and accurate co-circuits capable of handling the continuous integration of these intermediate points such that they not need be iterated at all.
fast as fast can be. you'll never catch me.
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/
Your CPU is not doing anything else, at least do something.
(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.
the more accurate the calculations became, the more the concepts tended to vanish into thin air. R. S. Mulliken
The rest is just footnotes.
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