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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.
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
Live life to the fullest. It's not that life is short, but that you are dead for so long.
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.
I think this internet thing sounds like a good idea
I learned two things studying for my degrees. One was memorizing what needed to be memorized, and two knowing the process by which one can derive those things I needed to know and had forgotten.
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.
... organic chem is not a life science
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.
--LWM
Flash cards.
I've hit Karma 50 and gotten a Score:5, Troll... I win!
Flashcards.
Hundreds of them.
'Nuff said.
Sucks, eh?
Favorite
Chemistry is not a life science, it is a hard science, like math or physics.
Although not the answer to your question, if you have any labs, get a copy of "the organic chem lab survival manual". It's good.
One of my organic profs once said that you can judge the quality of a basic organic textbook by what it weighs. Anything in the 10 pound range is sufficient. All the big authors keep tabs on the others and make sure they don't leave anything important out.
Opposite charges attract.
Oxygen and nitrogen are negative, and anything bonded directly to them is positive.
Then opposite charges attract and swap some electrons around when they get close enough.
Seriously, what you're describing is the next level of detail up (when multiple reactions are possible, you need to know a lot about rates to know which one will dominate), but you can get surprisingly far with this simple rule of thumb.
Sort your reactions by the charge distributions of the participating molecules and you'll find a lot of parallels.
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 use 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.
If you have to suffer the first sort of course, take my advice. Memorize it all the day before the exam. Drink it all away the night after the exam.
Check out freemind (I use it all the time): http://freemind.sourceforge.net/wiki/index.php/Mai n_Page
I believe what you are looking for is called physics.
you categorize the reactions by series, season and episode of Star Trek in which the reactions were featured.
Someone hates these cans.
We used a book for that. Come on man, you are just trying to find a way to postpone the inevitable. Learn hard and try to solve all the problems in your textbook, that's the only way to do this. There are things you can do without computers, and this is one of them.
-- Cheers!
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
Hey... I did organic some 6 years back. The best way to remember is to go through the basic 20-25 mechanisms at the electron transfer level. It seems a lot more logical. Just try understanding the mechanisms of wolf kishner, canizzaros, aldol condensation etc. I guess organic chemistry by Francis Carey is a very lucid text... much better than the old stuff like il finar or morrison n boyd. For cyclic compounds, get the reactions classified as groups which are electron injecting or electron extracting. Yea and also get to know all the condensation reactions peoperly. aldol, pinacole pinacolone (my favourite), etc. write to me at ch3.ch2.cho@gmail.com . i got a coupla brilliant sources for mechanisms. Dont recall now. Happy studying.
I've seen a diagram of the entirety of known human biochemistry. Printed out you could merrily cover the outside of a house with those 5mm arrows and 10pt labels. Gazing upon that chart was like staring into the maw of some terrible Lovecraftian creature beyond comprehension. My point? If you want to be able to cope with organic chemistry, I reccomend you deal with it one reaction at a time, and not try to link the whole thing together. Learning the whole reaction space is a daunting prospect. Learning the tools of functional group interconversion and retrosynthetic analysis isn't.
No kidding!!! What do you say at this point?
Petri Nets: Wikipedia
Tadao Murata has written an excellent paper about Petri Nets, courtesy of IEEE: PDF
"Nae Kin! Nae Quin! Nae laird! Nae master! We willna be fooled again!"
It has all of the reactions we needed to know for the final and such. The layout could be a little bit better, but you can edit it to suit your specs.
Oh.. BTW... Dr. Wamser at Portland Staue is not just the best O-chem prefessor out there. He is the best prof I have ever had.
Learning process involves iteration. Finding new contexts in which to iterate can be very useful. So finding a new environment into which to stick all these chemical reactions knowledge could be a good way to memorize it. So stop being so harsh on the original poster. He could learn a lot of the reactions just by making his diagram. And if he creates a pretty context in the process, he will also remember the result of his work -- a pretty pictures in which everything fits together. And, of course, this is exactly what one would hope for when trying to memorize a large chunk of information.
Any guest worker system is indistinguishable from indentured servitude.
that sounds like you're thinking about a database. in which you define something like a table of chemics And then create tables of reaction types then let each chemic be part of reaction type collections in combination with..... etc etc (but i'm not a DB expert, just translating your question to it's IT language) If it's just for school and get you're exam done, i remembered my chemics (school for painting industry) by creating my own symbolic language based on dots lines and 4 colors i could reduce a lot chemical formula's and remember a lot of them. But 'm also a bit of strange figure with strange ideas, you might try on your own to get to a simplified sysmbolic language, just for the purpose of remembering formula's. Reminder also in real databases use colors (then it's more easy to get support from manangement).
I know you're out there. I can feel you now. I know that you're afraid. You're afraid of us. You're afraid of change.
Surely you know exactly what you want. It shouldn't be too difficult to just throw something together. In fact, some of the languages nowadays are so easy to follow, it should be a breeze. I found a tutorial that should hopefully get you down the right path.
Random Musings
Have you tried Cmap? It's free and from what I remember, you can add hyperlinks, jpgs, small flash files; you can also share files and have others add to yours. Not hard to learn and it's better than a simple flowchart.
Hi there,
. toc.html
It really does take a while to get the "hang" of chemistry. Believe me, I know.
BTW organic chemistry isn't the "life sciences", a part of organic chemistry deals with life, but a lot of it really doesn't.
Do your best to organize the information as best as you can, courses (especially intro org.) don't offer the research experience you need to be able to understand the general concepts. The presentation is often extremely rushed, and many many students leave without even a little understanding of what organic chemsitry is, other than it is hard. There is a problem with organic chemistry when everyone leaves without ever hearing the words "subgraph isomorphism".
There isn't a really good magic chart out there that will help you, you are also restricted to learning things in the way your instructor is teaching you for the purposes of exams and stuff.
There isn't much one can do from here other than try to offer you some insight as to how chemical information is organized in the real world if you are really are interested in seeing how people organize chemical information in the real world.
Check out the daylight tutorials on how to represent molecules and reactions as SMILES strings:
http://www.daylight.com/dayhtml/doc/theory/theory
Check out the chem axon suite:
http://www.chemaxon.com/
If you know how to use a unix prompt, see if you can draw out general reactions and apply them (using the "react") program to starting materials you make up. This is a very slick software package that is free and makes chemistry a lot of fun.
Best of luck!