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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!"
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)
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 realize that this is probably COMPLETELY unrealistic, but I'm curious for an organo-chem geek oppinion on something. What would be the plausibility of cooking up either of the following two products:
:) I fully expect the answer to be "No way in hell".
Ac-Nle-cyclo[Asp-His-D-Phe-Arg-Trp-Lys]-NH2
or
Ac-Nle-cyclo[Asp-His-D-Phe-Arg-Trp-Lys]-OH
The common names are Melanotan II and PT-141. They just so happen to be the first known honest-to-god aphrodisiacs (nasal-spray administered). Chuckle.
Yeah yeah, I'm no organo-chem geek, but I do know a complex amino chain - a cyclo to boot - is seriously the sort of monster you want to harvest from a bioculture, but I just had to ask anyway
If you want to see the molecuar diagram or read other general info you can see it here.
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