Organizing Organic Chemical Reactions? 77
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!"
Now you want us to do your studying for you? (Score:4, Insightful)
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...
Re:Now you want us to do your studying for you? (Score:3)
Believe it or not, there are people who actually understand what all those stupid electrons do. Those are the ones who become chemists.
The rest of us, a category that includes you, me and (he leaves not the slightest doubt about this) the submitter, have no choice but to suck it up and memorize the damn things. Also, I'd suggest to him that organizing the reactions according to
Re:Now you want us to do your studying for you? (Score:3, Insightful)
Re:Now you want us to do your studying for you? (Score:5, Insightful)
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.
I'm one of those weirdos who always loved this stuff. Organic labs produce the most wonderfully indescribable odors. Even something mundane, like pyridene, has an odor I have never been able to adequately describe to anyone. You have to experience it. (DISCLAIMER: I do not recommend inhaling large amounts of pyridene vapor.)
Re:Now you want us to do your studying for you? (Score:1)
We will now wait for the circular logic of organic chemistry to melt the brains of the physics students.
Re:Now you want us to do your studying for you? (Score:2)
Re:Now you want us to do your studying for you? (Score:1)
Re:Now you want us to do your studying for you? (Score:2)
It's the difference between the white pages of the phone book, and the yellow pages. White pages = memorizing every freaking reaction. Yellow pages = finding some system for categorizing them.
The system in organic chemistry is "electrons flowing from source to sink." The electrons just roll downhill. This adds some memorization
Re:Now you want us to do your studying for you? (Score:2)
Re:Now you want us to do your studying for you? (Score:2)
I don't think there's much overlap between what you are saying and my comment. I agree wit
Re:Now you want us to do your studying for you? (Score:3, Interesting)
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 -
Re:Now you want us to do your studying for you? (Score:2)
Implying that you know better than the organic chemists how to best teach their material.
Organic chemistry isn't taught any differently than any other discipline. It starts out with sanitized examples in a clean room to familiarize the student with the basic principles. Once those basic principles are firmly in place then the student is allowed to see how they apply and are changed in a real world environment.
It's no different than doing 50 ma
Re:Now you want us to do your studying for you? (Score:3, Insightful)
The success of the home schooling community supports my assertion.
Similar to how Linux, the made at home alternative, is drawing the attention of Microsoft.
Big bad federal government with all its power and authority and tax money still can't educate our children near as well as their own parents can if they can afford the proper tools and time. It's just too bad The Man is keeping most people down with the tax rate.
Re:Now you want us to do your studying for you? (Score:1)
Re:Now you want us to do your studying for you? (Score:2)
That's a really dumb thing to say. The best assessment of homeschooling is "mixed." Many students have been homeschooled very well. Those who are taught by incompetent parents aren't as often reported.
For every competent, successful parent who homeschooled their children successfully, I'll show you a whackjob fundie moron who taught their kids nonsense. I'm not going to trash homeschooling, but to say it's wildly successful beyond public sch
Re:Now you want us to do your studying for you? (Score:2)
Like I said, some people can get their heads around electrons, or C pointers, or Gaussian statistics and some can't. If you're planning to become a chemist, abso100%lutely you have to understand the underlying principles. The rest of us often have no choice except to grind it out, get the B and finish off the prerequisite. It's not like (with one exception) I've ever needed any of that stuff in my career. And, if I may flatter myself, I was actual
Re:Now you want us to do your studying for you? (Score:2)
Re:Now you want us to do your studying for you? (Score:2)
Re:Now you want us to do your studying for you? (Score:1)
Re:Now you want us to do your studying for you? (Score:2)
When I read this the first thing that came to mind for me was calculus...God how I hate advanced calculus...
Re:Now you want us to do your studying for you? (Score:2)
Unfortunately the quantum physics that govern those electron bonds is incalculably difficult. A hydrogen or helium atom is one thing, but 'understanding' why complex organic molecules behave the way they do is beyond the scope of analytical quantum phy
Re:Now you want us to do your studying for you? (Score:2)
The rest of us, a category that includes you, me and (he leaves not the slightest doubt about this) the submitter, have no choice but to suck it up and memorize the damn things.
Have you ever seen the discussion of mappers vs packers at The Programmers Stone [reciprocality.org]?
Re:Now you want us to do your studying for you? (Score:2)
Re:Now you want us to do your studying for you? (Score:1)
I changed majors to avoid Organic at 8AM...
Mostly OT: a favorite organic reaction (Score:4, Interesting)
Re:Mostly OT: a favorite organic reaction (Score:2)
Re:Mostly OT: a favorite organic reaction (Score:2)
Re:Mostly OT: a favorite organic reaction (Score:2)
Carrying this out in water would shif the equilibrium to the left.
It's probably better to use ethanol as both reactant and solvent.
Re:Mostly OT: a favorite organic reaction (Score:2)
*: No kids, never stick your fingers in a light socket, never try to ride inside a dryer, and never drink battery acid.
-
Directed Graph Layout (Score:4, Informative)
Honestly... (Score:4, Insightful)
Electrons (Score:5, Informative)
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 (Score:2)
Re:Electrons (Score:5, Informative)
(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.)
Microstructured cellulose + patterned graphite (Score:4, Funny)
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?"
I don't know anything (Score:2, Interesting)
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
Re:I don't know anything (Score:2)
Re:I don't know anything (Score:1)
There are these great inventions... (Score:2)
Re:There are these great inventions... (Score:1)
Shapes (their properties, actually) in a Visio diagram can be linked to each other and to almost any database. The database connections can be uni or bi-directional . . . change the shape properties and the database reflects the cha
Pushing Electrons (Score:1)
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.
Re:Pushing Electrons (Score:2)
I had a brief look at the ToC. It starts out quite nicely. Chapter 1 is essential. Chapter 2 should be the characteristics of bonding. The proposed Chapter 2 should contain the current Chapter 2. Chapter 3 needs to be rewritten from the molecular orbital level. The proposed Chapter 2, Characteristics of Bonding, would prepare the reader adequately for molecular orbitals in the formation and breaking of bonds. A chapter should be inserted as Chapter 4, Mechanisms. This c
graphviz (Score:3, Informative)
The Obvious Solution (Score:4, Informative)
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.
Re:The Obvious Solution (Score:2)
Oh that's harsh! :) Inorganic is primarily facilitated by the arrogant molecule water. Organic, shared bonding (like shared source), seems to be the more natural order of things. :)
:)
Except in the sun, where everything is pretty ionic but even that organization has a shared component because, at that temperature, the photons matter more than the electrons.
Re:The Obvious Solution (Score:1)
Re:The Obvious Solution (Score:2)
ISIS Draw was inferior to CS ChemDraw or the offering from ACS Labs but ISIS Base, once you understand how the database infrastructure is designed, is probably one of the most powerful chemical databases I've come across.
Re:The Obvious Solution (Score:1)
The ChemOffice Suite (7, 9 or 9) is a wonderfully robust product, and CamSoft's chemical inventory product is awesome.
Thanks, btw.
Solve the Schrodinger equation... (Score:4, Funny)
Something like Visio work? (Score:2)
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
Simple set (Score:2)
The High Tech Solution (Score:2)
Hundreds of them.
'Nuff said.
Sucks, eh?
It depends immensely on the teacher (Score:2)
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.
read a physics book (Score:2)
I recommend (Score:2)
In my days... (Score:2)
Try this software... (Score:3, Informative)
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
use nucleophillic and electrophilic extensively (Score:1)
Terror! In the pit of your stomach! (Score:1)
check out ... (Score:1)
Tadao Murata has written an excellent paper about Petri Nets, courtesy of IEEE: PDF [berkeley.edu]
Advice from My O-Chem professor (Score:1)
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.
despite all the "obvious" advise here (Score:1)
many to many relations (Score:1)
Just write your own! (Score:2)
concept mapping (Score:1)