Organic chemistry reaction/reagent database for a student?
April 21, 2012 7:58 PM   Subscribe

I'm studying for my organic chemistry I final exam and I'm looking for some sort of searchable database of reactions and reagents to help me solve problems.

For example, right now I am stuck because I can't figure out how a 6 carbon molecule with an epoxide ring on one end and a double bond on the other end will react when treated with NaOEt and EtOH at 60 degrees Celsius. (Next it's treated with TsCl/pyradine and then NaCN/DMF and I have a faint idea that I'm going to be able to deal with that.) I've been searching through my textbook and tried googling it but the google results were too chemically complicated for me to extract any useful info.

Does anybody know of a resource to help me find this kind of info?

Bonus points if you can expand on what my professor said on the last day of class: that to figure out most syntheses, you should look at the target molecule, decide what's been added, and then decide if these functional groups have been added as an electrophile or a nucleophile.

This seems very sensible to me, but my first problem is that I'm getting confused about identifying nucleophiles from electrophiles. And my second problem is well, how on earth do I condense all these different reactions I've learned into just "adding as an electrophile or a nucleophile"??
posted by sunnichka to Science & Nature (12 answers total) 5 users marked this as a favorite
Does your school library have access to the Reaxys database?
posted by jenny76 at 8:01 PM on April 21, 2012

Yes! It is pretty overwhelmingly complicated at first glance though.
posted by sunnichka at 8:18 PM on April 21, 2012

Ha, I loved organic chem (although it's hard hard hard).

Anyway, these two sites might help you out:
posted by Hakaisha at 8:30 PM on April 21, 2012

Here's a Quick Reference guide to Reaxys that might help.
posted by jenny76 at 8:31 PM on April 21, 2012

A friend runs this site, which should include a reagent/reaction table:

He also has an iPad app which I think also includes one.
posted by beepbeepboopboop at 8:33 PM on April 21, 2012

BeepBeep'Boops Mastering Organic Chemistry PDF looks like exactly what I need, but the $25 will hurt a little.
posted by sunnichka at 8:40 PM on April 21, 2012

When I had to propose and conduct a quarter-long synthesis, I was taught to use Beilstein and Scifinder, but I don't think these would be very useful for studying for a largely theoretical exam because they would overwhelm you with all the myriad variations of ACTUAL CHEMISTRY. Whereas you'd probably benefit more from a cheat sheet to the small subset of clean, theoretical reactions covered in your textbook.

Does your textbook not summarize its reactions? Depending on how much time you have left, you might try manually curating these. Maybe you could enlist a few friends to divide the work. Then you can make either manual flashcards or a spaced-repetition set. I would recommend either Mnemosyne or (better) Anki if you go the spaced-repetition route.
posted by d. z. wang at 8:48 PM on April 21, 2012

Do not use Reaxys or Beilstein or Scifinder for this. You will be drinking from a firehose of reactions and search strategies. These are tools for working chemists to optimize existing syntheses and not for people who don't understand the underlying principles. Find another textbook on Google books that has a good guide to classification of reactions.
posted by benzenedream at 10:17 PM on April 21, 2012 [1 favorite]

The problem you're going to have is, well, if you put "sodium ethoxide" and epoxide into Google (just to use the most convenient example) you have to do some poking until you get to the answer you need. But if you just ask about nucleophilic attacks on an epoxide, you get there pretty quickly. (So let's look at what your instructor said.)

A nucleophile is an electron donating Lewis base. Back in the day, they called them anionoids with electrophiles being cationoids.

So look at what you have. Ethanol isn't all that reactive. but don't ever pour any sodium ethoxide on yourself, so that's got to be one of the reactants. Generally metals like sodium and potassium are not the preferred choice of organic molecules. Just like salt dissociating in water, they tend to go off on their own leaving Et-O:::- (Yeah, the electron pairs aren't drawn like you instructor would want). Given a choice, the first thing that ion is going to do is grab a hydrogen (Which is a lone proton which lives where? The nucleus, so this is a nuclophile) and become ethanol. But we're using ethanol as a solvent so if it does that we get another Et-OH:::- putting us back where we started. So the epoxide-ene has got to be the target.

If there was an electron withdrawing group near that double bond you might be able to add something across that, but look at that epoxide. It's a stressed ring and that oxygen is hogging the electrons so it's likely to be the star of the show. We've identified the ethoxide as a nucleophile, so it's nucleophilic attack.

I'm not sure what all your test is going to cover but my bet is it's going to be a lot of Lewis acids than bases either making off with weakly held hydrogens leaving to other reactant to cope as best it can, or breaking up perfectly happy covalent bonds so they can satisfy their own electronegativity issues.
posted by Kid Charlemagne at 10:18 PM on April 21, 2012 [2 favorites]

Thinking about this a bit more - try thinking about where the electrons are and where they want to be. Sodium and potassium ions are perfectly happy off on their own in a +1 state which is why KOH and NaOH are so basic. KOMe and NaOEt are just analogs of these but they're methoxide and ethoxide instead of hydroxide.

Oxygens are very electronegative. This means that they will have the electrons more than their share of the time in ethanol (an it's even worse with the two oxygens in an acetate ion) so the oxygen will go off on its own.

There are some other issues that matter (ring stress, steric hindrance and so on) but having an instinct for this kind of thing is all about know where the electrons are, and where, given the chance, they're going to go.
posted by Kid Charlemagne at 10:57 PM on April 21, 2012

Bless you Kid Charlemagne. I have 8 days before the final and I'm really hoping I can develop that instinct before then. Let me know if you think of any tips for further reading. I've been so overwhelmed with all the detail work that I'm having more trouble than usual grasping the grand vision of it all.
posted by sunnichka at 4:45 PM on April 22, 2012

I bought the reagent guide pdf on Master Organic Chemistry, and it's really helping too. Thanks everyone.
posted by sunnichka at 4:46 PM on April 22, 2012

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