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Category: Lindau • Science
Posted on: July 2, 2009 5:32 AM, by PZ Myers
Uh-oh. I'm trying to follow this talk, but it's one for the chemistry purists: I don't understand the words he's saying, starting with "olefin" and continuing with "metathesis". You'll have to look to one of the other Lindau bloggers with more chemistry to explain it, because Schrock seems to be assuming I understand all the basics already, and I don't.
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Comments
Posted by: Brian | July 2, 2009 5:37 AM
Maybe if you just smile and nod your head a lot, it'll get easier to understand later.
Posted by: Naked Bunny with a Whip
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July 2, 2009 5:50 AM
Sounds like the biology course I took in college, to be honest.
Posted by: Kevin Hunter
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July 2, 2009 5:52 AM
Oh no. PZ isn't omniscient, and the New Atheists have weaknesses! Quick, run and get one of the ignorant fools to write about this! I am sure this means a god exists...
Posted by: Kevin Hunter
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July 2, 2009 5:55 AM
Naked Bunny: I lost my bio prof somewhere between photoreceptor II and photoreceptor I... She must have said them backwards...
Posted by: PZ Myers
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July 2, 2009 5:59 AM
No, she didn't!
Posted by: Kevin Hunter
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July 2, 2009 6:07 AM
haha...
How could you miss that first (second) photoreceptor? I still don't get how they missed it and discovered it later... Perhaps I should look up something so simple on these internets... Or I could wait for someone to post it on here...
Posted by: Blugger | July 2, 2009 6:40 AM
I'm sure also many of the young researchers had their problems,-)
Posted by: Joe | July 2, 2009 7:13 AM
The basics aren't that bad, "olefin" is just the common name chemists use for alkenes - double bonds between carbon atoms. Metathesis is simply a reaction involving two alkenes (two molecules with double bonds between the carbon atoms), where the double bonds are broken and new double bonds are formed.
Posted by: Joe | July 2, 2009 7:18 AM
I guess I should add, though, that the devil is in the details...
Posted by: Nerd of Redhead, OM
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July 2, 2009 7:21 AM
What problem? The title is perfectly understandable. The olefin metathesis reaction can now use more metals than just ruthenium. Definitely hard core chemistry here.
Posted by: Doggles | July 2, 2009 7:39 AM
Ooh - proper chemistry! welcome to my world... come on in, the water's fine! - I'd love to have seen this one PZ. Schrock is a top name in this area - Grubbs is another metathesis name to look up for you young budding chemists out there. Metathesis is a great example of the extremely useful organic chemistry that can be done when you start throwing metal complexes into the mix. Reactions that would be very difficult to achieve under any other conditions suddenly become almost trivial - generally working quickly, cleanly and with high yields of the desired product. Other examples where metals get involved and help us organic chemists out can be found in the world of palladium and / or copper chemistry (the Suzuki, Sonogashira, Stille, Heck, and Buchwald/Hartwig reactions for instance). There is an unbelievably huge amount of work out there in this field though and it immediately thrusts us into real hardcore chemistry. There's a lot of organic chemists out there (myself included) who wouldn't pretend to know every last fine detail of these reactions so you can be forgiven for not following this one... Interestingly to the biologist, the importance of metal centers to get useful chemistry done is also abundantly obvious, as the haemoglobin in our blood demonstrated admirably.
Posted by: One Eyed Jack | July 2, 2009 7:58 AM
It's ALL physics.
Posted by: David Marjanović, OM | July 2, 2009 8:10 AM
I'm not quite sure what an alkylidene is – an alkene group bound to a metal (molybdenum or tungsten in this case)? Apart from that, everything's clear: "olefin" is a stupid ancient name for "alkene" (hydrocarbon with double bonds in it) that some chemists still use, and "metathesis" is switching the places of the double bonds and the hydrogen atoms around.
Posted by: Doggles | July 2, 2009 8:31 AM
@One Eyed Jack - ha ha - love it, yes it is indeed ALL physics. Reminds me of the xkcd comic where we all get pwned by the pure maths geek...
@David - yes in this case alkylidene does simply refer to the "alkene-like" carbon, which in this case will be bound to a metal. You can extend this to specifics, such as "benzylidene" which is used to refer to a benzyl group where the benzylic carbon is sp2 hybridised - ie: hooked up to something else via a double bond.
The "old names" issue is one that constantly comes up and it depends how far you want to push it to be correct before it just gets too pedantic - for instance I always refer to "acetic acid" and "acetic anhydride" rather than the perhaps more rigorous and less archaic "ethanoic" terminology - I don't know anyone who used "ethanoyl" in place of the simple "acetyl"! It's true that "olefin" does sound a little old and crusty to me too though.
Posted by: Doggles | July 2, 2009 8:38 AM
...by the way some of the differences between pronunciation between scientists in the US and the UK for these terms are quite comical at times - takes us a while to tune our ears in... for instance, Americans seem to pronounce carbonyl as "carbon-eel" whereas most of us in the UK say "carbon-"eye"-l"
ah well, potay-to potah-to...
Posted by: Kristoff | July 2, 2009 8:54 AM
From a linguistics perspective, "metathesis" is the phenomenon of sounds "switching place" in a word-Old English "brid" to "bird" for example, with the "replacement" word conforming to evolving phonetic paradigms within and among languages. Not really germane to evolutionary biology, per se, but still interesting parallel phenomena, nonetheless.
Posted by: Barney | July 2, 2009 9:45 AM
Here's the animated dance version of metathesis:
http://nobelprize.org/nobel_prizes/chemistry/laureates/2005/animation.html
There's a video somewhere of actual dancers doing this, but I can't seem to find a copy.
What Schrock was trying to say is that basic chemical research can be very very useful in the long run--he just got hung up on the details.
Posted by: Pablo | July 2, 2009 9:48 AM
Olefin metathesis is a remarkably powerful and simple approach to chemical synthesis. One problem, however, is that is such a relatively new methodology that it is having trouble finding it's way into Organic textbooks, which, of course, focus heavily on the basics. It is important to have the basics, of course, but I find it disheartening that new students are not getting an appreciation for life in modern organic chemistry.
For example, I just pulled a random Org text off my shelf. This is by a high-profile guy, and is the 2007 edition. No mention of olefin metathesis. Moreover, cross-coupling reactions are mentioned only as a "Chemical Highlight." These reactions make up a huge part of modern organic synthesis these days, and get only a passing mention? Especially given Louden's book (one of the best around) is better, with sections on both. Given that these are critical carbon-carbon bond forming reactions, that are part of almost any complex synthesis these days, they need to be taught.
Most organic courses have sections on synthesis, and when I teach that part, I always tell the students to not forget about metathesis and cross-coupling reactions, even if their book has. Particularly cross-coupling. I tell them that the reaction
R-M + R'-X --> R-R'
is usually going to work for almost any version of R and R', it's just a matter of chosing the right M and X. This is overstating things a little bit (there are combinations that don't work as well as others), but not by much. Especially if R and/or R' is unsaturated in some way.
Posted by: Barney | July 2, 2009 9:48 AM
Here's the animated dance version of metathesis:
http://nobelprize.org/nobel_prizes/chemistry/laureates/2005/animation.html
There's a video somewhere of actual dancers doing this, but I can't seem to find a copy.
What Schrock was trying to say is that basic chemical research can be very very useful in the long run--he just got hung up on the details.
Posted by: theophylact
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July 2, 2009 9:54 AM
Well, the days when a scientist could know all the science worth knowing probably ended before Whewell introduced the word "scientist". I'm an organic chemist myself; I've heard Schrock talk on olefin metathesis at one of the Gordon Conferences many years ago; but I don't really understand the structure of the catalysts involved because I'm not an organometallic chemist.
Still and all, PZ, I would have thought you'd know the word "olefin". You did take chemistry in high school, didn't you?
Posted by: Barney | July 2, 2009 9:58 AM
Sorry for the double. I didn't read so carefully.
I think there are at least two main reasons that the organometallic reactions don't get much more than a mention in most organic chemistry textbooks.
The first is that it takes a lot of effort on both the teacher's and students' parts to fit organometallic mechanisms (w/ multiple metal oxidation states) in with the rest of the basics.
The second more cynical reason is that it won't matter to most of the kids taking organic chemistry if they see a metathesis reaction or not. The small percentage who go in chemistry will most likely get to see all of these reactions in excruciating detail in a later class.
Posted by: Berner | July 2, 2009 12:37 PM
Barney:
It's also the case that a lot of these reactions aren't that well understood either. Their mechanisms can become very very complicated very quickly. This is where the theoretical chemists (computational/quantum) come in to propose a possible mechanism which can be checked against kinetcs (blech!).
When I was doing research with the computational group in my Univeristy we worked a lot with the organometallic researchers when they needed proposed mechanisms. We were also usually right!
Posted by: Pablo | July 2, 2009 2:19 PM
Organometallic mechanisms? I thought they were all
1) Oxidative addition
2) rearrangement
3) Reductive elimination?
:-)
The only question is how many empty orbitals are available on the transition metal. Of course, if any are you just throw ligands on...
BTW, Doggles, you forgot another important difference in proncunciation. The British (and Indians, FWIW) use long "e"s in the names in addition to the long Y. So instead of carbonyl, a better example is something like methyl. In american, it's "meth" with a short e (as in head) and "ill", but in british it's like "meeth-yle" (same with ethyl: "eth" - "ill" vs "eethyle")
And don't get me started on atomic number 13...
Posted by: MrFire | July 2, 2009 2:23 PM
Not so fast PZ...!
There has actually been a pretty useful application of olefin metahesis in the study of the BCL-2 protein family.
Basically, these proteins are involved in apoptosis, i.e. they cause defective cells to commit suicide. In tumor cells, they are compromised by various means such that the tumor can survive. What the guys above did was synthesize the active, pro-apoptotic fragment of the protein containing non-natural, olefin-bearing residues at specific positions. Then they used olefin metahesis to tie these two positions together, and presto chango! their fragment coiled up into an extremely stable alpha-helix that was resistant to degradation, and that strongly attenuated the growth of human leukaemia cells, presumably through re-establishing the apoptotic pathway.
Posted by: j a higginbotham | July 2, 2009 2:29 PM
Here's an old but nice overview:
http://www.umich.edu/~chem402/accountsOlefinMetathesis.pdf
Posted by: antistokes | July 2, 2009 2:56 PM
oook....I TAed the organic-for-premeds section a year ago at a Big Hospital U, and they did a whole freakin' section on organometallic reactions (there was a shortish "special section" in the text that the prof elaborated on). And o man was all that inorganic fun to explain. Personally, though, I thought it was fun, I love organic mechanisms, and did a few synth internships as an undergrad. And given the latest in metalloprotein mechanisms, this is kinda something the premeds ought to at least have heard of....
Posted by: MrFire | July 2, 2009 3:07 PM
If you're doing it in grad school, it's even less than that:
1) intractable, colloidal, tarry crap. That never, ever loses the brown color, even after five columns.
Touche. Though I've heard some Americans pronounce 'amide' as 'uhr-mid' and its makes my skin crawl every time ;)
Posted by: Berner | July 2, 2009 3:53 PM
Pablo:
It's step 2 that can be tricky. Also it depends on the hydrocarbon undergoing metathesis. Something like a straight chain (ethene, butene etc) is much more simple than something like bicyclics (norbornene, norbornadiene etc). With the bicyclics there are numerous possibilities for rearrangement ie C-C bond fission, 1,2 H-shift, C-W H-shift etc.
Posted by: doggles | July 2, 2009 5:47 PM
other pronunciation notes duly noted... "nations divided by a common language" also applies to science doesn't it - ha ha - we all know that our way is the right way though eh? - the amide one really does take some getting used to I must admit.
@ MrFire - have you ever tried solid phase extraction to remove the metal residues? - there are some organosulfur compounds immobilised on silica that can effectively remove Pd I think - Biotage make a few. Five fruitless columns is a hell no human should endure... at work I try to use these to take out metals prior to HPLC as the metals can ruin the HPLC columns pretty quick.
Posted by: 'Tis Himself
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July 2, 2009 6:05 PM
At least Americans don't stick extra syllables into alumininininininium.
Posted by: MrFire | July 2, 2009 6:28 PM
@doggles:
Thanks for the tip - next time I'll stink that Pd out of existence!
Posted by: Berner | July 2, 2009 6:55 PM
@'Tis Himself
Take a look at a periodic table. I'm pretty sure most of them have it spelled Aluminium rather than Aluminum. Being a chemist though I never write out the actual names. Using Al always looks better to me.
Posted by: j a higginbotham | July 2, 2009 7:08 PM
I think most periodic tables would have aluminum (certainly more popular in Google). See http://www.worldwidewords.org/articles/aluminium.htm for history.
Posted by: Pablo | July 2, 2009 9:07 PM
Colloidal AND tarry, Gracie?
Posted by: Kemist | July 2, 2009 10:01 PM
The trick I used is to drop a scoop of sodium borohydride in my crude product after disolving in methanol or THF. Reduces the metal, the complex is destroyed and it precipitates out. Cheap and fast, but your product has to be stable to reducing conditions.
Or you can try those high-priced scavenger resins, if your lab has the money.
I hate columns. Recristallisation rules.