4/11/2007

I've got a fever, and the only prescription is more BINAP

Apologies from Ψ*Ψ and I regarding the lack of posts as of late: we have been quite busy and, despite living in different states, we have come down with similar illnesses at the same time. Nevertheless, I believe it's time for another of my unnecessary advice posts. This week: how to distinguish between R- and S-BINAP.


BINAP is a chiral, bidentate phosphine ligand that's used a whole lot in asymmetric synthesis. One of its first and most well-known uses is in the Ru-BINAP catalyzed Noyori hydrogenation, which, with his other works, won Noyori a Nobel prize in 2001. It's an interesting molecule: it is chiral, yet it has no chiral center. It exhibits what is known as atropisomerism, where two stereoisomers are conformers of one molecule, separable only by hindered rotation about a bond. In BINAP's case, rotation about the bond between the two naphthalene units is strongly hindered by the phosphine units. If there were free rotation about that bond, the molecule would be achiral. You can racemize one enantiomer of BINAP by heating the hell out of it.

Whenever a prof showed BINAP in synthesis, they neglected to mention how the R- and S- designations are made, and I always had trouble distinguishing the two. Finally, one professor did manage to explain it simply to our class, and so, here is how you do it in case anyone else is in a similar position. This explanation works for BINAP and other atropisomers. Pretend as if you are walking on the naphthalenes of BINAP. Start at 12 o'clock and walk "up,". In this case, looking at the molecule from the side, "up" is coming toward you. In one enantiomer, you're always walking counterclockwise to go "up"- by convention, that is the S enantiomer. In the other one, you walk clockwise to go "up"- that is the R enantiomer.


You can do this with other atropisomers, like the cute helicenes. Same deal- just walk "up" the molecule. This might be easier to visualize.



Well, that's all for today's unnecessary advice post. I do enjoy writing these, and I hope someone gets something out of it. Maybe some real chemistry, with real pretty colors, next time!

16 comments:

Liquidcarbon said...

Bold bonds in (S)-BINAP sort of look like letter "S".

Kutti said...

Hey, that´s a great post! I like it very much.
By the way: is there a certain Document Setting that you are using for your drawings or is it just ACS Document 1996 with black background and changed Bold Width and Line Width?

milkshake said...

Bold bonds in (S)-BINAP look just like a swastika

(now - we have ways, to make you remember)

Excimer said...

milkshake- thank you for the first Godwin'd thread on CBC. You should be proud.

kutti- Thanks! I just use ACS document settings and change the line width and bold width. Structures look much better when you do a little tweaking.

Kutti said...

Do you know whether it is possible to create your own personalized "Document" so that one doesn´t have to apply the settings for every new drawing?

Felix said...

nomenclature is my favorite foreign language, pretty cool

Excimer said...

Kutti: i think you can do that with chemdraw ultra, but not standard... I don't know how though (I use standard myself). I just change the settings every time I do a post. Maybe someone else knows?

Liquidcarbon said...

File -> Apply document settings from -> Other. Other = any Chemdraw file as a template.

(Chemdraw Ultra 10.0

Excimer said...

oh, well how about that. that does, in fact, work in standard mode. thanks liquidcarbon.

Uncle Al said...

Another stereochemistry assignment nastiness: An undistorted tetrahedral sp3 carbon with four identical substituents can be chiral. Given enantiomeric chiral group R and S, CR4 and CS4 must be chiral centers. Which carbon is R and which is S? Go for the gold with C(CS4)4,

http://www.mazepath.com/uncleal/chiral2.gif http://www.mazepath.com/uncleal/chiral3.gif
[6.6]chiralane caused NIST to rewrite its commercial stereochemistry software. The carbon skeletons of convex molecules in point groups T, I, and presumably O (never could design that one) are *perfectly* chiral by Petitjean's quantitative measure,

J. Math. Phys. 40(9) 4587 (1999)

S-[6.6]chiralane has a calculated [alpha]D = +691.8 degrees (Jochen Autschbach, unpublished). That is pretty good for a saturated spherical molecule with no dipole moment and no chromophores. Every minimal ring is an identical twist boat cyclohexane.

Chemgeek said...

Any version of Chemdraw allows you to save setting in as a stationary file. (I think).

I use a Mac, so there may be some differences if you use a PC or a Commodore 64.

Open a new file.
Change all the settings you want.
Make sure the document is completely blank (unless you want something to appear everytime you open this type of file)
Save the document as a "ChemDraw Stationary" file (ends with .cds) in the "ChemDraw Items" folder. It must be in this folder.

[I save my most commonly used stationary with a space as the first character so it is listed first alphabetically]

Then when every you want to open this type of file with all of your custom settings you can chose "Open Special" or do what Liquid Carbon suggested.

Hope this helps

Oh, excimer, keep posting stuff like this. It is always useful if not interesting.

Dan said...

For BINAP, specifically, how about the fact that the bold bonds in the S isomer form... an S?

Excimer said...

I never found the S thing to be particularly appealing, because 1. I could never see it, 2. you orient it weird and it becomes nigh impossible for me to see it, 3. it doesn't explain where the R and S designations come from, 4. doesn't work for helicene. But, yes, the S thing for BINAP works too.

mevans said...
This comment has been removed by the author.
mevans said...

I'm an idiot; that's all there is to it.

sushi said...
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