About this Author
DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: Twitter: Dereklowe

Chemistry and Drug Data: Drugbank
Chempedia Lab
Synthetic Pages
Organic Chemistry Portal
Not Voodoo

Chemistry and Pharma Blogs:
Org Prep Daily
The Haystack
A New Merck, Reviewed
Liberal Arts Chemistry
Electron Pusher
All Things Metathesis
C&E News Blogs
Chemiotics II
Chemical Space
Noel O'Blog
In Vivo Blog
Terra Sigilatta
BBSRC/Douglas Kell
Realizations in Biostatistics
ChemSpider Blog
Organic Chem - Education & Industry
Pharma Strategy Blog
No Name No Slogan
Practical Fragments
The Curious Wavefunction
Natural Product Man
Fragment Literature
Chemistry World Blog
Synthetic Nature
Chemistry Blog
Synthesizing Ideas
Eye on FDA
Chemical Forums
Symyx Blog
Sceptical Chymist
Lamentations on Chemistry
Computational Organic Chemistry
Mining Drugs
Henry Rzepa

Science Blogs and News:
Bad Science
The Loom
Uncertain Principles
Fierce Biotech
Blogs for Industry
Omics! Omics!
Young Female Scientist
Notional Slurry
Nobel Intent
SciTech Daily
Science Blog
Gene Expression (I)
Gene Expression (II)
Adventures in Ethics and Science
Transterrestrial Musings
Slashdot Science
Cosmic Variance
Biology News Net

Medical Blogs
DB's Medical Rants
Science-Based Medicine
Respectful Insolence
Diabetes Mine

Economics and Business
Marginal Revolution
The Volokh Conspiracy
Knowledge Problem

Politics / Current Events
Virginia Postrel
Belmont Club
Mickey Kaus

Belles Lettres
Uncouth Reflections
Arts and Letters Daily
In the Pipeline: Don't miss Derek Lowe's excellent commentary on drug discovery and the pharma industry in general at In the Pipeline

In the Pipeline

« On the Uselessness of the MSDS | Main | Homeopathic Merchants Take Your Questions! Well, Sort Of. »

May 27, 2009

Surfin' On The Surface

Email This Entry

Posted by Derek

There are a lot of ways to think about the chemical reagents that we have stirring around in our flasks. But one of the basic ones, and one of the most useful, divides them into classes according to whether they’re in solution or not.

When things are in solution, they may act funny, but at least everything’s starting out on the same footing. If all the components are dissolved (and if everything’s stirring the way it should), then they all have the chance to find each other and do their respective things. But if some reagent is still a solid in there (powder, chips, what have you), that takes you into the nonintuitive world of surface chemistry.

This actually happens quite a bit. Plenty of standard organic reactions involve insoluble things where the chemistry takes place on the surface. There’s formation of a Grignard reagent from magnesium turnings, deprotonation with powdered sodium hydride, hydrogenation over palladium-on-charcoal – these are all classics. And I'm not even mentioning the surface-driven industrial scale catalyst systems today, which is unfair of me, since the economies of the entire industrialized world depend on them. But in all cases, the real details at the molecular level of these reactions are not easy to work out.

People are still arguing, for example, over just how catalytic hydrogenation works on the metal surface, although the general details of the mechanism are known. That one’s complicated by not just being the plain metal, but a weirdo solution of hydrogen in the metal lattice. There’s no dispute, though, that the reaction is taking place on the surface of the metal, and that the higher the surface area the better off you are.

That’s one big variable right there: surface area. Finely divided substances are very different players in these systems, and many chemists find (early in their lab careers) that they’ve unwittingly bought front-row seats for a demonstration of just how different they can be. Finely divided powders have a lot of surface area in them, and if that’s a rate-limiting factor, you can find yourself with something that’s easily a hundred times more reactive just by picking up a different bottle of what appears (at first glance) to be the same substance. I once saw someone substitute lithium powder for lithium sand in a prep without thinking about this issue, and not so much later, I got to see the same guy clean the inside of his fume hood out with a scrub brush.

But there’s more than just surface area affecting some of these reactions. Grignard formation, for example, seems to take place (at least initially) in fresh breaks or cracks on the magnesium surface. That exposes metal that hasn’t had a chance to become coated with anything (like a layer of magnesium hydroxide), and (zooming in) it also may reveal individual reactive magnesium atoms, left out on the edge and insufficiently surrounded by their teammates. Once these react and fly off into solution, the ones around them become exposed, and so on, and the oxidized layers become undermined and flake off. The standard Grignard-initiation tricks are all designed to speed this process along. A drop of iodine will react quickly with any magnesium points or edges, exposing still more fresh rough surface, as will reaching down under the solution and breaking the turnings with a spatula (or, alternately, grinding them with a heavy stir bar).

These days, what’s really complicating things is the ability to generate (and characterize) nano-sized particles. At some point, these things can stop behaving like tiny bits of the bulk substance (which can be enough of a difference in itself, as mentioned above), and start acting like completely new beasts. And the really nano-sized stuff has a better chance of actually being in solution – but that brings on various headache-inducing thoughts about what “being in solution” means on this scale. If you have clumps of (say) palladium a few dozen atoms wide, which manage to be solvated enough to float around, is that a heterogeneous reaction or a homogeneous one? At that size, is that a "surface", or not (and is the reaction really taking place on it?) What if the nanoparticles are immobilized on a solid support - do they stay and react there, or is the reaction driven by the few that escape? (That effect has been noted in the Heck reaction, among others).

We need to understand these things better than we do - there are surely a lot of very useful things that could be done if we had better control over catalysis and surface chemistry. It's going to keep a lot of people occupied for a very long time.

Comments (5) + TrackBacks (0) | Category: Inorganic Chemistry | Life in the Drug Labs


1. Retread on May 27, 2009 9:38 AM writes...

Along these lines, guess the total surface area of the air cells (alveoli) making up your lung.

No peeking !

It's about the size of a tennis court.

This is why pipe smoking is far less harmful than cigarettes (assuming you don't inhale -- which a cardiologist friend told me that ex-cigarette smokers do when they switch to a pipe, as I did years ago). You absorb far less gunk from your mouth.

Permalink to Comment

2. Norepi on May 27, 2009 3:36 PM writes...

Supposedly, ultrasonication is also good for kicking off stubborn Grignards. Never tried it meself though.

Permalink to Comment

3. The Beast on May 27, 2009 9:22 PM writes...

>Supposedly, ultrasonication is also good for kicking off stubborn Grignards. Never tried it meself though.

Ultrasonication? I think we are past that now. What started as "sonication," soon transformed into "supersonication," followed quickly by "ultrasonication." In this modern age, however, we are blessed to have "nanosonication."

Permalink to Comment

4. Anonymous on May 27, 2009 9:35 PM writes...

I love the numbers for Pd/C... ~1000 m2/g.

Permalink to Comment

5. Arjun on May 28, 2009 12:54 PM writes...

In a somewhat interesting twist, I am told that the preparation of adamantyl Grignard requires that you not stir. The reason, supposedly, is that the adamantyl radicals initially formed at the Mg surface need to stay there so that they can be further reduced to the Grignard. If you stir, the radicals diffuse away and you get mostly the diadamantyl homo-coupling product.

Permalink to Comment


Remember Me?


Email this entry to:

Your email address:

Message (optional):

The Last Post
The GSK Layoffs Continue, By Proxy
The Move is Nigh
Another Alzheimer's IPO
Cutbacks at C&E News
Sanofi Pays to Get Back Into Oncology
An Irresponsible Statement About Curing Cancer
Oliver Sacks on Turning Back to Chemistry