Kudos to the Fagnou Group

I am continuously impressed by the publications that have appeared since Prof. Keith Fagnou's shocking passing a little over a year ago. The chemical community still mourns; it is clear from these post-mortem publications that Fagnou's - and his clearly dedicated and talented graduate students and post-docs - brilliance lives on.

The chemistry that Fagnou has truly spearheaded, direct C-H functionalization, is a method of forming C-C, C-N, C-B, etc bonds without having to prepare one of the coupling partners, as in traditional transition-metal catalyzed cross-coupling reactions. Palladium, rhodium and ruthenium are commonly used catalysts in direct C-H functionalization reactions. Fagnou has published a great deal on arylation reactions of a wide variety of substrates and even a bit on direct benzylation reactions. Some fairly recent reviews are linked in a previous post.

A recent publication in Journal of Organic Chemistry (doi: 10.1021/jo102081a), "Predictable and Site-Selective Functionalization of Poly(hetero)arene Compounds by Palladium Catalysis," published by David Lapointe and coworkers, explores the development of two approaches to selectively functionalizing multi-ring systems - 1) using site-selective reaction conditions, and 2) a pathway with a particular order of reactivity according to a concerted metalation-deprotonation (CMD) mechanism. It is well-known in the field that a great many (hetero)arenes can be functionalized with (painfully) rigorous fine-tuning of the catalyst, ligand, additives, and other reaction conditions. Some substrates have been more difficult to functionalize than others, and selectivity of particular positions on these rings is always an issue - this publication tackles both issues.

To explore site-selective functionalization, the group used compounds with more than one available C-H bond for direct functionalization, and using multiple protocols specific for specific C-H bonds (Larossa's conditions for C2 arylation of indoles, Gaunt's Cu-catalyzed C3 arylation of indoles which is actually selective for meta to amido groups, and their own protocols for arylation of perfluorobenzenes and aromatic N-oxides) were able to successfully and selectively functionalize targeted C-H bonds in moderate yields. Here is an example with some decent yields, with reaction times ranging from 16 - 24 hours:

The alternative approach relies upon the CMD pathway as the operative mechanism, which favors electron-deficient substrates.  Several years ago, Echavarren published support of this mechanism by finding a preference for the most acidic C-H bond and requirement for a carbonate base, and Fagnou established the use of a pivalate additive, which was speculated to play a crucial role via CMD.   A recent mechanistic paper with aromatic N-oxides as the substrates strongly supports this mechanism.   The metal first inserts into the aryl-X bond, as expected, and in the key transition state, the pivalate coordinated to the metal deprotonates the C-H bond while the palladium forms a bond to the same C.  Reductive elimination (not shown) releases the arylated product.

In the current paper DFT calculations were found to agree quite well compared to competition reaction results of a series of heterocycles to elucidate the order of reactivity of the substrates.  Those presented in the paper are as follows, in order of reactivity - this is extremely convenient for the synthetic chemist who would like to utilize this chemistry.  And it's just plain neat - the kind of thing that will hopefully end up in a textbook someday. (Note: the last two substrates are either switched in the text or switched in the image - they don't agree in the paper and I haven't looked at the supporting information closely.)

Reaction conditions: 0.5 eq. of each of two heteroarenes in the competition experiment, 0.125 eq. 4-bromotrifluorobenzene, Pd(OAc)₂ 5 mol%, PCy₃.HBF₄ (10 mol%), PivOH (30 mol%), K₂CO₃ (1.5 eq.), DMA (0.3M), 100ºC.

And finally, for an example of the method in action - note that the difference between using this method and the previously described is that here, there aren't necessarily general optimized conditions available for each of the substrate classes here.  Examples of a few of these are peppered throughout the arylation literature but they aren't like indoles, pyridines, N-oxides, perfluorobenzenes, imidazoles, and pyrazoles and don't have their own special set of conditions (that I'm aware of at the moment).  Yields of included substrates range from 65-80%. Instead of optimizing conditions for each, the site of reactivity can be predicted with good specificity - here the indolizine C-H bond over the more electron-rich thiophene's:

Instead of an aryl bromide, benzyl chloride can be used as the coupling partner as well, with published yields from 55-84%.

• Lapointe, D., Markiewicz, T., Whipp, C. J., Toderian, A., Fagnou, K. (2011). Predictable and Site-Selective Functionalization of Poly(hetero)arene Compounds by Palladium Catalysis Journal of Organic Chemistry : 10.1021/jo102081a

Maker Faire 2010 has brought me back from the dead

It's been a long time since I've posted. I admit it. I'm not happy about it, but my energies have been unbelievably sapped. I attended an event last weekend that revitalized my faith in science as something FUN, though. (Note: this is the same post that I've also put at Chemistry Blog.)

The Maker Faire is a "World Science Fair" event conceived and organized by those who produce Make magazine, which is described as "a do-it-yourself technology magazine written by makers."  It was held in three cities this year - NYC, Detroit, and the Bay Area.  The Faire happened in NYC at the New York Hall of Science in Queens last weekend and was a fantastic, energetic composite of things going on.  Well worth the trek to get out that far into Queens!

The event embodied the "do-it-yourself technology" theme, featuring exhibits with a heavy focus on science, cool demonstrations, and lots of do-it-yourself booths where "makers" hosted hands-on activities for children and adults alike.   Naturally, something like this was irresistible to me, and I was able to attend for free since I was volunteering at a booth (unrelated to science or technology - I was with a group of a different kind of maker).  I didn't get too much of a chance to spend time at many of the huge number of booths and exhibits, unfortunately, which was a huge bummer.

The schedule was overwhelmingly packed - definitely intended for people to spend an entire day there.  There was a demonstration stage, multiple craft tents, a huge food area, a beer tent tucked in there (which seemed to result in me getting security to throw out one guy who was harassing one of the women I was working with), and a large handmade craft sale section hosted by BUST magazine called BUST Craftacular.

Activities included "Cardboard Music," where instruments were made from cardboard and found objects, a live presentation called "Thinking Like a Scientist" (some demonstrations of which are 200 years old) given by Wizard IV (Steve Jacobs), who also happens to be the science consultant for MythBusters.   MakerBot Industries was there - they create 3D printers that you assemble and then can then function as a little factory to make things for you (see the company website for more awesomeness).  One of the biggest pulls for visitors was the "Reverse Geocache (TM) Puzzle" - unlike using GPS to locate boxes around the country/world, you are given the box, but it won't open unless you are at particular coordinates that've been programmed into it, and you have a limited number of clues to find that exact location.   Add this fun kind of intellectually stimulating product, activities and ideas, to children's rides, music shows, tasty paella, and handmade crafts, and you've got one heck of a good sciencey time.

Check out images of the event on their own website, as well as those on CNET, guaranteed to be focused on the super techie stuff.

Some science for raw foodists

I once lived with a woman who insisted that cooking food broke down the enzymes that we so desperately need from the food.

...

This same roommate also insisted that water kept at room temperature was more "alkaline" than when it was cold.  (Though this website insists that the water must have a pH = 10 to have this effect, and that if you drink it, it will clean toxins from your body. She insisted temperature alone achieved this desired effect.) 

...

She was taking general chemistry at my university at the time, in my very department.  Apparently equilibrium means nothing to her... would you trust her as your doctor?  Excuse me, as your holistic natural medicine doctor who seeks to legitimize the profession by attending medical school.  I have zero beef with natural medicine, don't get me wrong, but more alkaline at room temp??  Is there a temperature dependence constant missing from H₂O → H⁺ + OH^- ??  F, man.  I have a beef with momos who deny the fundamentals of general chemistry.  Or who doesn't realize that the person or book that told her that might've said the pH was higher...

So, I acknowledge the health benefits of restricting the amount of processed food that one consumes, and in many fruits and vegetables, cooking does cause vitamins to leach from the greens into water, sometimes to an alarming degree.  Freezing in many cases also causes nutrient-dense foods to lose their potency.  Thanks to an article that just came out in Journal of Agricultural and Food Chemistry, we can now argue that at least eggplants do not behave the same way.  

Sample preparation:  Eggplant (the "black bell" variety) was grown in a research facility in Lodi, Italy, selected by visual inspection to be homogenous in size, color, and free from diseases or pests.  The fruits were cut into 1 cm slices and treated one of three ways - 1) kept raw (freeze-dried and lyophilized); 2) grilled on a surface of 190-210C such that the inside reached and stayed at 100C; 3) boiled in 10 min in tap water at a 1:10 fruit:water ratio such that the inside of the slices reached and stayed at 100C.  The grilled and boiled fruits were cooled for 1 minute at room temperature, then immediately frozen and lyophilized until constant weight was reached.   From these samples, 2 g samples were taken from each treatment group, treated twice with 55 mL 75% EtOH at 60C then dried with 20 mL acetone until constant weight to produce ethanol-insoluble residue, EIR.  (I bet you never thought about food sample preparation in science before, eh?)

Analytical chemical analyses:  

• Total polyphenol index was measured with RP-HPLC and the quantity of chlorogenic acid determined, since chlorogenic acid is the predominant polyphenol found in eggplant.  Anthocyanins from the peels were quantified as well.  
• Glycoalkaloid content (solamargine & solasonine, which you really don't want to eat in gigantic quantities as they are toxic in high doses) was determined from 0.5 g tissue treated with 95% ethanol and analyzed by RP-HPLC.  

• Antiradical activity, signified by superoxide anions and hydroxide radicals, was determined using ESR (electron spin resonsance) spectroscopy 1 minute after generating these species via:    
• Superoxide anions were generated by treatment of eggplant extract with 6.4 mM KO₂-18-crown-6 1:1 in DMSO followed by spin trapping with 25 mM 5,5-dimethyl-1-pyrrolin-N-oxide (DMPO)
• Hydroxyl radicals were generated by treatment of extract with 2 mM Fenton system (?) in 0.1M phosphate buffer (pH=7.4) followed by spin trapping with 10 mM DMPO

Biological assay:  Human polymorphonuclear neutrophils, which are the most common type of white blood cells (shown at the left surrounded by red blood cells), polymorphonuclear because their nuclei are often lobed -  are a type of granulocytes (dubbed so because their cytoplasms are granular in appearance).  These cells were isolated from human blood samples and chosen because when under oxidative stress, they produce oxidative species (as a good white blood cell should!) including superoxide anions, peroxides, oxygen radicals, hydroxyl radicals, and HClO, which are all considered "reactive oxidative species" (ROS).  The assay involved viewing the cells under a fluoroscence microscope to visualize the chemiluminescence produced by luminol when luminol is reacted with one of these ROS; this "luminol-amplified chemiluminescence" (LACL) assay allowed the researchers to measure oxidative bursts given off by the cells in response to varying concentrations of the eggplant extract; the fewer the bursts, the more antioxidant species the extract contains as the cells are emitting fewer ROS.

The authors found that cooking didn't affect the glycoalkaloid content, but the phenolic content was increased threefold, most likely due to greater extractability of the compounds by cooking.  The effect of the extract on the neutrophils was very marked, and the researchers were able to extrapolate that approximately 40 - 80 g of eggplant, which can be obtained in one serving, may be able to react with all the neutrophils in the body.   The following TOC graphic (black & white in the paper) shows that at higher concentration of extract, the inhibition of ROS is greater - though the concentrations needed to cause this effect are quite low.  Hope you like eggplant!  Make sure you grill the heck out of it.

• Lo Scalzo, R., Fibiani, M., Mennella, G., Rotino, G., Dal Sasso, M., Culici, M., Spallino, A., & Braga, P. (2010). Thermal Treatment of Eggplant (L.) Increases the Antioxidant Content and the Inhibitory Effect on Human Neutrophil Burst. Journal of Agricultural and Food Chemistry DOI: 10.1021/jf903881s