Abnormal NHC carbenes

23 October 2009 - Check this out

abnormal NHC Bertrand 2009
Check: Abnormal NHC carbenes (aNHC)
Check: variation of NHC carbene , a type of carbene that is stable at ambient temperature and can be isolated. In the regular NHC carbene carbon is flanked by two nitrogen atoms, in the aNHC it is just one. Requires steric protection by bulky diisopropylphenyl (dip) ligands. Central ring planar with 1.5 bond order bond lenghts consistent with ring delocalization. carbon NMR also indicates carbene.
Check: Published in Science , Aldeco-Perez et al. 2009 DOI Bertrand lab
Check: Substrate a imidazolium ion
Check: reagent KHMDS, a strong base removes the C5 proton
Check: utility as novel catalyst
Check: more on Guy Bertrand in this blog here, here and here

Asymmetric Strecker

21 October 2009 - Check this out

asymmetric Strecker Zuend 2009
Check: reaction type Strecker reaction
Check: keywords organocatalysis asymmetric synthesis
Check: Published in Nature Zuend et al. 2009 DOI Jacobsen lab.
Check: substrate imine
Check: reagents trimethylsilyl cyanide, methanol, a thiourea catalyst. See organocatalysis
Check: utility. The reaction product a chiral tert-butyl leucine can be used as a starting material for synthesis of HIV protease inhibitor atazanavir.
Check: More Strecker here

Single molecule white-light-emitter

16 October 2009 - Synthetic light

In regular fluorescence a material absorbs UV radiation and emits lower wavelength visible light. At the atomic level an electron is pushed to a higher energy level (excited state) and on relaxation it emits a photon with a wavelength inversely related to the energy jump. These jumps are quantized and the emitted light comes with a specific color. For example glow sticks are green, yellow or blue. The color white is not an option because white light is simply a mixture of all colors.



A recent report by a Korean / Spain based team (Park et al. 2009 DOI) of a single-molecule white-light-emitter should therefore raise some eyebrows. Yet, when you dissolve coolly named compound W1 (see graphic) in in chloroform and throw a UV lamp (254 nm incoming) at it, a beautiful color white (400-700 nm outgoing) beams back at you. So what is going on (pic here).

W1 is a dyad (linked by an ether group) of blue color emitting HPI and complementary color yellow emitting HPNI. When HPI and HPMI are mixed the color white does not appear because of energy transfer between excited donor HPI and ground-state acceptor HPNI but in the dyad this transfer is prohibited (frustrated) due to geometric constraints.


Instead with W1, emissions from both parts of the molecule occur independently and white light results. The full emission wavelength is also dependent on a keto-enol tautomerism process taking place: an enol exited state E* forms from the enol ground-state E which relaxes to a keto excited state K* in a so-called excited-state intramolecular proton transfer (ESIPT). The K* to K jump takes places next with a smaller energy gap (tunable inside visible spectrum) and a K to E conversion then completes the cycle.

Nanotech at the dentist

09 October 2009 - Self-assembly

Wouldn't that be just great, instead of having your cavities filled with resin or a metal alloy, simply regenerate the enamel at the cavity site. Sounds simple enough because enamel (the 2 mm thick outer layer of a human tooth) is just inorganic hydroxylapatite and the cells that made it have disappeared long ago when construction was done. Haifeng Chen et al. @ Peking University has this simple recipe (Yin et al. 2009 DOI): a human molar is etched with phosphoric acid and then put in a solution of calcium phosphate , the chelating agent N-(2-hydroxyethyl)ethylene-diamine-N,N,N-triacetic acid and KI at 37°C for 8 days.
Lo and behold new hydroxyapatite layer forms, nucleated from the surface of the existing enamel, 2 to 4 micrometer in thickness in typical enamel hexagonal rodlike crystals. In fact, the initial morphology is amorphous, it then changes to spherical crystals (Ostwald ripening) and finally (if you wait long enough) the thermodynamically favored nanorods form. The researchers also report comparable nanomechanical properties.

In 2008, US-based team investigated the role played by a enamel matrix protein called amelogenin (Wang et al. 2008 DOI). This team thinks the protein assists in the kinetic formation of the nanorods from nucleating nanoparticles via self-assembly.

Earlier in 2005, the Japanese competition prepared a ready-to-use paste for enamel restoration based on phosphoric acid / hydrogen peroxide / fluorized-apatite powder, that when applied to tooth at the site of a lesion (early stage of cavity formation) showed immediate results (20 micrometers growth) within 20 minutes with the the apatite crystals dissolving and regrowing (Yamagishi et al. DOI). To demonstrate the durability of the new layer the site was exposed to 10,000 brushing actions (150 rev./min, load force 200 g, brushing amplitude 30 mm) and luckily the Japanese invented a machine to do that for them.

The 2009 Nobel Prize in ChemBioPhysMed

07 October 2009 - interdisciplinary research

It is in a good tradition that each year the Royal Swedish Academy of Sciences awards the Nobel Prize in Chemistry to biochemists and this year is no exception: this year's winners are Venkatraman Ramakrishnan, Thomas A. Steitz and Ada Yonath for their work (involving a lot of crystallography) on the structure and function of the ribosome. Typically Wikipedia was ill prepared and the Ramakrishnan and Steitz bio pages were created minutes after the announcement was made. On the upside Wikipedia already had relevant citations from the three laureates on the ribosome page and more for Yonath on the collagen and 16S ribosomal RNA pages.

Luckily this year, the chemists have managed to snag a Nobel prize away from the physicists. After all the 2009 Nobel Prize in Physics is all about the wonderful material properties of glass, a substance that chemists have been tinkering with for over 2000 years. Charles K. Kao discovered how to purify glass for it to be useful in fiber optics.

Too bad the physicists in their turn were not able to get hold of the Nobel Prize in Physiology or Medicine, that would complete the circle and make everybody happy after all. In 2003 that prize went to physicist Peter Mansfield for his work on MRI, so it is not unthinkable. The medicine prize this year is all about certain biomolecular structures inside cells that assist in copying certain genetic material, not more ribosomes (that would be chemistry!) but this time DNA and telomerase.


Archive: Now worthless predictions

2009 Stoddart rotaxanes

05 October 2009 - Supramolecular chemistry

Supramolecular chemist James Fraser Stoddart moved to a new university this year and was dropped from the Thompson shortlist for the Nobel Prize in Chemistry 2009. Lets see what this blog's favorite has been up recently.

Enter the mechanised nanoparticle (MNP): a molecular machine that looks like a spigot capable of controlled release of encapsulated molecules (think drugs). In a recent incarnation the container is a nanoparticle made of mesoporous silica, the controlled substance (or cargo) is Rhodamine B (handy when it comes to spectroscopic identification), the stopper a pseudorotaxane based on viologen (thread) and cucurbituril (movable ring component and capping agent) and the switching trigger is local pH (the bloodstream has a neutral pH, cells are acidic). The cucurbituril unit is water soluble making the whole ensemble all the more biologically relevant (Khashab et al. 2009 DOI). A similar procedure has been described for a propidium iodide cargo with a hexamethylene diamine thread (Angelos et al. 2009 DOI). With two valves, one operating by light and one by pH the MNP can act as a molecular logic gate (Angelos et al. 2009 DOI)

A novel push-button molecular switch was designed with specification single pole, single throw (Spruell et al. 2009 DOI) as part of research into mechanically interlocked molecules. The contraption is based on a catanane (graphic here) where the ring containing a paraquat unit can only clip itself to one tetrathiafulvalene unit in the other ring. Synthesising the catenane required some template-directed synthesis made possible ("threading-followed-by-clipping") by copper assembling two alkyne termini in an Eglington coupling (image here). Reversible clipping and unclipping is a redox reaction. In another system recently developed (Zhao et al. 2009 DOI), one ring in the catenane can now clip itself redox controlled to two molecular units in the other ring (bistable) with both rings tethered to each other by a ethylene glycol unit as in a pretzelane.

Rotaxane complexity is increased when 4 rotaxanes are linked to a single porphyrin molecule and when the stopper contains a disulfide bond as an anchor for nanogold particles (sulfur looooves gold). The tetrameric rotaxane can thus reversibly pick up 4 gold NP's or release them by applying the electrochemical switch in the thread (image here). When the assembly is heated to 95°C, the 4 nanoparticles fuse leaving a tiny hole in the middle where the organic core once was (Olson et al. 2009 DOI). More solid-state chemistry: coat a microcantilever with gold, add a monolayer of redox-controllable rotaxane molecules and an artificial muscle (catilever bending by up to 500 nm) can be demonstrated by applying a voltage (Juluri et al. 2009 DOI). Rotaxanes can also be blended into metal-organic frameworks (Li et al. 2009 DOI)

And that is only a small sample of current Stoddart chemistry. So if ever you are desperate for tetrameric-fused-gold-nanoparticles-with-a-tiny-hole-in-it or a molecule-size-AND-gate, Stoddart is your man.