Saturday, February 28, 2009

The Force is strong here

If there is a gizmo I really crave to take control of, this is the one. As The NeoCube (Strong Force Inc.) website puts it,

The NeoCube is an entertainment device like no other in the world. Composed of 216 individual high-energy (whatever that means) rare-earth magnets, the NeoCube allows you to create and recreate an outrageous number of shapes and patterns... The NeoCube Alpha is perfect for gaming, expression, stress relief, dual hemispherical brain stimulation and much more.

The rare earth metal in question is neodymium, which, according to Wikipedia, is not that rare at all. Which is a good news for all of us needing affordable dual-hemisphere brain stimulation.

Sunday, February 22, 2009

Copper, zinc and haem in superoxide dismutase

Why bacterioferritin needs a haem anyway? It’s a very good question, and so far it does not have any good answer. The shortest one is, we don’t really know. There are ferritins (in Escherichia coli as well) having exactly the same architecture which do not bind any haem. Bacterioferritin is not alone: Cu,Zn superoxide dismutase from Haemophilus ducreyi contains not only, as one may guess, copper and zinc (all Cu,Zn-SODs do), but also, for no reason, a haem. Once again, it is bound at the dimer interface, although this time it is asymmetrically bound with two different histidine residues provided by the two subunits. The authors show that the introduction of only three mutations at the dimer interface of the Cu,Zn-SOD from a related species, Haemophilus parainfluenzae, is sufficient to induce haem-binding ability. However, it does not change anything: we still don’t know why the haem is there.

Friday, February 20, 2009

Zinc, haem and water in bacterioferritin

This structure is a beauty: Willies et al. solved the structure of bacterioferritin from Escherichia coli to 1.9 Å. The hollow shell of bacterioferritin is made up of 24 identical subunits organised as 12 dimers. The two metals that the ferroxidase centre binds have previously been assigned as manganese or as a mixture of iron and zinc; now it has been shown that both are zinc. The haem is coordinated by two Met-52 residues from two subunits forming a dimer. Interestingly,

At the resolution of the structure presented, the electron density clearly shows the binding of haem in both conformations, each at half occupancy with no preference for either conformation
(the authors consistently use “conformation” throughout the paper but they really should say “orientation”, as they do in the Figure 4 legend). For the first time, a link is described between the internal and the external environment of the bacterioferritin via the cluster of water molecules and the haem; the authors suggest that this could be an electron-transport pathway.

Saturday, February 14, 2009

Impossible figures

I am sure everybody can see that the drawing (a) is an impossible figure. So I expect nobody will draw cubane like this; the correct drawing is (b).

cubane (wrong)
cubane (right)

In fact, if you pay attention, you will notice that the chemical databases are full of impossible figures. I just have corrected the drawing in ChEBI entry for codeinone (c). Next release, it will look like (d).

codeinone (wrong)
codeinone (right)

Friday, February 13, 2009

Corrine, Corrina

The cover of Compendio de terminología química (the Spanish translation of IUPAC Gold Book) features the structure of corrin. So, I simply had to add the French (corrine) and Spanish (corrina) names to corrin entry. Undoubtedly, this will ensure that everyone who is googling for Corrine, Corrina will get to ChEBI. (Or maybe not: today there are about 315,000 results on Google, the top ones being the Wikipedia article and a Corrine, Corrina Home Page with a discography of over 160 different versions of this song.)

Compendio de terminología químicacorrinJohnny Carrol and His Hot Rocks

Thursday, February 12, 2009

The Darwin coin

Finally, something that has something to do with both Darwin and metals and that you can have in your pocket (quite unlike this bronze sculpture of young Darwin unveiled by Prince Philip today in Cambridge). To celebrate Charles Darwin's 200th birthday (today) and the 150th anniversary of the publication of On the Origin of Species, The Royal Mint issued a special Charles Darwin £2 Coin, although I am yet to see it in my change. (I am not talking here about £2 Silver Proof Coin or £2 Gold Proof Coin, which probably never will be in circulation.)

Friday, February 06, 2009

Heavy snow

Yesterday, the BBC weather people promised some “heavy snow” which had never materialised. But what exactly is “heavy snow”? I think the snow made of heavy water should be heavy. In that case, it is either a water enriched with dideuterium oxide (D2O) or heavy-oxygen water, H218O. Now, D2O has melting point 3.82 °C (0 °C “normal” water) and temperature of maximum density 11 °C (4 °C “normal” water). I got these data from our office copy of CRC Handbook of Chemistry and Physics (83rd Edition), p. 6-4. Unfortunately there are not that much data on physical proterties of D2O ice in this book, let alone snow. In fact, it does not contain the word “snow” in its index at all. It has SMOW though, literally on the next page. The table on p. 6-5
gives the density ρ of standard mean ocean water (SMOW), free from dissolved salts and gases, at a pressure of 101325 Pa.
(I wonder how much SMOW differs from any other water after all these purifications.) As for H218O, Handbook has nothing. Search in Gmelin database gives range of temperatures: from –0.01 to +0.3 °C. Hmm. Let’s just think that heavy water is D2O and heavy snow is D2O snow. According to this 3-year old thread (which has started with somebody asking this very important question: “Would it feel different to ski in snow made with heavy water?”), it may be pricey but at least it won’t melt at +3 °C. In the meantime, this BBC report tells us that
Some councils in England say they are running out of road salt.
I need to do some research on road salt next.

Tuesday, February 03, 2009

Metal snow, anyone?

It was snowing heavily yesterday, at least by English standards. Can I find something related to both snow and metal on the web? The googling for “metal snow” does not bring that many interesting results, mostly it’s all about metal tools related to snowy weather. All moderately interesting finds are rather old news. There are couple of papers from 1978 entitled “Plasma cooling by metal snow” (this and this). There, “metal snow” refers to the metal dust “liberated” from the walls of Tokamaks as a result of surface cracking. Another old news item concerns the heavy metal snow discovered on Venusian mountain tops back in 1995. According to Laura Schaefer and Bruce Fegley from Washington University in St. Louis (2004), this “snow” consists of compounds such as galena (lead sulfide), bismuthite (bismuth sulfide), and/or lead-bismuth sulfosalts. The most recent find (2008) is a photo promisingly titled Metal Snow Girl which does not show any snow either, but a snowman-like figure made of metal balls.