Saturday, January 31, 2009

Boron boride

All known structures of elemental boron contain icosahedral B12 clusters. Recently, a new form of elemental boron called γ-B28 has been characterised. Its structure resembles that of a sodium chloride, with the B12 icosahedra and B2 pairs playing the roles of anions and cations, respectively.

The example of γ-B28 shows that significant ionicity can occur in elemental solids”, the authors wrote. “Because of the charge transfer between these two components, the new phase can be regarded as a boron boride (B2)δ+(B28)δ–.”

Thursday, January 29, 2009

Molecules That Changed the World

We’ve got this wonderful, profusely illustrated book bought for the office, called Molecules That Changed the World, by K. C. Nicolaou and T. Montagnon. I’d say some of the molecules mentioned there (like LSD) change not so much the world per se but our perception of the world. Still, I’d recommend every chemistry or chemistry-related department/lab to have this book.

Molecules That Changed the World

On p. 42, it quotes Sir Robert Robinson’s wise words on the value of basic research (from his Nobel Lecture):
The synthesis of brazilin would have no industrial value; its biological importance is problematical, but it is worth while to attempt it for the sufficient reason that we have no idea how to accomplish the task. There is a close analogy between organic chemistry in its relation to biochemistry and pure mathematics in its relation to physics. In both disciplines it is in the course of attack of the most difficult problems, without consideration of eventual applications, that new fundamental knowledge is most certainly garnered.

Saturday, January 24, 2009

The Royal Society of Chemistry News

By some amazing coincidence, the same day as I have resuscitated this blog, the Royal Society of Chemistry has published the first issue of Metallomics, “a new journal covering the research fields related to biometals”. Good news is that the first issue is free. Check the “enhanced HTML articles” (for instance, this one) which provide “chemical ontology terms” which are nothing else but ChEBI ontology terms, with links to ChEBI.

On a lighter, but still metal-related note, the article on RSC blog entitled Gold saved! lists a winner and four more solutions to “The Italian Job problem”. Cool.

Tuesday, January 20, 2009


“Cucurbituril” may sound as a name of a natural product derived from some plant of Cucurbita genus. Wrong. There is a connection, though. According to this review,
In 1981, the macrocyclic methylene-bridged glycoluril hexamer (CB[6]) was dubbed cucurbituril by Mock and co-workers because of its resemblance to the most prominent member of the cucurbitaceae family of plants — the pumpkin.
My best 2-D representation for cucurbit[5]uril (a) does not look particularly pumpkiney. It is more like a sea urchin skeleton. Granted, its 3-D model (b) may look a bit like cleaned pumpkin devoid of top and bottom, but it still looks like a sea urchin skeleton (c) to me.

cucurbit[5]uril in 2-D
(a) cucurbit[5]uril in 2-D
cucurbit[5]uril in 3-D
(b) cucurbit[5]uril in 3-D
sea urchin skeleton
(c) sea urchin skeleton

Cucurbiturils, pumpkin-like or not, can be as useful as hunny pot that Pooh the Bear presented Eeyore: you can put things in them. For example, the platinum-containing anticancer drug oxaliplatin (d) can be put inside of cucurbit[7]uril to form a stable 1:1 complex (e). Jeon et al. suggest that this can increase the stability of the drug as well as to reduce unwanted side effects of oxaliplatin.

(d) oxaliplatin

cucurbit[7]uril-oxaliplatin complex
(e) cucurbit[7]uril-oxaliplatin

Saturday, January 17, 2009


I came across these “circumnames” quite by chance: several compounds were mentioned in this paper and some other can be found in this astrochemistry database. Is there any elegant way to name them systematically?

(a) circumpyrene
(b) ovalene
(c) pyrene

For instance, ACD/Name gives the molecule (a) a systematic name dinaphtho[2,1,8,7-hijk:2',1',8',7'-stuv]ovalene, i.e. two naphtho groups are fused to the top and bottom of the ovalene (b) molecule, while the non-systematic name “circumpyrene” means that pyrene (c) core is completely encircled by fused benzene rings. Unfortunately, I was unable to generate ACD/Names for bigger molecules, such as circumcoronene (d) [i.e. coronene (e) encircled by fused benzene rings] and circumovalene (f). Apparently, ACD/Name cannot name compounds with more than 15 fused rings.

(d) circumcoronene
(e) coronene
(f) circumovalene

If the “core” structure is surrounded by two rows of fused benzene rings, the doubly “circum” names like circumcircumpyrene (g) and circumcircumcoronene (h) appear.

(g) circumcircumpyrene
(h) circumcircumcoronene

Thursday, January 15, 2009

Deep Purple

Continuing with hard rock theme: the December 2008 ChEBI Entity of the Month was a natural fluorochrome epicocconone, also known as “Deep Purple” and “Lightning Fast”. I think that will increase our traffic a bit as more and more Deep Purple fans discover wonders of ChEBI.


Wednesday, January 14, 2009

Definitions of heavy metal

Anyone who wants to use the term “heavy metal” for any biological or chemical purpose, should consult this publication in Pure and Applied Chemistry first. It has great collection of useless definitions of this term and a conclusion:
The term “heavy metal” has never been defined by any authoritative body such as IUPAC. Over the 60 years or so in which it has been used in chemistry, it has been given such a wide range of meanings by different authors that it is effectively meaningless.
According to yet another definition (not included in the above paper),
Heavy metal is the 666th element in the periodic table of mixology. Heavy metal is the heaviest of the metals, even heavier than rocks.

Tuesday, January 13, 2009

A medication from the past

Today somebody sent this to the ChEBI help desk:
I find a capsule in my medicine chest that I don’t recognize and wonder if it’s a medication of some kind from the past that I should still be taking. It’s yellow and brown, more or less, and labeled #26666. Thank you!
Keep taking it, maybe you’ll remember what it was.

Monday, January 12, 2009

The definition of metallome

Just in case anyone wonders what the title of this blog means, here’s definition of metallome from Wikipedia.