Tuesday, March 31, 2009

Growing microtubes from polyoxometallate crystals

The long-awaited first issue of Nature Chemistry is out. It has a number of excellent reviews and research articles; best of all, it is all in free access. The cover shows the artist's impression of "a growing microtube with a single polyoxometalate ion visible at the open end of the tube" [see Ritchie et al. (2009) Nature Chemistry 1, 47–52, and comment, Constable, E. (2009) Nature Chemistry 1, 22–23].

Friday, March 27, 2009

Stories of chronomes and metallomes

I do not understand what principle is used by PubMed to indicate which papers are “related” to the one you are looking at. Take, for instance, the recent paper “Epigenetics: an important challenge for ICP-MS in metallomics studies” — among “Related Articles”, the top one is entitled “Chronoastrobiology: proposal, nine conferences, heliogeomagnetics, transyears, near-weeks, near-decades, phylogenetic and ontogenetic memories”. (Is that a real title? Yes it is.) True, the abstract, though truncated, makes an intriguing reading, but has it anything to do with metallomics (or epigenetics, for that matter)? The only passage related to any ome or omics is the following:
Structures in time are called chronomes; their mapping in us and around us is called chronomics. The scientific study of chronomes is chronobiology.
Well, I don’t know, Webster’s definition of chronobiology makes more sense to me and it does not use the dodgy concept of “chronome”. As for today, 27 March 2009, PubMed citations for chronome (61) and chronomics (39) visibly outnumber metallome (8) and metallomics (20), while there is none that combines any of the first pair of terms with any of the second pair of terms.

Monday, March 23, 2009

The enigmatic Metallosia

True, there is a lot of stuff on the web, but this is not remotely enough. Take, for example, Metallosia. The very short Wikipedia entry says:
Metallosia is a genus of moth in the family Arctiidae.
According to this taxonomy page,
There are approximately 3 species in this genus: M. chrysotis · M. nidens · M. nitens
(I wonder what “approximately 3 species” could possibly mean. Could it be that M. nidens and M. nitens is actually one species plus one typo? Can one say that 2 is approximately 3?) I also can find Metallosia mentioned in the Natural History Museum catalogue but not much factual information either. On the other hand, it is not listed in the NCBI taxonomy database, which indicates that no sequence data from these moths are available (and which makes it non-existent for bioinformatics). Internet, I am disappointed. Where can I see Metallosia? How can I recognise it if I see it? And most importantly, does it have anything to do with metals?

Saturday, March 21, 2009

Rhea has hatched

I am pleased to announce that after years of hard work, the Rhea database finally went online. Rhea is a freely available, manually annotated database of chemical reactions created as a collaboration between the EBI and SIB. From the Rhea website:
    In classical Greek mythology, Rhea (Greek Ρέα; /ˈriːə/) was the daughter of Uranus and Gaia, and was known as the mother of gods. Her name is often linked to the Greek word ρείν ("flow") but has no relation to the word "reaction". Rhea is the name of a genus of flightless birds, also known as ñandú. Rhea is also the name of the second-largest moon of Saturn, which contains up to 75% water and may have a tenuous ring system. The image of Rhea (moon) is used in Rhea (database) logo.
Rhea image

Saturday, March 14, 2009

Drawing ferrocene

Ferrocene was discovered in 1951 and we still do not know the proper way to draw it. CrossFire example recommends to connect every carbon atom of the ring to the central metal atom. Which is fair enough and will be a valid query for CrossFire Gmelin database. Similarly, both ChEBI and NIST Webbook use decacoordinate iron in ferrocene structure (a). In this representation, all carbon—carbon bonds are single. But, according to IUPAC Recommendations, section GR-1.7.2,
    coordination bonds to contiguous atoms (most commonly representing a form of π-bonding) should be drawn to indicate most clearly that special bonding pattern. Depictions that imply a regular covalent bond — and especially, depictions that show a regular covalent bond to each member of a delocalized system — are not acceptable.
In other words, the preferred representation is the one with bicoordinate iron and delocalised bond system (b). The problem with that is there is no agreed (as far as chemoinformaticans are concerned) way to do that, even though solutions for different applications (e.g. for Marvin Sketch) do exist. In MolBase, the coordination number of iron in ferrocene is 6 (and I do remember Mark Winter confirming that this is true). On yet another hand, Beilstein and ChemIDplus databases represent ferrocene as a standalone Fe2+ and two standalone cyclopenta-2,4-dienide anions (c), thus avoiding the question of coordination number altogether. Naturally, the decacoordinate-iron query will not work in Beilstein. (For InChI implications, see this discussion.)

ferrocene with 10-coordinate iron
ferrocene with bi-coordinate iron
ferrocene as three standalone entities

Friday, March 13, 2009


"Metallostar" is a relatively recent term: the oldest publication mentioning metallostars that I was able to find is dated 2000. It defines them as "complexes in which a single branching site bears a number of metallated arms". Something that looks too beautiful to be of any practical use, in fact metallostars appear to be promising MRI contrast agents. The metallostar of today's post, coming from the recent paper in Dalton Transactions, contains a central ruthenium atom and six lanthanoid(III) atoms (Y, Gd or Eu).

Saturday, March 07, 2009


I was given this wonderful Teaball as a present from my colleagues. Except from the wooden handle (the wood is not specified), the rest is 18/10 stainless steel. In case you are not familiar with this nomenclature (as I was until the arrival of the Teaball), "18/10" stands for 18% chromium and 10% nickel. It is a far cry from the other kind of stainless steel teapots you can find in this country — no need to use paper napkin etc.


Friday, March 06, 2009

Novel haem-degrading protein

This paper presents a beautiful octameric structure of HbpS, “a novel protein of previously unknown function from Streptomyces reticuli” complexed with iron. The authors “propose that the iron atom originates from the haem group and report subsequent biochemical experiments that demonstrate that HbpS possesses haem-degrading activity in vitro”. In the diagram taken from PDB:3FPW, the iron atoms are represented as grey spheres and phosphate ions are purple/red tetrahedra.

Sunday, March 01, 2009

PubChem takes liberties with hydrogens

The submitted structure (a) is C3H5O5P, the PubChem shows C3H4O5P+ (b). How did that happen? Why the deposited molecule lost hydride (H)?

3-[hydroxy(oxido)phosphoranyl]pyruvic acid


In the case of structure C16H36MoN6O4P2 (c), presumably submitted by NIST, it has acquired two hydrons in PubChem to become [C16H38MoN6O4P2]2+ (d).

3-[hydroxy(oxido)phosphoranyl]pyruvic acid