Thursday, June 16, 2016

The end of unun*iums is announced

So that’s it, then. Four new elements, ununtrium, ununpentium, ununseptium and ununoctium [1] are to be officially named nihonium (symbol Nh), moscovium (Mc), tennessine (Ts), and oganesson (Og), respectively [2]. So that for a while the periodic table will be free of ungainly “unun” names. The provisional recommendation is out [3], comments by 8 November 2016. I am going to send mine to IUPAC, but I’d like to share them with my readers first.

Let’s start with naming conventions [4]:

In keeping with tradition, elements are named after:
  1. a mythological concept or character (including an astronomical object),
  2. a mineral, or similar substance,
  3. a place, or geographical region,
  4. a property of the element, or
  5. a scientist.
Unfortunately, it is not required for the names to be aesthetically pleasing.

In absence of minerals (all four elements are artificial) and properties (apart from half-lives, which aren’t that long) to speak about, we are left with three options. Don’t you agree that the option (a) is the most interesting one? However, the discoverers have chosen easy and boring options (c) and (e). Well, I like nihonium, named after Nihon (ニホン), one of the Japanese names for Japan (literally, “the sun’s origin”). I can’t say the same about the rest.

Take moscovium:

It is proposed that the name moscovium and symbol Mc are given to element 115. Moscovium is recommended in recognition of the Moscow region and honoring the ancient Russian land that is home to the Joint Institute for Nuclear Research, where the discovery experiments were conducted using the Dubna Gas-Filled Recoil Separator in combination with the heavy-ion accelerator capabilities of the Flerov Laboratory of Nuclear Reactions, JINR.
I see. Not content with dubnium (element 105), Russian scientists™ insist on honouring Dubna one more time. But Dubna is not Moscow. The town is at least as old as the Russian capital and is situated on the very edge of Moscow Oblast, or Podmoskovye (Подмосковье). Shouldn’t dubnium 2.0 be called podmoskovium then? And why mention Moscow at all? After all, there are four elements named after Ytterby. The variations like dubinium, dubonium, or poddubnium spring to mind. Needless to say, “Mc” will have to go.

Personally, I would prefer the element 115 to be named lemmium in honour of the late Motörhead frontman Lemmy Kilmister. Alas, IUPAC’s set of absurd rules (see above) restricts people after whom the new elements could be named to “scientists”. I’ll come to that in a minute.

Now let’s look at tennessine. The ending -ine, by analogy with English names of other halogens, appears to be natural. However it simply shows that the authors of this proposal (from Tennessee region, I guess) did not think about languages other than English, although they should have, for “the names for new chemical elements in English should allow proper translationcinto other major languages” [3]. For instance, in Latin the halogen names are fluorum, clorum, bromum, iodum and astatum, in Spanish they are flúor, cloro, bromo, yodo and astato, while in German they are simply Fluor, Chlor, Brom, Iod und Astat. So in these languages the element 117 must be named tennessum, teneso and Tenness, respectively.

As for the symbol, I was about to complain that Ts is is a bad choice for an element symbol as Ts is widely used for tosyl group, and why not to use Tn given that TN is also an abbreviation for Tennessee. There was a similar story with copernicium a few years ago (originally proposed symbol Cp was later changed to Cn). It’s not that the authors of the recommendation aren’t aware of potential confusion:

NB: We are aware of the fact that Ts is often used as abbreviation for the tosyl chemical group. However, this was not considered to be a valid objection, given the fact that we also use the symbols Ac and Pr for chemical elements, while chemists also use these as abbreviations for the acyl and the propyl groups. Very common items like AcOH and PrOH are usually not taken for the hydroxides of actinium and praseodymium and a possible confusion with the tosyl group seem extremely low. On the other hand, the abbreviation Tn, that might have been a natural suggestion, is impossible given the earlier (1923) CIAAW-IUPAC acceptance of that symbol for thoron (220Rn), and its regular usage since then, see e.g. Journal of Environmental Radioactivity.
Still, I don’t find this convincing. If we ever get enough of ununseptium, we’ll find that its chemistry is nothing like that of actinium or praseodymium. Think of tosyl chloride, abbreviated TsCl. Now think of its tennessine analogue, abbreviated TsTs. That’s just silly. It’s a shame we can’t use “Tn” as TN is an abbreviation for the state of Tennessee. What about Tq then, after Tanasqui, the first recorded version of this toponym?

Finally, oganesson. Does it have to end with -on? Yes, most noble gases do (and, in contrast to meaningless -ine, the ending -on is present in other languages). Except helium, that is. Helium was named after Helios, the Greek god of the Sun, and is the only noble gas following the naming principle (a). Several “on” names are of Greek origin, namely νέον “new”, ἀργόν “inactive”, κρυπτόν “hidden” and ξένον “foreign”, whereas radon is a contraction of “radium emanation”. But oganesson... Please! It’s two syllables too many and feels out of place.

And another thing. I don’t know about you, but naming anything after a living person makes me uneasy. Seeing his surname mutilated this way should make Yuri Oganessian uneasy too. Come on, did we ran out of deserving dead scientists whose names, incidentally, can be used for the heaviest known element? For example, we can honour John Dalton, an English polymath best known for development of atomic theory; among other things, he invented his own symbols for chemical elements [5]. Or J. J. Thomson, discoverer of the electron. Or Francis W. Aston, discoverer of many naturally occurring isotopes. Or Arthur Compton, known for Compton scattering. Or C. T. R. Wilson, inventor of the cloud chamber. Or Fritz London, after whom the London dispersion forces are named. Or Ernest Walton, the first person to artificially split the atom.

To summarise: political considerations, inflated egos, and lack of imagination all may be responsible for some of the dismal proposals above. It does not mean we have to swallow them without fight. If you have better suggestions — and I’m sure you do — I urge you to write to IUPAC before 8 November.

  1. IUPAC announces the verification of the discoveries of four new chemical elements: The 7th period of the periodic table of elements is complete. IUPAC Press Release, 30 December 2015.
  2. IUPAC is naming the four new elements nihonium, moscovium, tennessine, and oganesson. IUPAC Press Release, 8 June 2016.
  3. Öhrström, L. and Reedijk, J. (2016) Names and symbols of the elements with atomic numbers 113, 115, 117 and 118. IUPAC Provisional Recommendation.
  4. Koppenol, W.H., Corish, J., García-Martínez, J., Meija, J. and Reedijk, J. (2016) How to name new chemical elements (IUPAC Recommendations 2016). Pure and Applied Chemistry 88, 401—405.
  5. Dalton, J. (1808) A New System of Chemical Philosophy, vol. I.

Sunday, April 03, 2016

Octahaem sulphite reductase MccA

The epsilonproteobacterium Wolinella succinogenes is able to grow by sulphite respiration with formate as electron donor [1], thanks to the octahaem cytochrome c MccA that catalyses the six-electron reduction of sulphite to sulphide:

HSO3 + 6 H+ + 6 e → HS + 3 H2O

The crystal structure of MccA has been determined at 2.2 Å resolution [2, 3]. The enzyme exists as a homotrimer showing a novel fold and haem arrangement. The heterobimetallic active centre contains a Cu(I) ion and a haem c with a Fe—Cu distance of 4.4 Å [4].

a, W. succinogenes MccA binds its substrate sulfite in the dehydrated form, SO2, at the distal axial position of haem 2. At 3.2 Å distance from the sulphur atom, a Cu(I) ion is nearly linearly coordinated by residues C399 and C495.

b, In respiratory haem–copper oxidases, CuB is a redox-active species liganded by three histidine residues and juxtaposed to a haem a3 moiety. The arrangement, with a Fe–Cu distance of 4.9 Å, is optimized to bind O2 and peroxide in a bridging fashion (PDB:3ABM).

  1. Kern, M., Klotz, M.G. and Simon, J. (2011) The Wolinella succinogenes mcc gene cluster encodes an unconventional respiratory sulphite reduction system. Molecular Microbiology 82, 1515—1530.
  2. PDB:4RKM
  3. PDB:4RKN
  4. Hermann, B., Kern, M., La Pietra, L., Simon, J., Einsle, O. (2015) The octahaem MccA is a haem c-copper sulfite reductase. Nature 520, 706—709.

Saturday, February 27, 2016

First eukaryotic photosystem II solved at 2.76 Å

The water-splitting reaction of photosynthesis is catalysed by photosystem II (PSII), a large protein complex located in thylakoid membranes of organisms ranging from cyanobacteria to higher plants [1]. During the last 15 years, a number of crystal structures of PSII from cyanobacteria have been solved. However, no structures of PSII from eukaryots have been reported until now, partly due to the instability of eukaryotic PSII upon isolation. Ago et al. [2] solved the structure of PSII from a red alga Cyanidium caldarium at 2.76 Å resolution [3]. This PSII contains four extrinsic proteins, including the three subunits found in cyanobacterial PSII and the fourth subunit PsbQ' homologous to the PsbQ protein of green algae and higher plants. Furthermore, two novel trans-membrane helices were found in the algal PSII which are not present in cyanobacterial PSII.

  1. Shen, J.-R. (2015) The structure of photosystem II and the mechanism of water oxidation in photosynthesis. Annual Review of Plant Biology 66, 23—48.
  2. Ago, H., Adachi, H., Umena, Y., Tashiro, T., Kawakami, K., Kamiya, N., Tian, L., Han, G., Kuang, T., Liu, Z., Wang, F., Zou, H., Enami, I., Miyano, M. and Shen, J.-R. (2016) Novel features of eukaryotic photosystem II revealed by its crystal structure analysis from a red alga. J. Biol. Chem., in press.
  3. PDB:4YUU

Saturday, January 30, 2016

Crystal structure of the DNAzyme 9DB1

The first ever crystal structure of a deoxyribozyme has been solved at 2.8 Å resolution [1—3]. The work by researchers from Max Planck Institute for Biophysical Chemistry (Göttingen, Germany) also sheds light on a difference in catalytic mechanism of ribozymes and deoxyribozymes [4]:

Ribozymes use RNA’s 2´-hydroxyl groups, which are absent in DNA, for structural interactions or directly for catalysis. The new structure shows why the lack of these groups doesn’t diminish the catalytic activity of DNAzymes. The missing hydroxyls make DNA’s sugar-phosphate backbone more flexible, allowing acrobatic conformations that compensate for the absent hydroxyls in DNAzymes.

  1. Ponce-Salvatierra, A., Wawrzyniak-Turek, K., Steuerwald, U., Höbartner, C. and Pena, V. (2016) Crystal structure of a DNA catalyst. Nature 529, 231—234.
  2. PDB:5CKK
  3. PDB:5CKI
  4. Borman, S. (2016) After two decades of trying, scientists report first crystal structure of a DNAzyme. Chemical & Engineering News 94, issue 2, p. 3.

Friday, December 25, 2015

Human Apaf-1 apoptosome at 3.8 Å

The apoptotic protease-activating factor 1 (Apaf-1) exists in normal cells as an autoinhibited monomer. Upon binding to  cytochrome c and dATP, Apaf-1 forms a heptameric complex known as the apoptosome. Zhou et al. report an atomic structure of an intact human Apaf-1 apoptosome at 3.8 Å resolution determined by single-particle, cryo-electron microscopy [1, 2].

  1. Zhou, M., Li, Y., Hu, Q., Bai, X.-c., Huang, W., Yan, C., Scheres, S.H.W. and Shi, Y. (2015) Atomic structure of the apoptosome: mechanism of cytochrome c- and dATP-mediated activation of Apaf-1. Genes & Development 29, 2349—2361.
  2. PDB:3JBT

Thursday, November 19, 2015

A magnetic protein biocompass?

A team of scientists from Peking University report a putative magnetic receptor (MagR) protein in Drosophila, CG8198 [1]. MagR binds an iron—sulphur cluster and interacts with photoreceptor cryptochrome (Cry) proteins to form a multimeric magnetosensing rod-like complex. Assemblies of these rods were observed orienting themselves in a weak magnetic field. Qin et al. speculate that these structures may function like compasses in living organisms, although the mechanism of magnetoreception in vivo remains a mystery [2].

A complete Cry/MagR magnetosensor protein complex structure model with 10 Crys helically binding to the rod-like MagR polymer consisting of 20 MagRs.
  1. Qin, S., Yin, H., Yang, C., Dou, Y., Liu, Z., Zhang, P., Yu, H., Huang, Y., Feng, J., Hao, J., Hao, J., Deng, L., Yan, X., Dong, X., Zhao, Z., Jiang, T., Wang, H.-W., Luo, S.-J. and Xie, C. (2015) A magnetic protein biocompass. Nature Materials, in print.
  2. Cyranoski, D. (2015) Long-sought biological compass discovered: Protein complex offers explanation for how animals sense Earth’s magnetic pull. Nature 527, 283–284.

Sunday, September 27, 2015

Nitrite binding modes in CuNIR

Fukuda and Inoue [1] have determined the crystal structure of the C135A mutant of thermostable copper nitrite reductase (CuNIR) from Geobacillus thermodenitrificans in complex with nitrite to 1.55 Å resolution. Interestingly, this high-temperature (320 K) structure [2] displays a near-bidentate binding mode of nitrite distinct from a monodentate mode in a cryogenic structure [3]:

To our knowledge, this is the first case in which the difference in substrate binding modes between cryogenic and high-temperature structures has been visualized by crystallography.
The copper site geometries are given in Table 1.

Table 1 (adapted from [4])

Cu—Ligand Distances (Å) 3X1N (320 K) 3WKP (100 K)
I. Type 1 Cu—residue distances
T1Cu—H95Nδ1 2.08 2.14
T1Cu—H143Nδ1 2.01 1.96
T1Cu—M148Sδ 2.13 2.07
II. Type 2 Cu—residue distances
T2Cu—H100Nε2 2.07 1.96
T2Cu—H134Nε2 2.00 1.95
T2Cu—H294Nε2 1.98 2.01
T2Cu—water 2.02 n/a
III. Type 2 Cu—nitrite distances
T2Cu—Oproximal 2.13 1.97
T2Cu—N 2.21 2.85
T2Cu—Odistal 2.52 3.41
  1. Fukuda, Y. and Inoue, T. (2015) High-temperature and high-resolution crystallography of thermostable copper nitrite reductase. Chemical Communications 51, 6532—6535.
  2. PDB:3X1N
  3. PDB:3WKP
  4. Fukuda, Y. and Inoue, T. (2015) High-temperature and high-resolution crystallography of thermostable copper nitrite reductase. Electronic Supplementary Material.