IUPAC periodic table?

The cover of the latest issue of Chemistry International features a fragment of Homenatge als elements (Hommage to the Elements) by the Catalan artist Eugènia Balcells. The display in the atrium of the Physics and Chemistry Library at the University of Barcelona takes the shape of the periodic table where each chemical element is represented by its emission spectrum [1]. According to the artist’s website, it “was born as a counterpoint” to the video installation Freqüències (Frequencies).

The Periodic Table Project at the University of Waterloo, Canada is another work of art,

designed by chemistry students from all Canadian provinces and territories, 20 U.S. states, and 14 countries. It can be viewed online and is available as a printed poster.

Also, as a free app for Apple or Android.

Both the Periodic Table Project and Hommage to the Elements use the medium-long form periodic table. The “IUPAC Periodic Table of the Elements” as published at the back of Chemistry International (in this issue, for the first time it includes flerovium and livermorium) has the same shape. Why the quotes? Because, as a matter of fact, there is no such thing as IUPAC-approved periodic table. Jeffery Leigh wrote three years ago that “there is unlikely to be a definitive IUPAC-recommended form of the periodic table” [2]. In my humble opinion, this is unfortunate that IUPAC refuses to take a position on this matter. Eric Scerri takes a view that “IUPAC should in fact take a stance on the membership of particular groups even if this has not been the practice up to this point” [3]. To illustrate this point, he goes to address the Group 3 question. He argues that the most logical composition of this group is Sc, Y, Lu and Lr (rather than Sc, Y, La and Ac), as shown below.

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

H

He

Li

Be

B

C

N

O

F

Ne

Na

Mg

Al

Si

P

S

Cl

Ar

K

Ca

Sc

Ti

V

Cr

Mn

Fe

Co

Ni

Cu

Zn

Ga

Ge

As

Se

Br

Kr

Rb

Sr

Y

Zr

Nb

Mo

Tc

Ru

Rh

Pd

Ag

Cd

In

Sn

Sb

Te

I

Xe

Cs

Ba

La

Ce

Pr

Nd

Pm

Sm

Eu

Gd

Tb

Dy

Ho

Er

Tm

Yb

Lu

Hf

Ta

W

Re

Os

Ir

Pt

Au

Hg

Tl

Pb

Bi

Po

At

Rn

Fr

Ra

Ac

Th

Pa

U

Np

Pu

Am

Cm

Bk

Cf

Es

Fm

Md

No

Lr

Rf

Db

Sg

Bh

Hs

Mt

Ds

Rg

Cn

Nh

Fl

Mc

Lv

Ts

Og

1

2

3

4

5

6

7

8

9

10

11

12

13

14

15

16

17

18

19

20

21

22

23

24

25

26

27

28

29

30

31

32

In addition to arranging all the elements in a more correct sequence of increasing atomic numbers, the decision to move to a long-form or 32-column table forces the periodic table designer towards just one possible option regarding the question of which elements to place in group 3.

I entirely agree with that. And yet Scerri stops short of proposing that IUPAC should support the 32-column (or “long, long form”, as Leigh put it) periodic table; in fact he explicitly states that he is not suggesting a change of IUPAC policy, viz. that of doing nothing about it. Why? That would be one of the most important and immediately noticeable changes sponsored by IUPAC in decades.

The problem is, sorting out the Group 3 does not resolve the problem how to number the f-block columns. If we stick with 18 groups (blue numbering on the top of the table), that would be really unfair towards the lanthanoids and actinoids. Why don’t we simply number groups from 1 to 32 (red numbers on the bottom of the table)? Sc, Y, Lu and Lr will find themselves in Group 17. So what? It’s not that many people will miss the current Group 17 — nobody really calls these elements anything but “halogens”. And 32 is even more convenient number than 18. I think it’s about time IUPAC took the lead and said how exactly the periodic table should look like.

1. Alvarez, S. (2012) An artist’s hommage to the elements. Chemistry International 34, 5.
2. Leigh, J. (2009) Periodic tables and IUPAC. Chemistry International 31, 4—6.
3. Scerri, E. (2012) Mendeleev’s periodic table is finally completed and what to do about group 3? Chemistry International 34, 28—31.

P. aeruginosa bacterioferritin—ferredoxin complex

The X-ray crystal structure of Pseudomonas aeruginosa bacterioferritin (Pa-BfrB) in complex with bacterioferritin-associated ferredoxin (Pa-Bfd) has been solved at 2.0 Å resolution [1, 2].

As the first example of a ferritin-like molecule in complex with a cognate partner, the structure provides unprecedented insight into the complementary interface that enables the [2Fe-2S] cluster of Pa-Bfd to promote heme-mediated electron transfer through the BfrB protein dielectric (~18 Å), a process that is necessary to reduce the core ferric mineral and facilitate mobilization of Fe²⁺. The Pa-BfrB—Bfd complex also revealed the first structure of a Bfd, thus providing a first view to what appears to be a versatile metal binding domain ubiquitous to the large Fer2_BFD family of proteins and enzymes with diverse functions.

1. Yao, H., Wang, Y., Lovell, S., Kumar, R., Ruvinsky, A.M., Battaile, K.P., Vakser, I.A. and Rivera, M. (2012) The structure of the BfrB—Bfd complex reveals protein—protein interactions enabling iron release from bacterioferritin. J. Am. Chem. Soc. 134, 13470—13481.
2. PDB:4E6K

Crystal structure of HGbI

Hell’s Gate globin I from an obligate methanotroph Methylacidiphilum infernorum. Poetry.

1. Teh, A.-H., Saito, J.A., Baharuddin, A., Tuckerman, J.R., Newhouse, J.S., Kanbe, M., Newhouse, E.I., Rahim, R.A., Favier, F., Didierjean, C., Sousa, E.H.S., Stott, M.B., Dunfield, P.F., Gonzalez, G., Gilles-Gonzalez, M.A., Najimudin, N. and Alam, M. (2011) Hell’s Gate globin I: An acid and thermostable bacterial hemoglobin resembling mammalian neuroglobin. FEBS Lett. 585, 3250—3258.
2. Pechkova, E., Scudieri, D., Belmonte, L. and Nicolini, C. (2012) Oxygen-bound Hell’s gate globin I by classical versus LB nanotemplate method. J. Cell Biochem. 113, 2543—2548.
3. PDB:3S1I
4. PDB:3S1J
5. PDB:3UBC
6. PDB:3UBV

Polyoxomolybdate clusters of Mo/W-storage protein

Five years ago, Schemberg et al. reported the crystal structure of molybdenum/tungsten storage protein from Azotobacter vinelandii complexed with polyoxotungstates [1, 2].

Now Kowalewski et al. report the 1.6 Å X-ray structure of the same protein containing a variety of polyoxomolybdate clusters, from Mo₃ to Mo₈ [3].

Some N₂-fixing bacteria prolong the functionality of nitrogenase in molybdenum starvation by a special Mo storage protein (MoSto) that can store more than 100 Mo atoms. The presented 1.6 Å X-ray structure of MoSto from Azotobacter vinelandii reveals various discrete polyoxomolybdate clusters, three covalently and three noncovalently bound Mo₈, three Mo_5–7, and one Mo₃ clusters, and several low occupied, so far undefinable clusters, which are embedded in specific pockets inside a locked cage-shaped (αβ)₃ protein complex. <...> The formed polyoxomolybdate clusters of MoSto, not detectable in bulk solvent, are the result of an interplay between self- and protein-driven assembly processes that unite inorganic supramolecular and protein chemistry in a host–guest system.

1. Schemberg, J., Schneider, K., Demmer, U., Warkentin, E., Müller, A. and Ermler, U. (2007) Towards biological supramolecular chemistry: a variety of pocket-templated, individual metal oxide cluster nucleations in the cavity of a Mo/W-storage protein. Angewandte Chemie International Edition 46, 2408—2413.
2. PDB:2OGX
3. Kowalewski, B., Poppe, J., Demmer, U., Warkentin, E., Dierks, T., Ermler, U. and Schneider, K. (2012) Nature’s polyoxometalate chemistry: X-ray structure of the Mo storage protein loaded with discrete polynuclear Mo–O clusters. J. Am. Chem. Soc. 134, 9768—9774.

P450-flavodoxin fusion enzyme XplA

XplA is a P450-flavodoxin fusion enzyme that mediates the metabolism of the military explosive RDX (1,3,5-trinitro-1,3,5-triazinane) in Rhodococcus rhodochrous 11Y [1]. Bui et al. have conducted a detailed spectroscopic and crystallographic study of this unusual hemoflavoprotein [2, 3].

The XplA P450 has evolved as a reductase (rather than oxidase) of RDX and structural alterations to its heme- and FMN-binding domains have led to reduction potentials for low-spin heme iron Fe³⁺/Fe²⁺ and FMN_SQ/HQ couples being much more positive than those seen in typical P450s and flavodoxins, but consistent with non-oxidative P450 catalysis. These evolutionary steps have also led to a constricted P450 active site with high affinity for RDX (but also for the small heterocyclic inhibitor imidazole), and also to substantially diminished affinity for FMN in the flavodoxin domain.

1. Rylott, E.L., Jackson, R.G., Sabbadin, F., Seth-Smith, H.M.B., Edwards, J., Chong, C.S., Strand, S.E., Grogan, G. and Bruce, N.C. (2011) The explosive-degrading cytochrome P450 XplA: biochemistry, structural features and prospects for bioremediation. Biochim. Biophys. Acta 1814, 230—236.
2. Bui, S.H., McLean, K.J., Cheesman, M.R., Bradley, J.M., Rigby, S.E.J., Levy, C.W., Leys, D. and Munro, A.W. (2012) Unusual spectroscopic and ligand binding properties of the cytochrome P450-flavodoxin fusion enzyme XplA. J. Biol. Chem. 287, 19699—19714.
3. PDB:4EP6

Stachydrine demethylase

Crystal structures were determined for the Rieske-type monooxygenase, stachydrine demethylase, in the unliganded state (at 1.6 Å) and in the product complex (at 2.2 Å) [1—3].

1. Daughtry, K.D., Xiao, Y., Stoner-Ma, D., Cho, E., Orville, A.M., Liu, P. and Allen, K.N. (2012) Quaternary ammonium oxidative demethylation: X-ray crystallographic, resonance Raman, and UV-visible spectroscopic analysis of a Rieske-type demethylase. J. Am. Chem. Soc. 134, 2823—2834.
2. PDB:3VCA
3. PDB:3VCP

FAD/NADPH-domain of flavocytochrome P450 BM3

The crystal structure of the FAD/NADPH-binding domain of the Bacillus megaterium flavocytochrome P450 BM3 has been solved in both the absence and presence of the ligand NADP⁺ [1—3].

1. Joyce, M.G., Ekanem, I.S., Roitel, O., Dunford, A.J., Neeli, R., Girvan, H.M., Baker, G.J., Curtis, R.A., Munro, A.W. and Leys, D. (2012) The crystal structure of the FAD/NADPH-binding domain of flavocytochrome P450 BM3. FEBS J. 279, 1694—1706.
2. PDB:4DQK
3. PDB:4DQL

Carbon—carbon quadruple bond

Quadruple and higher order metal—metal bonds are known for transition metals, lanthanoids and actinoids. But for main group elements? Using four different computational methods, Shaik et al. [1] show that

C₂ and its isoelectronic molecules CN⁺, BN and CB⁻ (each having eight valence electrons) are bound by a quadruple bond. The bonding comprises not only one σ- and two π-bonds, but also one weak ‘inverted’ bond, which can be characterized by the interaction of electrons in two outwardly pointing sp hybrid orbitals.

According to Shaik, the existence of the fourth bond in C₂ suggests that it is not really diradical C₂^2• [2]:

If C₂ were a diradical it would immediately form higher clusters. I think the fact that you can isolate C₂ tells you it has a barrier, small as it may be, to prevent that.

1. Shaik, S., Danovich, D., Wu, W., Su, P., Rzepa, H.S. and Hiberty, P.C. Quadruple bonding in C₂ and analogous eight-valence electron species. Nature Chemistry 4, 195—200.
2. Extance, A. Calculations reveal carbon-carbon quadruple bond. Chemistry World, 29 January 2012.

Collaborative Computational Technologies for Biomedical Research

It’s been a while since I read a science/technology book from back to back. And was it worth it? Definitely.

The book is about collaboration and is a collaboration. Ironically, the best-written chapters almost invariably are those by single authors. Which confirms my own theory that writing (including scientific writing) is not exactly collaborative activity. The contributions by Robert Porter Lynch [1], Robin W. Spencer [2], Victor J. Hruby [3], Edward D. Zanders [4], Brian Pratt [5] and Keith T. Taylor [6] are especially worth noting — I wish the whole book was written at the level of these chapters. Then again, collaboration is always a compromise. The material presented here is diverse and heterogeneous — what did you expect?

I am sure there are people who do all sorts of stuff using their smartphones, including scientific database browsing and chemical structure drawing [7]. This latter activity does not strike me as especially productive or convenient. (Also, makes me glad that the use of mobile phones while driving is outlawed in most of Europe.) In my view, for the purposes of computer graphics bigger is better: if I had a choice, I’d go for HIPerWall (25,600 × 8000 pixels) or, better still, HIPerSpace (35,840 × 8000 pixels) display walls [8]. Then I could draw some really large (in many senses) molecules.

As much as I enjoy reading the real (hardcopy) book, it could be nice to see it online, preferably in open access. For instance, Chapter 25 [9] has 196 references, all of them are URLs, and some of them are rather long ones. I’d love to be able to click on them rather than type!

Will the wikis, virtual communities and cloud computing replace the behemoth pharma companies and NCBI? A man can dream. Ekins et al. write [10]:

As a result of the recent recession there is a lot of drug discovery and development talent available now due to company lay-offs. If the software or other tools to enable this workforce to be productive and collaborate were available and they participated in the existing scientific collaboration networks, then there may be potential for enormous breakthroughs.

I wish I could share the authors’ optimism. Yes there is potential, but it is highly unlikely that unemployed researchers are in the mood to collaborate. In case you wonder why: being unemployed is a full-time occupation, which leaves preciously little spare time. I rather inclined to agree with Robin W. Spencer [2]:

Especially for cutting-edge scientific challenges, the participants you need are probably well paid and not particularly enthused by another tee shirt, coffee cup, or $100 voucher.

More quotes from this book can be found here.

I use this opportunity to lament the decline of old-fashioned copy editing [11]. I get used to the lack of any such luxury in open access publications: if the paper is accepted, the publisher tends to keep all your typos intact. But when you buy a book from John Wiley & Sons for a hundred something bucks, you’d expect some editorial intervention. (To be honest, I did not buy it. I can’t afford buying books at such prices anyway.) The major and minor irritations include:

• Typos: “chpater” instead of “chapter” (p. 281) — I thought by now the text editing software should take care of these.
• Tautologies: ‘The institutes of the national Institutes of Health’ (p. 496); ‘... we need to consider standards specifically for chemistry and biology. In chemistry specifically...’ (p. 202).
• Impenetrable sentences, e.g. ‘Many aspects should be considered, such as a regulatory path for filing, potential market size, differentiability of the therapeutic and experience with and difficulty to carry out clinical trials in the disease of interest’ (p. 252) or ‘This will only be done by drawing from the mental resources of an extended scientific community in an innovative and complex, yet “daily practice”, manner that promises a profound impact on our ability to use existing data to generate new knowledge with the maximum conceivable serendipity’ (p. 454). You what?
• Overabundance of acronyms (have a look at p. 497 and you’ll see what I mean).
• Overabundance of buzz-words of yesteryear: crowdsourcing (see below), integration, leveraging, paradigm, stakeholder and so on. The worst offenders, however, are clear and clearly. Clearly, when these words is used too often, it is clear that something is not quite clear.

Now for “crowdsourcing”: I find the term not only ugly but offensive. As a scientist (once a scientist, always a scientist), I am open to collaboration. Also, as a scientist, I detest being part of a crowd. Period.

Don’t get me wrong: it is a good book. I wouldn’t hesitate to recommend it to any decent scientific library. But it could have been a great book.

1. Lynch, R.P. Collaborative innovation: essential foundation of scientific discovery. In: Ekins, S., Hupcey, M.A.Z. and Williams, A.J. (eds.) Collaborative Computational Technologies for Biomedical Research. John Wiley & Sons, Hoboken, 2011, pp. 19—37.
2. Spencer, R.W. Consistent patterns in large-scale collaboration. Ibid., pp. 99—111.
3. Hruby, V.J. Collaborations between chemists and biologists. Ibid., pp. 113—120.
4. Zanders, E.D. Scientific networking and collaborations. Ibid., pp. 149—160.
5. Pratt, B. Collaborative systems biology: open source, open data, and cloud computing. Ibid., pp. 209—220.
6. Taylor, K.T. Evolution of electronic laboratory notebooks. Ibid., pp. 303—320.
7. Williams, A.J., Arnold, R.J.G., Neylon, C., Spencer, R.W., Schürer, S. and Ekins, S. Current and future challenges for collaborative computational technologies for the life sciences. Ibid., pp. 491—517.
8. He, Z., Ponto, K. and Kuester, F. Collaborative visual analytics environment for imaging genetics. Ibid., pp. 467—490.
9. Bradley, J.-C., Lang, A.S.I.D., Koch, S. and Neylon, C. Collaboration using open notebook science in academia. Ibid., pp. 425—452.
10. Ekins, S., Williams, A.J. and Hupcey, M.A.Z. Standards for collaborative computational technologies for biomedical research. Ibid., pp. 201—208.
11. Clark, A. The lost art of editing. The Guardian, 11 February 2011.

Kilogram, pterin, selenium

I really enjoyed the latest issue of Chemistry International. Did you know that pterin is called “pterin” because it was first isolated from butterfly wings, and folic acid is “folic” because it was first found in leafy vegetables (from Latin folium)? I just learned that from Edward Taylor’s illuminating article on Alimta [1].

Next, two papers on kilogram in the “New SI”. Currently, kilogram is defined as a unit of mass equal to mass of the international prototype kilogram (IPK), which is a cylinder made of 90% platinum—10% iridium alloy kept at the International Bureau of Weights and Measures in France. The problem is, IPK is losing mass! But even if it did not, it is still not good that one of SI base units is linked to an artifact rather than to something more fundamental. The chemist in me prefers the definition of kilo based on carbon-12 mass [2] to the one based on Planck constant [3].

Finally, essay by Jan Trofast on discovery of selenium [4]. I didn’t know that Swedes discovered so many elements!

1. Taylor, E.C. (2011) From the wings of butterflies: The discovery and synthesis of Alimta. Chemistry International 33, 4—8.
2. Censullo, A.C., Hill, T.P. and Miller, J. (2011) Part I — From the current “kilogram problem” to a proposed definition. Chemistry International 33, 9—12.
3. Mills, I. (2011) Part II — Explicit-constant definitions for the kilogram and for the mole. Chemistry International 33, 12—15.
4. Trofast, J. (2011) Berzelius’ discovery of selenium. Chemistry International 33, 16—19.

Icosahedrite

In 1982, Dan Shechtman observed unusual diffraction pattern in aluminium—manganese alloy [1, 2]. Almost 30 years later, he was awarded The Nobel Prize in Chemistry 2011 “for the discovery of quasicrystals”.

Earlier this year, the first naturally occurring quasicrystal was described. Icosahedrite Al₆₃Cu₂₄Fe₁₃ is a new mineral found in southeastern Chukhotka, Russia. It is named “for the icosahedral symmetry of its internal atomic structure, as observed in its diffraction pattern” [3].

1. Shechtman, D., Blech, I., Gratias, D. and Cahn, J. (1984) Metallic phase with long-range orientational order and no translational symmetry. Physical Review Letters 53, 1951—1953.
2. Fernholm, A. (2011) Crystals of golden proportions. Nobelprize.org.
3. Bindi, L., Steinhardt, P.J., Yao, N. and Lu, P.J. (2011) Icosahedrite, Al₆₃Cu₂₄Fe₁₃, the first natural quasicrystal. American Mineralogist 96, 928—931.

Do we need the terminal e?

Chemical English, after all, is just a subset of English. As such, it suffers the same problem as English in general: the pronunciation of the words is far from obvious. What makes it worse for chemistry is absence of any authoritative pronunciation guide. (Since the last year’s post on this topic, the audio guide “Pronunciation of Chemical Terms”, originally hosted by Hong Kong Cyber Campus, has disappeared from the web.)

You’d think that the chemical terminology was developed after the Great Vowel Shift and therefore there must be less of gap between the spoken and written word. You’d be wrong. The gap is there, a-gaping.

For instance, the effect of silent terminal e on pronunciation of English words, including chemical terms, is simply unpredictable. Sometimes the terminal e makes no difference: both thiamine and thiamin are pronounced and mean the same. (Cf. “win” and “wine”.) In some other cases, it makes a lot of difference: chlorine (chemical element number 17) and chlorin (tetrapyrrole), or silicon (chemical element number 14) and silicone (a class of silicon-containing polymers).

Protein vs cysteine; cisplatin vs astatine; krypton vs ketone; phenol vs pyrrole — what is the point of terminal es? Wouldn’t we all be better off without them? That will spare us a few rules about elision of terminal vowels, for example.

Sometimes metal just plain rusts

Our stainless steel forks and knives, which in England were literally stainless, even spotless, for years, here on Fuerteventura developed rust stains in a matter of days. What’s the matter?

I found this lovely quote from Brion Toss’s book [1]:

Sometimes metal just plain rusts. Stainless steel rusts more slowly, but tropical climates will get to it in just a few years. Galvanized steel left untended can dissolve in a matter of months.

Well said, but what exactly is wrong with “tropical climates”? High humidity and high temperature, that’s what.

But wait. Humidity in Fuerteventura is not higher than in England, right? We hardly have any rain on this island. But the temperature is definitely higher. As is the case with most chemical reactions, the corrosion rate increases with increasing temperature. Add to this salt air. (Salt acts as a catalyst of rusting.) No wonder cars rust quickly here.

Ah well, we always can use the chopsticks.

1. Toss, B. (1998) The Complete Rigger’s Apprentice: Tools and Techniques for Modern and Traditional Rigging. International Marine/Ragged Mountain Press, Camden, Maine.

CYP7A1—cholest-4-en-3-one complex

The crystal structure of human CYP7A1 (cholesterol 7α-monooxygenase) in complex with cholest-4-en-3-one has been solved [1].

1. PDB:3SN5

Phe—Val crosslink in symerythrin

The crystal structure of diiron protein symerythrin from Cyanophora paradoxa reveals a novel C—C cross-link between valine and phenylalanine residues [1].

1. Cooley, R.B., Rhoads, T.W., Arp, D.J. and Karplus, P.A. (2011) A diiron protein autogenerates a valine-phenylalanine cross-link. Science 332, 929.

Open and closed P450 2B4

The crystal structures of rabbit P450 2B4 covalently bound to the mechanism-based inactivator 4-tert-butylphenylacetylene in closed (a) and open (b) conformations have been solved [1].

(a)

(b)

1. Gay, S.C., Zhang, H., Wilderman, P.R., Roberts, A.G., Liu, T., Li, S., Lin, H.-l., Zhang, Q., Woods, V.L., Jr., Stout, C.D., Hollenberg, P.F. and Halpert, J.R. (2011) Structural analysis of mammalian cytochrome P450 2B4 covalently bound to the mechanism-based inactivator tert-butylphenylacetylene: insight into partial enzymatic activity. Biochemistry 50, 4903—4911.

Importance of being obsessive-compulsive

Never underestimate the importance of naming. For instance, I would probably never read the excellent paper by Kuhn and Wahl-Jensen [1] if not for its title. (Seriously, read it. Although the note appears in Binomina, it is relevant to scientific nomenclature and terminology in general, not just biological taxonomy.) They write:

When terms get renamed just for the sake of renaming them then outrage at nomenclature experts is justified. But it is a two-way street. Nomenclature without discourse with the scientific community working in laboratories is useless — but science without nomenclature cannot be performed, either.

Conversely, Roderic Page argues that “quite a lot” of biology can be performed without “proper” taxonomic names [2], even though his

definition of “proper” name is a little loose: anything that had two words, second one starting with a lower case letter, was treated as a proper name.

Just imagine the fury of those who are “obsessive-compulsive about terminology” on reading that! Surely not any binomial name is “proper”? However, that is beyond the point. Linnaean names are just labels. They may be preferable to NCBI tax_id codes because of aesthetic considerations but ultimately they are dispensable. We only cling to them because we believe that these labels have, as Robert M. Pirsig put it, “an intrinsic sacredness” of their own [3]:

One finds that in the Judeo-Christian culture in which the Old Testament ‘Word’ had an intrinsic sacredness of its own, men are willing to sacrifice and live by and die for words.

But what about chemistry? On the one hand, chemistry appears to be in a better position because of superiority of chemical nomenclature over, well, any other known nomenclature. The name constructed according to the rules of systematic chemical nomenclature holds the key to the structure of the entity in question. It does not mean that there could or should be only one “proper” name for one structure. For example, “tetrafluoridolead” (additive nomenclature) and “tetrafluoroplumbane” (substitutive nomenclature) correspond to the same entity, PbF₄. You don’t have to know it, because you can figure it out. Compare this with the situation in biology: there is no way to deduce that, say, Prunus dulcis and Amygdalus communis are synonyms.

On the other hand, we chemists often fall into the same trap as anyone else: we tend to believe that “proper” naming of a compound (of known structure) automatically improves our knowledge of it. But why? The terms can change. The nomenclature rules are changing. For a structure of certain complexity, the application of the same rules by different chemists (or different naming software) may result in different systematic names. Some structures as yet cannot be named by any software. So what? It is highly unlikely that a name which takes more than 100 characters will be used in any discourse. I distinctly remember thinking about it a few years ago while reading the draft of IUPAC Recommendations for rotaxane nomenclature [4]. Why not to use the (equally unpronounceable but more useful) InChI string instead?

Still, I wouldn’t dismiss the aesthetics that easily. For me, concise, clear, elegant is good; long, ambiguous, ugly is bad. And coming back to the title of [1]: “being obsessive-compulsive about terminology and nomenclature” is neither a vice nor a virtue. It is a mental condition that some people (myself included) have, for better or for worse.

1. Kuhn, J.H. and Wahl-Jensen, V. (2010) Being obsessive-compulsive about terminology and nomenclature is not a vice, but a virtue. Bionomina 1: 11—14.
2. Page, R. (2011) Dark taxa: GenBank in a post-taxonomic world.
3. Pirsig, R.M. (1974) Zen and the Art of Motorcycle Maintenance.
4. Yerin, A., Wilks, E.S., Moss, G.P. and Harada, A. (2008) Nomenclature for rotaxanes and pseudorotaxanes (IUPAC Recommendations 2008). Pure Appl. Chem. 80, 2041—2068.

Amethyst

Last Summer, we bought this crystal-growing kit in Oxfam. It contains ingredients and instructions to grow several types of crystals. Those nicknamed “quartz” and “emerald” in fact are monoammonium phosphate, NH₄H₂PO₄, while “amethyst” and “fluorite” are grown from a solution of potassium aluminium sulphate, KAl(SO₄)₂. Our latest experiment was to grow an “amethyst” crystal cluster. Timur and I prepared the solution, poured it over two stones from our garden and left to grow for a week. Here’s the result.

Chlorite dismutase

Photosynthesis is not the only dioxygen-evolving biological process. For instance, chlorite dismutase (Cld; EC 1.13.11.49) catalyses the production of O₂ from chlorite (1):

ClO2− → Cl− + O2

(1)

The reaction (1) is not really disproportionation, and NC-IUBMB made a valid point that the term “chlorite dismutase” is “misleading”. Even so, the NC-IUBMB-approved, sorry, “accepted” name “chlorite O₂-lyase” for an oxidoreductase is equally absurd; I am going to ignore it.

Chlorite dismutase from Azospira oryzae exists as a homohexamer [1] while Cld from Dechloromonas aromatica [2] and enzyme from Candidatus Nitrospira defluvii [3] are homopentamers.

The active site contains a single haem group [Fe(ppIX)] coordinated by a proximal histidine residue. Goblirsch et al. [2] propose the mechanism where the reaction of chlorite within the distal pocket of Cld generates hypochlorite (ClO⁻) and a compound I intermediate [Fe(ppIX)O] (1a). Then ClO⁻ rebounds with compound I forming the chloride and dioxygen (1b):

ClO2− + [Fe(ppIX)] → ClO− + [Fe(ppIX)O]	(1a)
ClO− + [Fe(ppIX)O] → Cl− + O2 + [Fe(ppIX)]	(1b)

1. de Geus, D.C., Thomassen, E.A.J., Hagedoorn, P.-L., Pannu, N.S., van Duijn, E. and Abrahams, J.P. (2009) Crystal structure of chlorite dismutase, a detoxifying enzyme producing molecular oxygen. J. Mol. Biol. 387, 192—206.
2. Goblirsch, B.R., Streit, B.R., DuBois, J.L. and Wilmot, C.W. (2010) Structural features promoting dioxygen production by Dechloromonas aromatica chlorite dismutase. J. Biol. Inorg. Chem. 15, 879—888.
3. Kostan, J., Sjöblom, B., Maixner, F., Mlynek, G., Furtmüller, P.G., Obinger, C., Wagner, M., Daims, H. and Djinović-Carugo, K. (2010) Structural and functional characterisation of the chlorite dismutase from the nitrite-oxidizing bacterium “Candidatus Nitrospira defluvii”: Identification of a catalytically important amino acid residue. J. Struct. Biol. 172, 331—342.

Femtosecond X-ray nanocrystallography of PSI

It is a well known fact (to those who know it well) that in order to obtain a decent diffraction pattern one has to grow a decent-size crystal first. Well, that is about to change. The PDB entry enigmatically named “femtosecond X-ray protein nanocrystallography” [1] in fact contains the structure of the photosystem I (PSI) from Thermosynechococcus elongatus solved by this new method [2]. In this work, more that 3 million diffraction patterns were collected from really small PSI crystals (from ~200  nm to 2  μm in size) illuminated by the new femtosecond X-ray laser, the Linac Coherent Light Source in Stanford. According to the authors,

We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes.

1. PDB:3PCQ
2. Chapman, H.N., Fromme, P., Barty, A. et al. (2011) Femtosecond X-ray protein nanocrystallography. Nature 470, 73—77.

P450 from Actinoplanes teichomyceticus

The crystal structure of the P450 monooxygenase from Actinoplanes teichomyceticus (CYP165D3) involved in biosynthesis of antibiotic teicoplanin has been solved [1].

1. Li, Z., Rupasinghe, S., Schuler, M. and Nair, S.K. (2011) Crystal structure of a phenol-coupling P450 monooxygenase involved in teicoplanin biosynthesis. Proteins: Structure, Function, and Bioinformatics 79, 1728—1738.

P450 monooxygenase AurH from S. thioluteus

The first crystal structures of the unique P450 monooxygenase AurH from Streptomyces thioluteus have been solved [1].

1. Zocher, G., Richter, M.E.A., Mueller, U. and Hertweck, C. (2011) Structural fine-tuning of a multifunctional cytochrome P450 monooxygenase. J. Am. Chem. Soc. 133, 2292—2302.

Natural products

Do a Google search and you’ll find all sorts of stuff claimed to be “natural products” — amazingly, some of them even are “chemical-free”! Now seriously. To quote IUPAC’s 1999 recommendations [1],

The nomenclature of natural products has suffered from much confusion.

That does not surprise me. What is surprising, however, that neither these nor the previous recommendations [2] tell us what the “natural products” are. Ditto the Gold Book. It may define terpenoids as “natural products and related compounds formally derived from isoprene units” but the natural products go without explanation. (Nor is it clear what “related compounds” are.) The very same Gold Book says that natural graphite is “a mineral found in nature”. Therefore, “natural” means “found in nature”. Right? Right. Is natural graphite a natural product? I am not sure.

Let us look in Webster then:

A chemical substance produced by a living organism; — a term used commonly in reference to chemical substances found in nature that have distinctive pharmacological effects. Such a substance is considered a natural product even if it can be prepared by total synthesis.

Is that any better? Both dioxygen and nitric oxide are produced by living organisms and have rather distinctive pharmacological effects, yet most chemists would hesitate to call them natural products. In The Concise Oxford Dictionary, the first definition of “natural” is

existing in or caused by nature; not artificial.

Of course human beings are parts of nature, but maybe this negative definition, “not artificial”, is indeed most useful?

In ChEBI, natural product (no definition so far) is an organic molecular entity (so no O₂ or NO here) and includes the following classes:

• alkaloid
• carbohydrate
• cyclitol
• heterocyclic natural product
• lipid
• peptide
• phenylpropanoid
• polyphenol

On the first glance, nothing looks particularly disturbing here. But I see a bit of a problem with ontology. First, all is a children of natural product have to be natural products. What if we have, say, (artificially) fluorinated carbohydrates? Are they still carbohydrates? If no, then the True path rule is broken. If yes, then some “unnatural” compounds will be considered natural products. I don’t mind that — perhaps that will cover “related compounds” (whatever they are) nicely.

Second, CHEBI:33243 belongs to chemical entity ontology, which is (or at least it should be) purely structure-based. The origin does not enter here. There is no such thing as intrinsic “naturalness” in a natural product molecule: natural product remains a natural product even if (artificially) prepared by total synthesis.

Natural products often are equated with secondary metabolites. This does not seem right. In ChEBI, secondary metabolite (“A metabolite that is not directly involved in the normal growth, development or reproduction of an organism” — another negative definition?) belongs to role ontology. (The role ontology sounded such a good idea at the time... no, don’t get me started.) At best, one can say some natural products have role “secondary metabolite”. Yuck.

To summarise: “natural product” appears to be a rather useless top-level term. Let us look at the sources of natural products: plants, fungi, bacteria, animals. What if, instead of saying “fungal natural product”, we say “fungi-specific compound”? In this case, we discard primary metabolites, other simple compounds found just about everywhere in the universe and are left with exactly what we want: molecules isolated from and specific for fungi.

Or are we? Antibiotics, naturally synthesised by fungi, are not naturally found in humans. But when we take them, they are naturally metabolised in our liver and eventually excreted with urine. Are these metabolites the natural products? If yes, are they fungal or animal or neither?

1. Revised Section F: Natural products and related compounds (IUPAC Recommendations 1999). Pure Appl. Chem. 71, 587—643 (1999).
2. Nomenclature of Organic Chemistry. Section F: Natural Products and Related Compounds. Recommendations 1976. Eur. J. Biochem. 86, 1—8 (1978).

It’s elementary

According to IUPAC’s Principles of Chemical Nomenclature [1],

An element (or an elementary substance) is matter, the atoms of which are alike in having the same positive charge on the nucleus (or atomic number). In certain languages, a clear distinction is made between the terms ‘element’ and ‘elementary substance’. In English, it is not customary to make such nice distinctions, and the word ‘atom’ is sometimes also used interchangeably with element or elementary substance. Particular care should be exercised in the use and comprehension of these terms. An atom is the smallest unit quantity of an element that is capable of existence, whether alone or in chemical combination with other atoms of the same or other elements.

You can’t help noticing the circular nature of these definitions: An element is matter, the atoms of which have the same atomic number; while an atom is the smallest unit quantity of an element. And what are “atoms of the same or other elements” if not just “any atoms”?

Of course it is not helpful that ‘element’ is used for either ‘elementary substance’ or ‘atom’. The ChEBI solution was to get away from ‘element’. Instead, there are either atoms or elemental molecular entities. These belong to different branches of ontology, so they should not really be confused. Or at least, that was the idea.

In ChEBI, ‘elemental’ applies to any class of molecular entities which consist of only one type of atom, be they mono- or polyatomic. For instance, elemental oxygen can be mono-, di- or triatomic. On the other hand, the oxygen atom can be part of a non-elemental molecular entity.

If there is a scope for confusion, people will get confused. Here’s a question I heard on more than one occasion: what is the difference between monoatomic oxygen and oxygen atom? After all, any form of monoatomic oxygen, viz. oxide(•1−), oxide(2−), or neutral monooxygen, can also be referred to as an ‘oxygen atom’. Ditto any of the monooxygen groups: oxido (—O⁻), oxo (=O) and oxy (‒O‒). The thing is, they belong to different universes (which, properly, should be made disjoint):

• monoatomic oxygen is a monoatomic entity is a molecular entity
• monooxygen group is a group
• oxygen atom is a atom

A group does not exist on its own: it is always a part of polyatomic entity and consists of at least one atom plus at least one bond. Monoatomic entity consists of one (and only one) atom and does exist on its own. Since we need ‘atom’ to define both groups and molecular entities, it is a good idea to keep atoms in an independent, disjoint branch.

1. Leigh, G.J., Favre, H.A. and Metanomski, W.V. Principles of Chemical Nomenclature: A Guide to IUPAC Recommendations. Blackwell Science, 1998, p. 3.

Ontology and reality

One of these days, I keep promising myself, I am going to publish something incredibly clever about chemistry, ontology and/or chemical ontology. Then again, I need some incentive to do so, and there’s none in my view. In the meantime, I am happy that somebody else has bothered to write a paper dealing with so-called “realist” approach to ontology [1].

Personally, I never cared much about the “reality” as used in context of OBO Foundry Principles [2]:

Terms in an ontology should correspond to instances in reality.

Worse still is its “corollary”:

Ontologies consist of representations of types in reality — therefore, their preferred terms should consist entirely of singular nouns.

(Why? Does “reality” really consist of singular English nouns?)

Now Lord and Stevens confirm my gut feeling that “realism” (the authors take care to clarify that “realism” in [1] stands for “realism as practiced by BFO”) applied to ontology building often results in unnecessary complexity. Everybody who ever studied physics (or English) in school would agree that expression |dr/dt| is much better definition of speed than the one provided by PATO: “A physical quality inhering in a bearer by virtue of the bearer’s rate of change of position”. To quote [1],

It makes little sense to replicate the models of physics using English instead of a more precise mathematical notation.

Alas, this is exactly what BFO (and most of OBOs) are trying to do. By going “where science has gone before” without learning the language of the science, BFO & Co. keep reinventing the square wheel.

OK, what about chemistry? Chemistry has developed its own language which makes the plain-text definitions for molecular entities redundant. The 2-D diagram (connectivity) defines the molecule of interest better than a paragraph in English. In theory, the systematic name should provide the exactly same information (and thus to be usable as a definition). However, the systematic names for even relatively small molecules often are too complicated to be widely (or ever) used.

Take the systematic name (a) for beauvericin. You are extremely unlikely to either hear it (because it is more or less unpronounceable) or see it (it takes more than one line of text, which is annoying). More importantly, there is a certain limit of molecular complexity above which the systematic names (according the existing nomenclature rules, that is) simply cannot be generated. On the other hand, the diagram (b) is both beautiful and useful.

(a)	(3S,6R,9S,12R,15S,18R)-3,9,15-tribenzyl-4,10,16-trimethyl-6,12,18-tri(propan-2-yl)-1,7,13-trioxa-4,10,16-triazacyclooctadecane-2,5,8,11,14,17-hexone
(b)

Not only are the 2-D diagrams self-defining, they provide all the information needed to build the consistent ontology for molecular entities. With a few simple rules, the ontology will build itself from scratch, I promise. But this is a topic for another post.

1. Lord, P. and Stevens, R. (2010) Adding a little reality to building ontologies for biology. PLoS ONE 5, e12258.
2. OBO Foundry Principles.

Terminology vs nomenclature

First published 8 September 2010 @ just some words

According to The Concise Oxford Dictionary,

nomenclature n. 1 a person’s or community’s system of names for things. 2 the terminology of a science etc. 3 systematic naming. 4 a catalogue or register.

terminology n. (pl. -ies) 1 the system of terms used in a particular subject. 2 the science of the proper use of terms.

I must say that these definitions do not add much clarity. Do you see any difference between “system of names for things” and “system of terms”? Moreover, the nomenclature (2) appears to be equated with the terminology. As for terminology (2), it is akin to terminology as defined by Wikipedia: “the study of terms and their use”, although I have my doubts whether there is such thing as “the science of the proper use of terms”. As was mentioned before, “logy” does not always mean “a subject of study or interest”. And what is “proper”?

On the other hand, Merriam-Webster defines terminology as

1 the technical or special terms used in a business, art, science, or special subject
2 nomenclature as a field of study

No, this does not help at all. Let us agree on the following: terminology is not nomenclature, and nomenclature is not terminology. I suggest these working definitions:

terminology: a set of terms used in a particular field.
nomenclature: a system of generating new terms for a particular field.

Completely different things. Terminology is a subset of vocabulary and, therefore, is part of the language. Nomenclature is a set of external rules. A good nomenclature system has few rules all of which should be understood and applied, preferably with reproducible results, by more than one person.

That is not to say that terminology does not depend on nomenclature or vice versa. Terms can be formed by systematic application of nomenclature rules — that’s what the nomenclature is devised for. But they also can arise by different mechanisms, just like any new words do. Often, terms are recruited from the existing lexicon and conferred new meanings. For instance, the word “residue” acquired specific meanings in fields of math, chemistry or law.

The Russian word for nomenclature, номенклатура, has an additional meaning: the bureaucratic class of Soviet Union and its descendants (as in “post-Soviet nomenklatura”).

Spoken chemistry

As I was going, for the n^th time, through the draft of the “new Blue Book”, it did strike me how much attention is paid to the appearance of a printed word. It is discussed in length what type of dash or bracket to use, which part of term has to be italicised and so on, whereas we often do not even know how to pronounce it. Which is a shame really, because I think IUPAC should take care of pronunciation (and comprehension of a spoken word) when coming with nomenclature recommendations. These are meant to improve the quality of chemical language, right? But the language where words cannot be pronounced is dead. (Think ancient Egyptian.)

Imagine we are given a task of recording an audio book on chemical nomenclature. Suddenly the names that look neat on paper become next to useless. Why? We do not pronounce parentheses (brackets, braces). We can’t pronounce sub- or superscripts. Ditto dashes, full stops and colons, which all can be parts of systematical names. Not to mention white space.

No, in olden days the pronunciation of your chemicals was taken seriously. Back in 1949, Dr. W. Bryce Orme wrote in a letter to British Medical Journal [1]:

Doctors and chemists are aware that difficulties occur in reaching consistency in the pronunciation of certain chemical terms, such as benzene and benzine, but generally it is conceded that the former should be rendered as ben'zēn and the latter ben'zin. It was, however, a shock to hear several highly qualified and distinguished chemists at a well-known pharmaceutical laboratory all referring to the radical CH₃ as mēthyl. I had the temerity to correct them and pointed out that the term was derived from the Greek μεθυ = wine + ύλη = wood. . . . Neither Dorland’s Medical Dictionary nor our old school friend, Liddell and Scott’s Lexicon, refers to any latitude in the pronunciation of methyl.

Well I never. American Chemical Society had a Nomenclature, Spelling and Pronunciation Committee, which even came up in 1934 with a list of recommended pronunciation for 437 terms [2]. Apparently, one even could order the complete report by writing to the chairman of the committee:

A charge of five cents per reprint (postage acceptable) to cover costs is made.

Sounds like a bargain, but that was quite a while ago. So far I was unable to get hold of the report. However, I found the next best thing: a list of about 400 common chemical terms that originally appeared on an audio tape prepared by Dr. M.P. Sammes and the Hong Kong Association for Science and Mathematics Education in 1988 [3]. Now, at long last, I know how to say “2-ethanoyloxybenzenecarboxylic acid”.

1. Orme, W.B. (1949) Points from letters: Pronunciation of chemical terms. Br. Med. J. 2 (4638), 1236.
2. Crane, E.J. (1934) The pronunciation of chemical words. J. Chem. Educ. 11, 454.
3. Sammes, M.P. Pronunciation of Chemical Terms.

Don’t trust your eyes

Ultramarine differs from other inorganic pigments in that it does not contain any transition metals. It is the sulfur species that confer the colour: S₃^•− (blue ultramarine), S₂^•− (yellow ultramarine) or S₄ (red ultramarine). Green ultramarine contains both S₂^•− and S₃^•− [1].

You’d think that by now they should know what the structure of ultramarine is. But no. In the Inorganic Crystal Structure Database I’ve found only two structures called “ultramarine” (ICSD 27523 and 27524), both associated with a paper from 1936 [2]. The composition of ICSD 27523 is given as Na₈Al₆Si₆O₂₄S_2.5·(H₂O)_0.6. The structure (see figure below) is an aluminosilicate cage containing sodium cations and beautiful octahedral sulfur clusters. Wait a minute. S₇ clusters? Never heard about those before.

A more recent structure of deuterated lazurite, Na_7.5Al₆Si₆O₂₄S_4.5·(D₂O)_0.5 (ICSD 63022), also featuring S₇ octahedra, provided an explanation. The authors [3] wrote that

to accommodate the indications emerging from the difference maps, the octahedral model of sulfur occupancy was modified to reproduce a more even density inside cage by adding a further sulfur to the hollow octahedral shell, with sulfur occupancies rescaled accordingly to maintain S₃ overall.

I feel relieved if slightly disappointed.

1. Landman, A.A. (2003) Aspects of solid-state chemistry of fly ash and ultramarine pigments. Doctoral Thesis, University of Pretoria.
2. Podschus, E., Hofmann, U. & Leschewski, K. (1936) Röntgenographische Strukturuntersuchung von Ultramarinblau und seinen Reaktionsprodukten. Zeitschrift für anorganische und allgemeine Chemie 228, 305—333.
3. Tarling, S.E., Barnes, P. and Klinowski, J. (1988) The structure and Si,Al distribution of the ultramarines. Acta Crystallographica B44, 128—135.

Rhodothermus marinus HiPIP at 1.0 Å

Meike Stelter and colleagues have solved the crystal structure of the reduced form of a high-potential iron–sulfur protein (HiPIP) from the thermophilic eubacterium Rhodothermus marinus.

This is the first structure of a HiPIP isolated from a nonphotosynthetic bacterium involved in an aerobic respiratory chain. The structure shows a similar environment around the cluster as the other HiPIPs from phototrophic bacteria, but reveals several features distinct from those of the other HiPIPs of phototrophic bacteria, such as a different fold of the N-terminal region of the polypeptide due to a disulfide bridge and a ten-residue-long insertion.

Popular health supplements

David McCandless and Andy Perkins have created a generative data-visualisation of scientific evidence for popular health supplements. The more Google hits, the bigger the bubble. The greater the evidence for its effectiveness (according to PubChem abstracts and The Cochrane Collaboration), the higher a bubble. The evidence ranges from “none” to “strong” (through “slight”, “conflicting”, “promising” and “good”). This visualisation generates itself from this spreadsheet. As you can see, these supplements are quite a mixed bag, e.g.

• L-lysine
• (unspecified) arginine
• selenium (in which form?)
• fish oil
• probiotics

Interestingly, of all the metals used as “health supplements”, only calcium (effective only for the specific condition of colorectal cancer) is above “worth it” line.

Hydrogen

I say, Hydrogen is a bit unusual name for a boat. But here she is, the Thames sailing barge Hydrogen (1906) in Maldon, Essex.

She circumnavigated Great Britain for Bells Whisky and became charter barge based Maldon.

This page contains some historic photographs of Hydrogen.