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.

Aluminium ion clock

The scientists at the National Institute of Standards and Technology (NIST) created a new optical clock of unprecedented precision.

The clock, which is based on a single aluminium ion, could remain accurate to within one second over 3.7 billion years. The previous record was held by a clock with one mercury ion, which was good to one second in 1.7 billion years.

My, these are some mind-boggling figures.

I thought that one ²⁷Al⁺ ion should not take much space. But then, they needed another “logic ion”, ²⁵Mg⁺. And a vacuum chamber. And two lasers. (Not three lasers, as in earlier model which used Al⁺/Be⁺ pair, so I presume the new clock is more compact.) I couldn’t find in the preprint what are the dimensions of the whole contraption. However, the NIST press release features the photo of one of the authors, Chin-wen Chou, together with the famous clock. The caption says that

The ion is trapped inside the metal cylinder (center right).

Not exactly wristwatch size but easily fits in Big Ben.

Selenite

1. In chemistry, selenite, [SeO₃]²⁻, is a diconjugate base of selenous acid, H₂SeO₃.
2. In mineralogy, selenite is a variety of gypsum, CaSO₄·2H₂O.
3. In science fiction, e.g. in The First Men in the Moon by H. G. Wells, the native inhabitants of the Moon are referred to as “Selenites”.

All three words are derived from Σελήνη, Greek for the Moon. Ironically, only fictitious Selenites have a “real” lunar connection.

(1)

(2)

Selenite (1) — not to be confused with selenate or selenide — is named similarly to other oxoanions of “ous” acids, such as sulfite or nitrite. The systematic name recommended by the Red Book is trioxidoselenate(2−). Now, Berzelius gave the element selenium its name by analogy with tellurium, which, in its turn, was named after Tellus, Latin for Earth. (Do you follow the logic?) The Mineral Information Institute gives an alternative explanation:

This is a reference to the silvery-gray color of metallic, non-crystalline selenium.

A similar line of thinking is responsible for naming of selenite (2):

From the Greek σελήυη, for “moon”, in allusion to the moon-like white reflections of the mineral or to the quality of the light transmitted by semi-pellucid gypsum slabs of cleavages used as windows.

Fine, but not as touching as this childhood belief:

When we were studying chemistry and the teacher talked about selenium, I thought that selenium was named after a Mexican pop star Selena who died during my childhood.

Speaking of Mexico: the world’s largest natural crystals, some as long as 11 meters, consist of selenite (2) and are found in Cueva de los Cristales in Chihuahua, Mexico.

The rise and fall of the Zinc World

I like the way the journals such as Biology Direct now publish reviewers’ comments and authors’ responses together with a final version of the paper. The fact that reviewers’ names are made public ensure that reviewers are properly acknowledged as well as share some responsibility for releasing another pointless paper into the wild. The discussion is often more interesting than a paper. Take the couple of recent highly speculative articles on Zinc world and origin of life [1, 2]. Even though I myself would not recommend any of these manuscripts for publication (luckily nobody asked me), I am glad that these were eventually published, because I really enjoyed reading the reviews — and, occasionally, the authors’ responses.

Reviewer 4: Last but not least I find the last sentence of the paper rather revealing: what could the aesthetics of minerals to do with a scientific argument on the origin of life?

Author’s response: Aesthetic criteria are of great importance in scientific research <...> For example, my initial opposition to the idea of abiogenesis at the floor of the Hadean ocean, when I first heard about it, was purely aesthetic. I simply did not like the idea of the origin of life being in complete darkness.

Similarly, it could have been stated “I simply liked the idea of using a single type of metal cation to fulfill all life’s metal needs”. The authors acknowledge the need for transition metal ions for origin of life but argue that the zinc is preferred to other transition metals because it is not redox-active. (According to modern view, zinc is not a transition element at all — why to bring transition metals in the first place?) For example, both papers contain the statement that “iron, unlike zinc, is redox-active”. Wait a minute. Is it bad? Since zinc is not redox-active, it cannot be used as a redox cofactor, therefore there won’t be any oxidoreductases utilising zinc. But fear not; apparently, the authors think that NAD(P)H, FAD and FMN evolved before primitive life forms learned how to use Fe²⁺ ions safely.

Incidentally, the only danger of redox-active iron mentioned in these papers seems to be the “harmful hydroxyl radicals”. I would not worry much about them though because I don’t think they were the main hazard in largely anoxygenic environment. In general, conditions on Earth at the time were rather harsh. You would’t go outside without an oxygen mask and a very thick (a few inches?) layer of sunscreen. Now add, on top of that, ZnS-catalysed photosynthetic production of formaldehyde [2, equation 1]... yep, sounds a plausible enough way to kick off that life thing.

1. Mulkidjanian, A.Y. (2009) On the origin of life in the Zinc world: 1. Photosynthesizing, porous edifices built of hydrothermally precipitated zinc sulfide as cradles of life on Earth. Biology Direct 4, 26.
2. Mulkidjanian, A.Y. and Galperin, M.Y. (2009) On the origin of life in the Zinc world. 2. Validation of the hypothesis on the photosynthesizing zinc sulfide edifices as cradles of life on Earth. Biology Direct 4, 27.

BioMetals 2010

Online registration for 7^th International Biometals Symposium (BioMetals 2010) is now open. The meeting will take place in Tucson, Arizona, USA, July 25—30, 2010.

Sessions are planned on Arsenic: Toxicity and Transformation; Siderophores and Iron Transport; Interplay of Metals; Metals and Gene Regulation; Metals in Disease and Metal Transport. See the current list of invited speakers.

The conference is limited to 200 participants, so early registration is recommended.

Metals in ancient Egypt

The al of “alchemy” is an Arabic article, but what about the rest of the word? Wikipedia mentions theories favouring Egyptian, Greek or Persian origin of the root. Whatever the etymology, it looks like ancient Egyptians knew quite a lot of chemistry.

This table of Egyptian symbols for the metals (don’t think any of them is in Unicode) misses two or three metals known to ancient Egyptians. According to Hamed A. Ead,

tin was used in the manufacture of bronze, and cobalt has been detected as a coloring agent in certain specimens of glass and glaze. Neither metal occurs naturally in Egypt, and it seems probable that supplies of ore were imported from Persia.

Mercury <...> is stated to have been found in Egyptian tombs of from 1500—1600 B.C.

Perhaps not surprisingly, the terminology used in ancient Egyptian chemical literature sometimes was deliberately misleading:

The use of the trade names for the purpose of concealing the character of the substance used where secrecy seemed desirable was not unknown at that period.

The secret names as the later alchemists used extensively: “blood of the serpent”, “blood of Hephaistos”, “blood of Vesta”, “seed of the lion”, “seed of Hercules”, “bone of the phyasimian”, etc.

The term “blood of the dove” used in the papyrus, von Lippmann has identified from other sources as meaning red lead or sometimes cinnabar.

Below minus forty

Cold snap, you say? I do remember one New Year’s Day when the temperature in the Moscow region dropped below −40°. (Celsius or Fahrenheit? In this particular case, it’s the same: −40 °C = −40 °F = 233.15 K.) On 1 January 1979, we woke up in the (late) morning only to discover that we are stuck without any tea or hot food. We couldn’t switch on the gas cooker, which was running on propane/butane mixture. Why? As explained in this useful guide,

When the temperature of the liquids falls below its current boiling point the pressure inside the canister will no longer drive vapour out.

The boiling point of butane is −0.5 °C and that of propane is −42 °C; the temperature outside was below −42 °C, and the gas canisters were outside!

My mum called for a friendly neighbour who was better equipped than us. We kids did not worry too much about a guy warming up a gas canister with a blow torch. Anyway, everything went just fine and we had a wonderful day.

Seizure

With all these holidays, it seems that I missed another great exhibition: “Seizure” by Roger Hiorns (open until 3 January 2010). According to The Guardian,

Hiorns filled a bedsit with 75,000 litres of copper sulphate solution, which hardened over several weeks into crystals. The installation secured him a nomination for the Turner Prize.

What you see on the walls (floor, ceiling etc.) is copper sulfate pentahydrate (CuSO₄·5H₂O). A stylish way to refurbish the apartment.

Cobalt chlorium G and water fluoridation

Two chemistry-related quotes from Dr. Strangelove:

You’ve obviously never heard of cobalt chlorium G. It has a radioactive half-life of 93 years.

Have you ever heard of a thing called fluoridation of water?

In contrast to fictitious “cobalt chlorium G”, water fluoridation is real. So is opposition to it. To quote the recent Australian study, “water fluoridation appears to be a low-risk, high-outrage controversy”. Luckily, the communist threat is no longer mentioned — or so I thought until I came across a recent publication quoting a Californian mum who wondered whether the dentist was “one of those socialists trying to poison us with fluoride”. From The Fluoride Wars: How a Modest Public Health Measure Became America’s Longest Running Political Melodrama:

It seemed such simple act at the time <in 1945>. A tap was turned, and water that had been chlorinated for many years without much fuss now carried a second chemical supplement to help keep us healthy. Soon, the taps would be turned in city after city across the nation. For most, it was another blessing bestowed on us by modern medical science. But for some, it was one chemical too many.

The Gold Book

The Gold Book and the Silver Book (currently under revision) are two of the so-called colour books. Which kind of implies that gold and silver are colours. Not that IUPAC ran out of ‘real’ colours — e.g. they still could have chosen pink or yellow or black. For long time I thought that the reason behind naming the Gold Book ‘Gold Book’ was its (intended) role as a gold standard for chemical terminology. I was wrong. It was named in honour of Victor Gold (1922—1985), the British chemist who was the first author and compiler of the book. No such story with the Silver Book, I am afraid.

One of problems with the Gold Book (as opposed to other colour books) is that it deals with ‘general’ chemical nomenclature. Therefore, when it comes to terms which are different meanings in different fields of chemistry, the Gold Book gives more than one definition. Which one should be used? Take ligands. The definition 1 (coordination chemistry) is short and nice, while the definition 2 (biochemistry) is long and horrible. At least it mentions that in bioinorganic chemistry, one should be careful which definition to use.

In case of sulfides, there are three different meaning. Sulfides 1 (organic chemistry) is the replacement term for obsolete but less ambiguous ‘thioethers’, while sulfides 2 (inorganic chemistry) are “salts or other derivatives of hydrogen sulfide”. I am happy with salts but not with the “other derivatives”. Is sulfenic acid (IUPAC name ‘sulfanol’) a sulfide? As for sulfides 3, the definition goes “a term used in additive nomenclature”. Excellent.

Similarly, there is a consistency problem with related terms that are derived from different IUPAC recommendations. The entry for dipolar bond (1994) says:

The term is preferred to the obsolescent synonyms ‘coordinate link’, ‘coordinate covalence’, ‘dative bond’, ‘semipolar bond’.

And yet the more recent entry for dative bond (1999) does not mention that the term is obsolete. It is even states that

In spite of the analogy of dative bonds with covalent bonds, in that both types imply sharing a common electron pair between two vicinal atoms, the former are distinguished by their significant polarity, lesser strength, and greater length.

A textbook example of dative bond is the one in ammonium. Of course, all the N—H bonds are exactly the same, even if you choose to represent one of them with an arrow.

Visual maths

Many old jokes are based on the stereotype of mathematicians as impractical freaks (as opposed to, say, chemists). Here’s one from my university days (as told by the lecturer in physical chemistry):

How to calculate the area of this figure? (Draws a squiggly figure on a blackboard.) A mathematician spends three days establishing the nature of the function and two days taking the integral. By the end of the week, the problem is solved. A chemist draws the figure on graph paper, cuts it out and weighs it on an analytical balance. The problem is solved in 10 minutes.

Note that the chemist, apart from being ‘simply’ practical, also provides more direct answer to the question.

I prefer graphics to formulae. If I can’t draw a graph, I won’t grasp a concept. Luckily, there are some great resources on the web. For instance, MatematicasVisuales contains a nice collection of Java applets which elegantly visualise a number of mathematical concepts. Examples range from geometry to probability.

This applet illustrates some aspects of the braid theory. Click on ‘draw’, enter a braid word, e.g. BcbACb, and see your braid! The applet also can ‘reduce’, or simplify, the braid diagram, as well as to solve the braid isotopy problem (‘compare’).

=

=

Chromium

The name of chromium is derived from the Greek χρωμα (colour), because many of chromium compounds have bright colours. Chromium is also the name of the open-source browser project behind Google Chrome. Chrome is a hacker slang for the graphical user interface. The Chrome logo (a) features Google colours while the Chromium logo (b) is almost monochrome.

a	b

I liked the idea of Chrome for Linux without Google’s branding. I have followed this instruction to the letter to install Chromium on my Acer Aspire One netbook and it worked beautifully. Chromium certainly lacks lot of Firefox’s functionality but it does most things I need. Plus, it is very fast and you can change the appearance of browser using themes.

Some ChEBI news

Wow. Today’s ChEBI news inform that

ChEBI release 62 is now available, containing 455,788 total entities, of which 19,236 are annotated entities and 607 were submitted via the ChEBI submission tool.

Looking back, I must say that ChEBI news lack consistency and therefore the users are bound to be confused. Before, we never said how many entities ChEBI contained in total. For the previous release, only “annotated” entities were counted:

ChEBI release 61 is now available, containing 18933 annotated entities, with 413 of those submitted via the ChEBI submission tool.

And a few releases back, “annotated” was not mentioned at all:

ChEBI release 58 contains 18186 entities with 175 of those submitted via the ChEBI submission tool.

Does “annotated” matter? Most ChEBI entries are annotated is some way. That includes all these thousands of compounds which just came from ChEMBL. What is meant here really is “annotated and approved by ChEBI curators”. But wait:

With this release, we’ve incorporated the compound records from the ChEMBL dataset and introduced a starring system to identify core (3-star) annotated ChEBI entries from entries annotated by the ChEMBL project and ChEBI submitters.

This is unfortunate that ChEBI introduced stars to signify entry quality. I think I am not the only one who firmly associates stars with user’s (external reviewer’s) rating. “Thou shalt not award no stars to thyself.” In addition, the star rating system usually implies that stars can be lost as well as gained, which is not the case in ChEBI: once the three-star status is reached, the entry stays as it is.

Oh well. Sure ChEBI is not perfect, but what is? Perhaps in a couple of releases we’ll see another change, stars replaced by other celestial bodies or flowers or traffic signs. Good night.

Metalloproteomics

“Metalloproteomics” is a relatively new and not that widely known term. Today (20 October 2009), PubMed search produces only 13 hits. (The search for “metallomics” gives only twice as many hits.) The earliest use of the term is by Alfredo Sanz-Medel and by Scott et al. — incidentally, both papers were published online 23 December 2004.

Metalloproteomics by Eugene Permyakov (Wiley-Interscience, 2009) gives us a definition of the term:

Metalloproteomics is a proteomics of metal-binding proteins.

That’s easy, right? But wait. Check out the table of contents. It looks to me like another bioinorganic chemistry book, and a rather pricey one. It mostly deals with metalloproteins, but there are also Chapter 15, Interactions of metal cations with nucleic acids, and Chapter 16, “Nonphysiologic” metals. Nothing here is specifically proteomic or metallomic. I suppose that Chapter 3, Experimental methods used for studies of the binding of metal cations could be of some relevance to metalloproteomics. Then again, maybe not: how come that mass spectrometry, the most obvious proteomics technique, is not mentioned at all? And why metal cations only? Some metalloproteins contain vanadate. Maybe I am jumping to conclusions here (without even reading the book!), but this title is simply misleading.

Metal instruments

This post was prompted by my recent exercises with trombone. Like many (but not all) brass instruments, trombone is actually made of brass, i.e. alloy of copper and zinc. Thus the English term “brass” is more pertinent than French cuivre or Russian медные (both mean “copper”). Still, it is misleading: saxophones (which are woodwind instruments) are also commonly made of brass. But then, I also heard of all-aluminium double bass which was patented in 1934 under the inconspicuous name “Musical instrument of the viol and violin type”.

Can one distinguish the sound of a silver flute from the sound of a gold flute? This study attempted to answer this question with a scientific experiment. Here’s the experimental setup:

A silver coated, full silver, 9 carat gold, 14 carat gold, 24 carat gold, platinum coated and all-platinum flute was played by 7 professional flutists (members of Viennese orchestras including the Vienna Philharmonic orchestra) in an anechoic chamber.

And the result?

As expected, the most significant assigned expressions for all instruments were the “contradictionary <contradictory?> expressions”: for example, the sound color of each instrument was evaluated as “bright” and simultaneously as “dark” or “full/round” and “thin/sharp”.

Tests with experienced professional flutists and listeners and one model of a flute made by Muramatsu from 7 different materials showed no evidence that the wall material has any appreciable effect on the sound color or dynamic range of the instrument. The common stereotypes used by flutists and flute makers are exposed as “stereotypes”.

So there. It’s a shame that Muramatsu does not make aluminium flutes.

Uranyl-binding protein

“Uranyl ion” is the traditional name of dioxidouranium(2+), [UO₂]²⁺. According to Wikipedia, [UO₂]²⁺ is “the most common species encountered in the aqueous chemistry of uranium”. Wegner et al. designed a uranyl-selective DNA-binding protein using the template of NikR, a nickel-dependent transcriptional repressor from E. coli. The binding site of wild-type NikR was modified by a series of mutations (Val72Ser, His76Asp and Cys95Asp) to introduce extra hard equatorial ligands to favour binding of [UO₂]²⁺.

Wild-type NikR binds to its promoter DNA in the presence of Ni²⁺ ions, and a number of other divalent metal ions such as Cu²⁺, Zn²⁺, Co²⁺, Mn²⁺, and Cd²⁺ can also induce protein-DNA complex formation. However, NikR does not bind to DNA in the presence of 50 μM UO₂²⁺. The <triple> mutant NikR′ binds to DNA neither in the absence of metal ions nor in the presence of Ni²⁺ ions, but it forms a protein-DNA complex in the presence of UO₂²⁺. In comparison to NikR, the metal selectivity of NikR′ has been altered. Experiments with other metal ions show that the mutant protein only forms the protein-DNA complex in the presence of the uranyl cation while Ni²⁺, Zn²⁺, Co²⁺, Cu²⁺, Cd²⁺, Mn²⁺, and Fe²⁺ ions do not result in any observable complex formation. Attempts to load NikR with uranyl or NikR′ with Ni²⁺ did not yield any observable metal binding. Thus, this mutant NikR′ shows a uranyl-specific DNA-binding ability.