Online registration for 7th 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.
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.
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.
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.
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 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.
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.
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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’).
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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.
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| a | b |
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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.
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” 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.
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.
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.
The colouring <of the niobium insert> is made by a so called anodic oxidation of the material. With this treatment, by electrochemical processing a very thin niobium oxide layer is formed under controlled conditions. By refraction of light in the oxide layer so called interference colours are created which gives the colouring of the niobium. Depending on the processing parameters, the thickness of the oxide layer can be very well controlled, and gives the niobium its noble appearance. Depending on the thickness of the layer different colours are producible.For instance, Latvian bimetallic Coin of Time (struck by Münze Österreich) consists of beautiful blue niobium centre enclosed in an outer silver ring. The obverse of the coin features the heraldic rose and the tiny Gothic script letters ℌ and ℜ standing for Heinrich Rose (1795—1864), discoverer of niobium.
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Although the magnetic monopoles were postulated by Paul Dirac in 1931, the existence of these particles remains an open problem. This article surveys the recent breakthrough discoveries concerning magnetic monopoles within spin ice materials, dysprosium titanate (Dy2Ti2O7) and holmium titanate (Ho2Ti2O7).
The recent paper in Science describes the sulfilimine (sulfimide, in IUPACese) bond, “not previously found in biomolecules”, identified in collagen. The bond (>S=N–) cross-links methionine and hydroxylysine residues of adjoining protomers.
Following the call to the community from Antony Williams, I indulged in some chemical drawing. I did redraw structure 1 from this paper from scratch to get (a). This is very much like structure of digitonin in ChEBI (b), except for methyl group at C-20 which goes up in (a).
 (a) |  (b) |
Muhr et al. wrote:
With our investigations, it was possible for the first time to confirm beyond all doubt the structure suggested by Tschesche and Wulff for digitonin by means of modern NMR techniques, and to assign all proton and carbon resonances.
Now I was not able to get to the full text of Tschesche and Wulff, but at least their abstract contains the German name “3[β-D-Glucopyranosyl(I)(1→3Galakt.II)-β-D-galaktopyranosyl(II)(1→2Gluc.III)-β-D-xylopyranosyl(1→3Gluc.III)-β-D-glucopyranosyl(III) (1→4Galakt.IV)-β-D-galaktopyranosyl(IV)(1→3-Digitog.)]5α,20βF,25α Spirostantriol(2α,3β,15β)”, which kind of confirms 20β configuration. (The default configuration of spirostan is 20α.)
I guess this still does not answer what the “correct” structure of digitonin is. All we can say that Muhr et al. reported the structure (a).
Here’s something one doesn’t see in a chemistry textbook. The recent perspective paper in Nature Chemistry deals with a distinct class of electron-pair bonding called “charge-shift” (CS) bonding, which exists alongside classical covalent and ionic bonding. And in not-so exotic molecules.
<A> striking example is the difference between H2 and F2; two homonuclear bonds that by all criteria should be classified as covalent bonds, but exhibit fundamental differences. Consider the energy curves (Fig. 1) of the two bonds calculated recently. Figure 1a shows that the H—H bond is indeed covalent; its covalent structure accounts for most of the bonding energy (relative to the ‘exact’ curve). By contrast, for the F—F bond in Fig. 1b, the covalent structure is entirely repulsive, and what determines the bonding energy and the equilibrium distance is the covalent–ionic mixing. This mixing leads to a resonance energy stabilization, which we have termed the ‘charge-shift resonance energy’ (RECS). Thus, despite their apparent similarity, the two bonds are very different; whereas the H—H bond is a true covalent bond, the F—F bond is a CS bond that is completely determined by the RECS quantity.
No less striking example is so-called inverted C—C bond in [1.1.1]propellane (described in a paper from the same group of authors), which “closely resembles the single bond of difluorine”.
Antarcticite is a mineral form of calcium dichloride hexahydrate. It was first discovered in Don Juan Pond in Antarctica, which is probably the saltiest (47% w/v) body of water on earth. Looking at crystal structure of antarcticite (below), one can see that both name “calcium dichloride hexahydrate” and formula CaCl2·6H2O are misleading, for there are two kinds of water in it. The structure comprises the alternating layers of (i) trigonal planar triaquacalcium(2+) ions and (ii) water and chloride ions. I suppose it should be named “triaquacalcium dichloride—water (1/3)” or “triaquacalcium dichloride trihydrate”, with formula [Ca(OH2)3]Cl2·3H2O.
I always thought that ferrochelatase (EC 4.99.1.1) has an absurd systematic name: “protoheme ferro-lyase (protoporphyrin-forming)”. Why? According to Enzyme Nomenclature,
Lyases are enzymes cleaving C—C, C—O, C—N and other bonds <in other words, any bond> by other means than by hydrolysis or oxidation.
“Protoheme ferro-lyase” implies that the reaction goes in the direction:
| protoheme + 2 H+ → protoporphyrin + Fe2+ | (a) |
while ferrochelatase, in fact, catalyses the reverse reaction:
| protoporphyrin + Fe2+ → protoheme + 2 H+ | (b) |
Usually, to release iron from protoheme, you have to break it. Heme oxygenase (EC 11.14.14.18) does it by sequential oxidation of heme into the linear tetrapyrrole, biliverdin.
However, this paper demonstrates that there could be another way to do it.
Until today, all known enzymes performing iron extraction from heme did so through the rupture of the tetrapyrrol skeleton. Here, we identified 2 Escherichia coli paralogs, YfeX and EfeB, without any previously known physiological functions. YfeX and EfeB promote iron extraction from heme preserving the tetrapyrrol ring intact. This novel enzymatic reaction corresponds to the deferrochelation of the heme. YfeX and EfeB are the sole proteins able to provide iron from exogenous heme sources to E. coli.
Thus, deferrochelatase catalyses the reaction (a) and, indeed, can be named “protoheme ferro-lyase (protoporphyrin-forming)”.
During the IUPAC International Chemical Identifier (InChI) Subcommittee meeting in Glasgow last month, we touched upon the issue of normalisation of metal complexes. I did not realise before that even simple entity such as chromate(2−), drawn in different ways (a)—(c), will give different InChIs. (And different standard InChIs as well; and InChIKeys too.) This is, I am told, because the current InChI algorithm involves “disconnection” of metals before “normalisation”, while it really should do normalisation first. Bother.
![[Cr(O)2(O-)2]](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiMl79HNr0UpiyYYGh19PXfrVS8tgjZpGFAXZVCc4UOf9mkbRi22X04ihTqlc4kIt3MhjkoadFSu1o4S_bm2B_MrMmvKwlJB__guvw6LTHk2KhQpN1daOMI2lDyeUkHefZXhMy2pw/s320/%5BCr(O)2(O-)2%5D.png)
InChI=1/Cr.4O/q;;;2*-1 | ![[Cr(O)4]2-](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEig_6nDbBjkdqedyqMZqcaqsMjAKQTNTh6qfYC695EGI2cTTKtyAbJh13mjeVrv_7wLrr6mcW1FMJVxrR1n9JCZHH9R5Dwb-gWMGpJSDl2_VwEirZWvOGQv359HmZuN3mLmDDS19A/s320/%5BCr(O)4%5D2-.png)
InChI=1/Cr.4O/q-2;;;; | ![[Cr(2+)(O-)4]](https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhcX_-K6YsWcufdFVEykYISID9dKdDFxNYAtXgcZvGq4cOeyXrwgE4DhOAAQVRu23tiP0soKyY7s05pGIabeMwIZX1YoPhL73RGw6zuauvpkJ9w5DQMnLqzS9PTzcO0tsKc1yoYVg/s320/%5BCr(2+)(O-)4%5D.png)
InChI=1/Cr.4O/q+2;4*-1 |
| (a) | (b) | (c) |
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