Wednesday, April 29, 2009

How to draw a nitro group

In our IUPAC Recommendations, section GR-8, “the nitro problem” is discussed in detail. To quote:
“The nitro problem” is one of the most familiar issues in chemical informatics: How should a nitro group be best represented? Experimentally, the two oxygen atoms are equivalent, so it would make sense to depict them symmetrically. However, any way to depict them symmetrically will either violate the popular “octet rule” or force a double positive charge on the nitrogen atom. Conversely, any attempt to honor the octet rule results in oxygen atoms that appear to be non-equivalent. Similar problems arise for molecules based on sulfur, phosphorus, and related elements. Furthermore, all of these are fairly common functional groups, and cannot readily be pushed aside as “unusual” cases.
The recommended representation of nitrobenzene is either (a) or (c) while (b) is not acceptable. Needless to say, (b) is exactly the way this compound is drawn in Beilstein database, while the search with charge-separated nitro query will not work.

nitrobenzene with charge separation
nitrobenzene with pentavalent nitrogen
nitrobenzene with text NO2 group

But what is wrong with representation using “pentavalent” nitrogen? In my view, nothing. How else one should draw nitrogen dioxide (d)? One can think of nitro group as of nitrogen dioxide with a single bond instead of the unpaired electron.

nitrogen dioxide

For purely aesthetic reasons, the multiple charge-separated nitro groups are not good: too many charges without good reason. For example, hexanitroplatinate(2–) looks much nicer when the sketch shows only one charge, 2– (e), rather than 13 assorted charges as in (f).

hexanitroplatinate(2-) with pentavalent nitrogen
hexanitroplatinate(2-) with charge-separated nitro groups

Sunday, April 26, 2009

Chinese element symbols in Unicode

According to Chinese philosophy, there are only five elements:

The union of five elements is known as 五行 (Wǔ xíng). In Chinese Periodic Table, 金 (jīn) on its own means ‘gold’ while all other solid metals consist of two symbols, jīn + something else, for instance 金 + 白 = 鉑 (platinum). The only liquid metal at room temperature, mercury (汞), does not include 金 but has 水 (shuǐ) instead. There are many versions of Chinese Periodic Table on the web but personally I like this interactive one. Bizarrely, Unicode has three flavours for each of Chinese elements: ‘parenthesized’, ‘circled’ and ‘simple’. Again, I am sure that many people will not see these characters correctly.

PARENTHESIZED IDEOGRAPH FIREU+322B㈫㈫Fire (traditional element) or Tuesday
PARENTHESIZED IDEOGRAPH WATERU+322C㈬㈬Water (traditional element) or Wednesday
PARENTHESIZED IDEOGRAPH WOODU+322D㈭㈭Wood (traditional element) or Thursday
PARENTHESIZED IDEOGRAPH METALU+322E㈮㈮Metal (traditional element) or gold (element) or Friday
PARENTHESIZED IDEOGRAPH EARTHU+322F㈯㈯Earth (traditional element) or Saturday

Thursday, April 23, 2009

Another mystery solved

Here’s a short fragment of Accident by Agatha Christie.

Evans paid no attention, but went on. ‘You interrupted me just now. After Marsh’s test, Merrowdene heated a substance in a test tube, the metallic residue he dissolved in water and then precipitated it by adding silver nitrate. That was a test for chlorates. A neat, unassuming little test. But I chanced to read these words in a book that stood open on the table. “H2SO4 decomposes chlorates with evolution of Cl2O4. If heated, violent explosions occur, the mixture ought therefore to be kept cool and only very small quantities used.”’
What book was that? Googling gave me The Elements of Chemical Arithmetic with a Short System of Elementary Qualitative Analysis by J. Milnor Coit, Ph.D., published in 1886. On page 80, section 103, I’ve found the original description (shortened in Agatha Christie’s version):
H2SO4 decomposes chlorates with evolution of Cl2O4, a greenish-yellow gas having a powerful odor. If heated, violent explosions occur; the mixture ought therefore to be kept cold, and only very small quantities should be used.
The full text of this, apparently, still very useful book is copyright-free.

Tuesday, April 21, 2009

Chemical symbols in Unicode

I was told that the Unicode atom symbol (which appeared in my previous post) is not represented correctly in other browsers, or, indeed, other PCs. This is because not all PCs have the fonts installed that can show these characters; or even when the font is there, one has to tell the browser to use it, e.g. <font></font>. That’s annoying.

Given a number of various symbols present in Unicode, I am surprised how little of them are genuinely related to chemistry, without having any other meaning. In fact, just three. Two of them, and , mean the same and are quite useless — I’d prefer them rotated 90° so one could attach them by “bonds” to something else inline. The third, , means “chemical term” (in dictionary etc.); the scales, , even though may appear related to chemistry, really mean “legal term”. See the little table below for these and a few others which may be of some chemical relevance.

SUNU+2609&#9737;&#x2609;Sun (astrology) or gold (alchemy)
FIRST QUARTER MOONU+263D&#9789;&#x263d;Moon (astrology) or silver (alchemy)
MERCURYU+263F&#9791;&#x263f;Mercury (astrology) or mercury (alchemy)
FEMALE SIGNU+2640&#9792;&#x2640;Venus (astrology) or copper (alchemy)
EARTHU+2641&#9793;&#x2641;Earth (astrology) or antimony (alchemy)
MALE SIGNU+2642&#9794;&#x2642;Mars (astrology) or iron (alchemy)
JUPITERU+2643&#9795;&#x2643;Jupiter (astrology) or tin (alchemy)
SATURNU+2644&#9796;&#x2644;Saturn (astrology) or lead (alchemy)
BENZENE RINGU+232C&#9004;&#x232c;Benzene ring (Kekulé structure)
BENZENE RING WITH CIRCLEU+23E3&#9187;&#x23e3;Benzene ring (delocalised)
SKULL AND CROSSBONESU+2620&#9760;&#x2620;Poison (chemistry etc.)
RADIOACTIVE SIGNU+2622&#9762;&#x2622;Radioactivity
BIOHAZARD SIGNU+2623&#9763;&#x2623;Biohazard
SCALESU+2696&#9878;&#x2696;Legal term
ALEMBICU+2697&#9879;&#x2697;Chemical term
ATOM SYMBOLU+269B&#9883;&#x269b;Nuclear installation

Friday, April 17, 2009

Metals and toponymy

Some years ago, I’ve circulated this list among my colleagues at the EBI. I think it may be of interest to the readers of this blog as well. Here goes:

Copper was named after Cyprus, francium and gallium after France, germanium after Germany, polonium after Poland, ruthenium after Russia, and americium after (the United States of) America. Magnesium was named after Magnesia region in Greece, hassium after the land of Hesse (Hessen) in Germany, and californium after California. In addition, europium got his name after (continent of) Europe while the names of both scandium and thulium have something to do with Scandinavia. However, indium was named not after India but because of blue (indigo) line in its atomic spectrum. As for cities and villages, lutetium was named after Paris, hafnium after Copenhagen, holmium after Stockholm, strontium after Strontian in Scotland, berkelium after Berkeley in California, dubnium after Dubna in Russia*, and rather unpronounceable darmstadtium after Darmstadt in Germany. Four elements (yttrium, erbium, terbium, ytterbium) took their names after otherwise little known Ytterby in Sweden. Rhenium was named after the (river) Rhine. All the place-name elements, except for germanium, are metals.

Apart from Argentina, I cannot think of any other country named after a metal or any other element (unless you count Cyprus again, which well could have been named after copper; the history is not very clear here). According to the Wikipedia, the smallest of Canary Islands, El Hierro (Spanish for ‘iron’) originally had a name ‘Hero’, later mutated into ‘Hierro’ and further latinised as ‘Ferro’ while having nothing to do with iron. Lead, South Dakota also has nothing to do with lead (metal). I am sure there are plenty of placenames featuring coinage metals (gold, silver, copper) in a variety of languages, but I better stop for now.

* Dubna is the only town I know that has both flag and coat of arms featuring a ‘popular culture’ atom symbol

Sunday, April 05, 2009

On biological role of titanium

According to WebElements, “titanium has no biological role”. Having recently acquired a titanium (or rather, Ti6AlV4 alloy) dental implant, I am not convinced. To be a dental implant sounds like a perfectly valid biological role to me. Apparently, osteoblasts like to attach to titanium surface (more precisely, to titanium dioxide, TiO2). However, it is not just the material that matters, it is the shape of the material as well. In the recent paper, in vivo bone binding to TiO2 nanotubes and TiO2 gritblasted surfaces was investigated. The authors have found that

after four weeks of implantation in rabbit tibias, pull-out testing indicated that TiO2 nanotubes significantly improved bone bonding strength by as much as nine-fold compared with TiO2 gritblasted surfaces.
Earlier this year, another study has demonstrated that the fate of human mesenchymal stem cells can be affected solely by the geometry of TiO2 nanotubes:
Small (≈30-nm diameter) nanotubes promoted adhesion without noticeable differentiation, whereas larger (≈70- to 100-nm diameter) nanotubes elicited a dramatic stem cell elongation (≈10-fold increased), which induced cytoskeletal stress and selective differentiation into osteoblast-like cells...